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At least 217 records · Page 12Linked to original sources

Collaborative social and medical service application.

Baylor College of Medicine has five Teen Health Clinics (THC) dispersed throughout Harris county. The population served by the clinics includes inner-city adolescent boys and girls 19 years of age and under. Patients receive services such as family planning, sexually transmitted disease screening and treatment, perinatal care, counseling, and support services. Adolescents may receive services at any one of the clinics at no cost to the adolescent or their dependents. Given the geographical distribution of the clinics and the reliance on paper-based records, client services cannot be provided efficiently or expeditiously. According to the statistics developed by Clinic staff, ineffective coordination of service needs and client schedules undermine the follow-up needed for effective care. For example, a counselor will often need to balance a school schedule, clinic visits, well baby follow-up, and the Best Friends Program for a new mother. In addition, the lack of ready access to patient information impairs the ability of clinical and social service staff to provide continuity of care. In fact, some cases of client dropout are attributable to these difficulties. We have developed the Collaborative Social and Medical Service Application (CSMSA) to facilitate the provision of social and medical services to this population. The CSMSA is a domain-specific application based on a robust infrastructure known as the Ambulatory Services Architecture (ASA). This system is designed to support integrated social and ambulatory care. The ASA is a Baylor developed application framework and architecture for the computerization of the patient medical record in the ambulatory care setting. The working environment for the CSMSA user is an integrated desktop which provides an operating environment for both third-party applications and the CSMSA, as well as a fundamental set of services. The integrated desktop services include a mechanism for object organization or grouping, a facility for the management of desktop objects including disposal and storage, and an embedded search utility to assist in the location of desktop objects as well as other application objects. The access control mechanism will provide the security for the desktop environment by requiring the user to log into and out of the environment. This security mechanism will also enable/disable CSMSA tools based on the user's role at the clinic. The CSMSA is designed to provide work process, functionality and data access appropriate to the responsibilities of the user, e.g., a THC clerk may have permission to view a patient's orders but does not have the facility to create an order. Patient context is defined through a patient browser containing the master patient index or a user defined patient list. Patient encounters are managed using forms based on the process for each encounter type (e.g., initial visit). Forms are used for data entry and for queries. Data entry forms are only committed to the patient database (i.e., making the patient data available to other users who have permission to access the data) when the user approves the data. The CSMSA provides a means to suspend an entry into a chart by saving incomplete or non-committed data entry forms as part of the desktop state which is restored when the user logs into the system. CSMSA was designed to provide a robust, expandable application capable of accommodating the changes in health care and social services delivery while encompassing evolving software standards and new technology. This goal was achieved using object-oriented methodologies and technologies, combined with an object-oriented database management system as the foundation of our server to facilitate the evolution of our data model.

Adolescent↗

A COSTAR interface using WWW technology.

The concentration of industry on modern relational databases has left many nonrelational and proprietary databases without support for integration with new technologies. Emerging interface tools and data-access methodologies can be applied with difficulty to medical record systems which have proprietary data representation. Users of such medical record systems usually must access the clinical content of such record systems with keyboard-intensive and time-consuming interfaces. COSTAR is a legacy ambulatory medical record system developed over 25 years ago that is still popular and extensively used at the Massachusetts General Hospital. We define a model for using middle layer services to extract and cache data from non-relational databases, and present an intuitive World-Wide Web interface to COSTAR. This model has been implemented and successfully piloted in the Internal Medicine Associates at Massachusetts General Hospital.

Ambulatory Care Information Systems↗

The TIGR Rice Genome Annotation Resource: improvements and new features.

In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42,653 non-transposable element-related genes encoding 49,472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13,237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31,739 gene models), representing approximately 50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

DNA Transposable Elements↗

Obstacles and approaches to clinical database research: experience at the University of California, San Francisco.

With increasing availability of clinical data in machine-readable form, and decreasing cost of storing and manipulating that data, retrospective research using clinical databases has become more feasible. Nonetheless, much of the potential for clinical research using these data remains unrealized. Obstacles to clinical database research include difficulty accessing data, difficulty using retrospective data to draw valid inferences about medical tests and treatments, and a shortage of investigators trained and interested in using a clinical database to answer their questions. At the University of California, San Francisco, we have developed a Clinical Database Research Program (CDRP) to try to overcome these obstacles. The CDRP maintains a relational database of patient data obtained from diverse sources and a small staff dedicated to providing such data to researchers. The CDRP staff also provides support for design and analysis of studies using the database--the development of methods for such studies is our primary research interest. Finally, to increase the number of investigators using the database for research, we are integrating training in clinical epidemiology and clinical research methods into residency and fellowship training, and offering an elective in clinical database research for trainees who wish to undertake a specific project.

Databases, Factual↗

Computational Science and Engineering Online (CSE-Online): a cyber-infrastructure for scientific computing.

With the expansion of the Internet and World Wide Web (or the Web), research environments have changed dramatically. As a result, the need to be able to efficiently and securely access information and resources from remote computer systems is becoming even more critical. This paper describes the development of an extendable integrated Web-accessible simulation environment for computational science and engineering called Computational Science and Engineering Online (CSE-Online; http://cse-online.net). CSE-Online is based on a unique client-server software architecture that can distribute the workload between the client and server computers in such a way as to minimize the communication between the client and server, thus making the environment less-sensitive to network instability. Furthermore, the new software architecture allows the user to access data and resources on one or more remote servers as well as on the computing grid while having the full capability of the Web-services collaborative environment. It can be accessed anytime and anywhere from a Web browser connected to the network by either a wired or wireless connection. It has different modes of operations to support different working environments and styles. CSE-Online is evolving into middleware that can provide a framework for accessing and managing remote data and resources including the computing grid for any domain, not necessarily just within computational science and engineering.

Engineering↗

SORTEZ: a relational translator for NCBI's ASN.1 database.

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Algorithms↗

Health care access problems of medically indigent emergency department walk-in patients.

OBJECTIVES: To obtain health care access data on emergency department walk-in patients and to determine factors associated with delayed access to care. DESIGN: Survey of stable ED walk-in patients in the triage area. SETTING: University of California Irvine Medical Center, an urban, 493-bed, noncounty, Level I teaching hospital treating 38,000 emergency patients annually. PARTICIPANTS: A quota of 1,000 consecutive patients derived from a representative selection of service days was included; 94% of eligible patients agreed to participate. Patients with obstetrical problems (more than 20 weeks' gestation) were excluded. INTERVENTIONS: Pretested health access survey, available in both Spanish and English, administered by investigator. RESULTS: Public aid/self-pay insurance status was significantly associated with routine use of the ED for care (P less than .003), income of less than $10,000 (P less than .0002), refusal of care by health provider (P less than .001), refusal of care at an ED (P less than .03), and delay in seeking health care (P less than .0002). Income of less than $10,000 was significantly associated with routine use of the ED for care (P less than .02), and delay in seeking health care (P less than .04). Statistical analysis done using chi 2 with continuity correction and with the binomial test for comparison of two proportions. CONCLUSION: Among stable ED walk-in patients surveyed at our facility, low-income individuals and those with public aid/self-pay insurance status were significantly more likely to use the ED as a routine source of health care, and more likely to delay in seeking needed health care, than higher income and fully insured individuals. These data should be useful to health policymakers in formulating rational, cost-effective strategies that improve access to early treatment and prevention.

Adult↗

Emergency department access to a longitudinal medical record.

Our goal is to assess how clinical information from previous visits is used in the emergency department. We used detailed user audit logs to measure access to different data types. We found that clinician-authored notes and laboratory and radiology data were used most often (common data types were used up to 5% to 20% of the time). Data were accessed less than half the time (up to 20% to 50%) even when the user was alerted to the presence of data. Our access rate indicates that health information exchange projects should be conservative in estimating how often shared data will be used and the wide breadth of data accessed indicates that although a clinical summary is likely to be useful, an ideal solution will supply a broad variety of data.

Emergency Service, Hospital↗

Adopting a database as a solution to managing electron image data.

A database was used for data management and interprogram communication in an image processing and three-dimensional reconstruction program suite for biological bundles. The programs were modified from the MRC crystallographic package. The database server works with local and remote programs and data sets, allows simultaneous requests from multiple clients, and maintains multiple databases and data tables within them. It has built-in security for the data access. Several graphical user interfaces are available to view and/or edit data tables. In addition, FORTRAN interface and function libraries are written to communicate with image processing software. The data management overhead is inexpensive, requiring only narrow bandwidth from the network. It easily handles several data tables with over 1000 entries.

Computer Communication Networks↗

[Sample survey of persons insured in statutory health insurance institutions in Hessen--concept and realisation of person-related data base].

Statutory health insurance data are being increasingly used for secondary data research. Longitudinal data can be prepared for research in health care, epidemiology or demand planning, in particular through the person-related nature of the data which is a precondition for the creation of inter-sector and inter-period data sets. This application possibility was introduced in a method study "person-related sampling of statutory health insurance data" and is now translated into practice on a larger scale for the first time in the regional sample "Versichertenstichprobe AOK Hessen/KV Hessen". For the collection and use of these data, model procedures were designed which take account of organisational (data access, contractual agreement, advisory board), technical (sampling, collection and storage of data) and confidentiality (data protection concept, pseudonymisation) aspects. The insured person-related sample may thus serve as a basis for the data pool planned for the national health system (Social Security Regulation 303 a-SGB V).

Community Participation↗

The European Bioinformatics Institute's data resources: towards systems biology.

Genomic and post-genomic biological research has provided fine-grain insights into the molecular processes of life, but also threatens to drown biomedical researchers in data. Moreover, as new high-throughput technologies are developed, the types of data that are gathered en masse are diversifying. The need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation is greater than ever. The European Bioinformatics Institute's (EBI's) databases and tools have evolved to meet the changing needs of molecular biologists: since we last wrote about our services in the 2003 issue of Nucleic Acids Research, we have launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI). Our existing core databases have continued to evolve to meet the changing needs of biomedical researchers, and we have developed new data-access tools that help biologists to move intuitively through the different data types, thereby helping them to put the parts together to understand biology at the systems level. The EBI's data resources are all available on our website at http://www.ebi.ac.uk.

Computational Biology↗

Digital image archiving: challenges and choices.

In the last five years, imaging exam volume has grown rapidly. In addition to increased image acquisition, there is more patient information per study. RIS-PACS integration and information-rich DICOM headers now provide us with more patient information relative to each study. The volume of archived digital images is increasing and will continue to rise at a steeper incline than film-based storage of the past. Many filmless facilities have been caught off guard by this increase, which has been stimulated by many factors. The most significant factor is investment in new digital and DICOM-compliant modalities. A huge volume driver is the increase in images per study from multi-slice technology. Storage requirements also are affected by disaster recovery initiatives and state retention mandates. This burgeoning rate of imaging data volume presents many challenges: cost of ownership, data accessibility, storage media obsolescence, database considerations, physical limitations, reliability and redundancy. There are two basic approaches to archiving--single tier and multi-tier. Each has benefits. With a single-tier approach, all the data is stored on a single media that can be accessed very quickly. A redundant copy of the data is then stored onto another less expensive media. This is usually a removable media. In this approach, the on-line storage is increased incrementally as volume grows. In a multi-tier approach, storage levels are set up based on access speed and cost. In other words, all images are stored at the deepest archiving level, which is also the least expensive. Images are stored on or moved back to the intermediate and on-line levels if they will need to be accessed more quickly. It can be difficult to decide what the best approach is for your organization. The options include RAIDs (redundant array of independent disks), direct attached RAID storage (DAS), network storage using RAIDs (NAS and SAN), removable media such as different types of tape, compact disks (CDs and DVDs) and magneto-optical disks (MODs). As you evaluate the various options for storage, it is important to consider both performance and cost. For most imaging enterprises, a single-tier archiving approach is the best solution. With the cost of hard drives declining, NAS is a very feasible solution today. It is highly reliable, offers immediate access to all exams, and easily scales as imaging volume grows. Best of all, media obsolescence challenges need not be of concern. For back-up storage, removable media can be implemented, with a smaller investment needed as it will only be used for a redundant copy of the data. There is no need to keep it online and available. If further system redundancy is desired, multiple servers should be considered. The multi-tier approach still has its merits for smaller enterprises, but with a detailed long-term cost of ownership analysis, NAS will probably still come out on top as the solution of choice for many imaging facilities.

Capital Expenditures↗

Visualization and analysis of microarray and gene ontology data with treemaps.

BACKGROUND: The increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the challenge of integrating experimental results with information resources. The use of Gene Ontology enables researchers to summarize results of quantitative analyses in this framework, but the limitations of typical browser presentation restrict data access. RESULTS: Here we describe extensions to the treemap design to visualize and query genome data. Treemaps are a space-filling visualization technique for hierarchical structures that show attributes of leaf nodes by size and color-coding. Treemaps enable users to rapidly compare sizes of nodes and sub-trees, and we use Gene Ontology categories, levels of RNA, and other quantitative attributes of DNA microarray experiments as examples. Our implementation of treemaps, Treemap 4.0, allows user-defined filtering to focus on the data of greatest interest, and these queried files can be exported for secondary analyses. Links to model system web pages from Treemap 4.0 enable users access to details about specific genes without leaving the query platform. CONCLUSIONS: Treemaps allow users to view and query the data from an experiment on a single computer monitor screen. Treemap 4.0 can be used to visualize various genome data, and is particularly useful for revealing patterns and details within complex data sets.

Animals↗

Web-accessible scientific workflow system for performance monitoring.

We describe the design and implementation of a web-accessible scientific workflow system for environmental performance monitoring. This workflow environment integrates distributed automated data acquisition with server side data management and information visualization through flexible browser-based data access tools. Component technologies include a rich browser-based client, a back-end server for methodical data processing, user management, and result delivery, and third party applications which are invoked by the back-end using web services. This environment allows for reproducible, transparent result generation by a diverse user base, and provides a seamless integration between data selection, analysis applications, and result delivery. This workflow system has been implemented for several sites and monitoring systems with different degrees of complexity.

Databases, Factual↗

AIM Project A2002: CAMARC-II (computer aided movement analysis in a rehabilitation context-II).

CAMARC-II intends to establish a European network of clinical and research centres, interconnected with the manufacturers of the relevant instrumentation and with 'end-users' like insurance companies, which will allow a standardised approach to the Functional Assessment (FA) of the motor (dis)ability of the motor impaired and/or the elderly. The objectives of the project are: to build-up a Europe-wide network to practice Movement Analysis; to define agreed clinical and experimental protocols; to integrate existing and new instrumentation; to define suitable User Interfaces driving the clinician in the tests; to define a comprehensive Knowledge Base (KB) of the MA experience: to build-up suitable databases (DB) of MA data accessible through the Network; to assess criteria for the definition of normative data for a conventional age-related classification of normality, impairment and disability for the motor behaviour. A number of achievements are mentioned in the paper.

Aged↗

Towards interoperability of information sources within a hospital Intranet.

Information is usually available in heterogeneous data format and various legacy sources. Interoperability appears to be a major approach for applications to access information. The project ARIANE is devoted to provide end-users with an easy to use and natural access to information databases. In this frame we defined actors able to operate the mediation between end-users and information servers: a "broker" which selects appropriate resources and "mediators" which access data suppliers. We have implemented a web-oriented stand-alone prototype accessing three types of information sources: a bibliographical server, a SQL database server and a hypertext server. Both broker and mediators exploit the Unified Medical Language System knowledge sources, especially the Information Sources Map which allows a way to identify information servers.

Computer Communication Networks↗

The Portable Dictionary of the Mouse Genome: a personal database for gene mapping and molecular biology.

The Portable Dictionary of the Mouse Genome is a database for personal computers that contains information on approximately 10,000 loci in the mouse, along with data on homologs in several other mammalian species, including human, rat, cat, cow, and pig. Key features of the dictionary are its compact size, its network independence, and the ability to convert the entire dictionary to a wide variety of common application programs. Another significant feature is the integration of DNA sequence accession data. Loci in the dictionary can be rapidly resorted by chromosomal position, by type, by human homology, or by gene effect. The dictionary provides an accessible, easily manipulated set of data that has many uses--from a quick review of loci and gene nomenclature to the design of experiments and analysis of results. The Portable Dictionary is available in several formats suitable for conversion to different programs and computer systems. It can be obtained on disk or from Internet Gopher servers (mickey.utmen.edu or anat4.utmen.edu), an anonymous FTP site (nb.utmem.edu in the directory pub/genedict), and a World Wide Web server (http://mickey.utmem.edu/front.html).

Animals↗

In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes.

Low accessibility of the rRNA is together with cell wall impermeability and low cellular ribosome content a frequent reason for failure of whole-cell fluorescence hybridization with fluorescently labeled oligonucleotide probes. In this study we compare accessibility data for the 16S rRNA of Escherichia coli (gamma Proteobacteria, Bacteria) with the phylogenetically distantly related organisms Pirellula sp. strain 1 (Planctomycetes, Bacteria) and Metallosphaera sedula (Crenarchaeota, Archaea) and the 18S rRNA accessibility of Saccharomyces cerevisiae (Eucarya). For a total of 537 Cy3-labeled probes, the signal intensities of hybridized cells were quantified under standardized conditions by flow cytometry. The relative probe-conferred fluorescence intensities are shown on color-coded small-subunit rRNA secondary-structure models. For Pirellula sp., most of the probes belong to class II and III (72% of the whole data set), whereas most of the probes targeting sites on M. sedula were grouped into class V and VI (46% of the whole data set). For E. coli, 45% of all probes of the data set belong to class III and IV. A consensus model for the accessibility of the small-subunit rRNA to oligonucleotide probes is proposed which uses 60 homolog target sites of the three prokaryotic 16S rRNA molecules. In general, open regions were localized around helices 13 and 14 including target positions 285 to 338, whereas helix 22 (positions 585 to 656) and the 3' half of helix 47 (positions 1320 to 1345) were generally inaccessible. Finally, the 16S rRNA consensus model was compared to data on the in situ accessibility of the 18S rRNA of S. cerevisiae.

Bacteria↗