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At least 469 records · Page 26Linked to original sources

PubMed1999

Computers and connectivity in Illinois emergency departments.

UNLABELLED: Although the Internet has been described as "ubiquitous," little is known about the extent to which physicians have access to the Internet while providing clinical care. OBJECTIVE: To assess the extent of Internet connectivity within the clinical area of every ED within the state of Illinois. METHODS: This was a prospective observational study. Each Illinois ED listed in a published directory was called by telephone, and a responsible party was identified to provide information regarding the type and size of the ED, patient demographics, the types of personal computers (PCs) available in the ED (if any), the types of operating systems used, the availability of access to the World Wide Web (Web), and the highest speed at which an Internet connection could be established. Responses regarding the presence and types of PCs and the types of operating systems used were assessed using one-factor chi-square. Univariate and multivariate predictors of the type of PC used, the presence or absence of Web access, and the highest speed of Internet access were evaluated using optimal discriminant analysis and nonlinear classification tree analysis, respectively. RESULTS: One hundred ninety-eight of the 199 EDs in the state of Illinois (99.5%) completed the survey. Of the responding EDs, 50.5% had PCs, but only 17.6% had Web access. When Web access was available, it was most often available through a high-speed Internet connection that was faster than a dial-up modem. Most departments (68.1%) with PCs used the Windows 95 or Windows 98 operating systems. A majority (62.5%) used the Netscape browser exclusively. Larger EDs (more than six ED beds) in rural or suburban areas were more likely to have a PC compared with smaller EDs (six or fewer beds). Large EDs (more than 12 ED beds) in private tertiary care or academic hospitals were most likely to have Web access. CONCLUSIONS: Although half of Illinois EDs have PCs, only one in six has access to the Internet; thus, most emergency physicians do not have ready access to the Web from the site where they deliver clinical care.

Analysis of Variance↗

PubMed1998

Trends in medical information retrieval on Internet.

Information on the World Wide Web is unstructured, distributed, multimedia and multilingual. Many tools have been developed to help users search for useful information: subject hierarchies, general search engines, browsers and search assistants. Although helpful, they present serious limitations, mainly in terms of precision, multilingual indexing and distribution. In this paper, we cover some on-line solutions to medical information discovery and present our own approach, the MARVIN (multi-agent retrieval vagabond on information network) project, which tackles medical information research with specialized cooperative retrieval agents. We also draw some outlines for future extensions.

Computer Systems↗

PubMed2004

Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma.

BACKGROUND: Rhabdomyosarcoma is a relatively common tumour of the soft tissue, probably due to regulatory disruption of growth and differentiation of skeletal muscle stem cells. Identification of genes differentially expressed in normal skeletal muscle and in rhabdomyosarcoma may help in understanding mechanisms of tumour development, in discovering diagnostic and prognostic markers and in identifying novel targets for drug therapy. RESULTS: A Perl-code web client was developed to automatically obtain genome map positions of large sets of genes. The software, based on automatic search on Human Genome Browser by sequence alignment, only requires availability of a single transcribed sequence for each gene. In this way, we obtained tissue-specific chromosomal maps of genes expressed in rhabdomyosarcoma or skeletal muscle. Subsequently, Perl software was developed to calculate gene density along chromosomes, by using a sliding window. Thirty-three chromosomal regions harbouring genes mostly expressed in rhabdomyosarcoma were identified. Similarly, 48 chromosomal regions were detected including genes possibly related to function of differentiated skeletal muscle, but silenced in rhabdomyosarcoma. CONCLUSION: In this study we developed a method and the associated software for the comparative analysis of genomic expression in tissues and we identified chromosomal segments showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma, appearing as candidate regions for harbouring genes involved in origin of alveolar rhabdomyosarcoma representing possible targets for drug treatment and/or development of tumor markers.

Chromosome Mapping↗

PubMed2006

iHAP--integrated haplotype analysis pipeline for characterizing the haplotype structure of genes.

BACKGROUND: The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations. RESULTS: To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded. CONCLUSION: The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.

Algorithms↗

PubMed2006

Array2BIO: from microarray expression data to functional annotation of co-regulated genes.

BACKGROUND: There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. RESULTS: Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1) comparative analysis of signal versus control and (2) clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. CONCLUSION: We have developed Array2BIO - a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

Algorithms↗

PubMed2001

Distance learning in the digital environment.

The expansion of radiology departments and divisions often can not occur in adjacent geographic locations. This leads to a greater separation of staff and residents, as well as workers in similar divisions. This makes traditional teaching difficult in academic institutions. The economic drive forcing many departments to investigate more isolated outpatient imaging centers has further hindered the ability to continue effective academic training at many facilities. The ability to easily share a digital environment across physical distance can greatly enhance the teaching experience, as well as be a valuable tool for consultation and case discussion with referring clinicians. The transition to a filmless environment with picture archiving and communication systems (PACS) can be utilized for distance learning in addition to the clinical arena. It is possible to take advantage of the digital transformation to PACS and case-viewing browser programs to conduct improved interactions with referring clinicians as well as radiologic teaching with relatively minimal hardware and software demands. The integration of web-based teleradiology programs with business networking software can be used for effective distance learning in the digital environment, sufficiently closing the distance on our rapidly expanding departments. This same technology allows for greater interaction with referring clinicians for real-time consultation and enhanced case discussion to entrench a supportive referral base for the radiologic community.

Humans↗

PubMed2006

Ontology annotation treebrowser : an interactive tool where the complementarity of medical subject headings and gene ontology improves the interpretation of gene lists.

Gene expression and proteomics analysis allow the investigation of thousands of biomolecules in parallel. This results in a long list of interesting genes or proteins and a list of annotation terms in the order of thousands. It is not a trivial task to understand such a gene list and it would require extensive efforts to bring together the overwhelming amounts of associated information from the literature and databases. Thus, it is evident that we need ways of condensing and filtering this information. An excellent way to represent knowledge is to use ontologies, where it is possible to group genes or terms with overlapping context, rather than studying one-dimensional lists of keywords. Therefore, we have built the ontology annotation treebrowser (OAT) to represent, condense, filter and summarise the knowledge associated with a list of genes or proteins. The OAT system consists of two disjointed parts; a MySQL database named OATdb, and a treebrowser engine that is implemented as a web interface. The OAT system is implemented using Perl scripts on an Apache web server and the gene, ontology and annotation data is stored in a relational MySQL database. In OAT, we have harmonized the two ontologies of medical subject headings (MeSH) and gene ontology (GO), to enable us to use knowledge both from the literature and the annotation projects in the same tool. OAT includes multiple gene identifier sets, which are merged internally in the OAT database. We have also generated novel MeSH annotations by mapping accession numbers to MEDLINE entries. The ontology browser OAT was created to facilitate the analysis of gene lists. It can be browsed dynamically, so that a scientist can interact with the data and govern the outcome. Test statistics show which branches are enriched. We also show that the two ontologies complement each other, with surprisingly low overlap, by mapping annotations to the Unified Medical Language System. We have developed a novel interactive annotation browser that is the first to incorporate both MeSH and GO for improved interpretation of gene lists. With OAT, we illustrate the benefits of combining MeSH and GO for understanding gene lists. OAT is available as a public web service at: http://www.ifm.liu.se/bioinfo/oat.

Algorithms↗

PubMed2004

GOChase: correcting errors from Gene Ontology-based annotations for gene products.

SUMMARY: The Gene Ontology (GO) is a controlled biological vocabulary that provides three structured networks of terms to describe biological processes, cellular components and molecular functions. Many databases of gene products are annotated using the GO vocabularies. We found that some GO-updating operations are not easily traceable by the current biological databases and GO browsers. Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based high-level analyses. GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.

Database Management Systems↗

PubMedDate not supplied

Internet case management: finding information on the World Wide Web.

In conclusion, the World Wide Web offers an incredible variety of resources, many of which are available free of charge. To begin accessing these resources, one must first become comfortable with using browser software. Once this is done, master the basics of searching. Keep in mind that for a search to be efficient, you should have a clear understanding of why you are doing the search, the basis of a Purpose-Focus-Assessment analysis. With this information in hand, you can dive in, using methods that range from broad and general--such as brute force--to highly focused and specific literature searching. Remember that although the most effective searches are those that are tailored to the situation at hand, all searching on the Internet requires persistence, tenacity, and a good dose of creative thinking!

Case Management↗

PubMed2006

Lowering the barrier to a decentralized NHIN using the open healthcare framework.

In this paper, we discuss two important elements to lowering the barrier to creation of a National Health Information Network. The first element is the adoption of standards that will enable interoperability while guarantee open interfaces (and preventing vendor lock-in). The second element is the role of open source. While adoption of open standards by large EMR vendors is critically important to enterprise healthcare providers and payors, the availability of inexpensive (or free) standardized Healthcare Information Technology for small physician practices is critical. By analogy to the emergence of the World Wide Web, a framework for creating inexpensive and open source applications for physicians will be as important to realizing a National Health Information Network as availability of free browser technology was to the growth of the internet.

Ambulatory Care Information Systems↗

PubMed1997

Electronic forms: benefits drawbacks of a World Wide Web-based approach to data entry.

It has long been realized that, compared to paper-based records, electronic record systems provide many advantages in the healthcare environment, including increased availability, improved legibility, long-term accessibility, (potentially) greater completeness, data encoding, and automated decision support and analysis. In spite of these recognized benefits, collection of patient data at the point of service generally does not occur, in large part because each such effort usually requires application-specific software and hardware, and, most significantly, provider time. Given the presence of WWW browsers now available on nearly every desktop, the support and access concerns for data entry applications can be substantially lessened. Despite these advantages, there are also downsides to the use of the WWW for data entry, including user interface issues and security. At CPMC, we are currently using web-based forms to gather patient charge data from physical and occupational therapists. Benefits of this approach have included a 98.2% user compliance rate for at least weekly data entry, and the reduction of charge posting from an average of 24.3 days to 2.3 days following the date of service. Drawbacks to WWW-based applications have included increased security exposure and persistent human tendencies to enter data in batches rather than at the time of service. A final conclusion was that, in the absence of a strong central mandate, providers must perceive a clear benefit in order to be willing to learn and use a new technology.

Attitude to Computers↗

PubMed1998

A multi-agent softbot to retrieve medical information on Internet.

World-Wide Web is a media where information is unstructured, distributed, multimedia and multilingual. Many tools have been developed to help users search for information: subject hierarchies, general search engines, browsers and search assistants. Although helpful, they show serious limitations, mainly in terms of precision, multilingual indexing and distribution. The M.A.R.V.I.N. project (Multi Agent Retrieval Vagabond on Information Networks) proposes solutions with a distribution of the indexing task in agents specialized in a given domain. M.A.R.V.I.N. has been successfully applied to the medical domain. The medical index and its associated search engine MedHunt (Medical Hunter) demonstrate the interest of such an approach with currently 50,000 indexed medical sites and more than 100,000 accesses each month.

Abstracting and Indexing↗

PubMed2005

Design and utility of a web-based computer-assisted instructional tool for neuroanatomy self-study and review for physical and occupational therapy graduate students.

The cadaver continues to be the primary tool to teach human gross anatomy. However, cadavers are not available to students outside of the teaching laboratory. A solution is to make course content available through computer-assisted instruction (CAI). While CAI is commonly used as an ancillary teaching tool for anatomy, use of screen space, annotations that obscure the image, and restricted interactivity have limited the utility of such teaching tools. To address these limitations, we designed a Web-based CAI tool that optimizes use of screen space, uses annotations that do not decrease the clarity of the images, and incorporates interactivity across different operating systems and browsers. To assess the design and utility of our CAI tool, we conducted a prospective evaluation of 43 graduate students enrolled in neuroanatomy taught by the Divisions of Physical and Occupational Therapy at the University of Utah, College of Health. A questionnaire addressed navigation, clarity of the images, benefit of the CAI tool, and rating of the CAI tool compared to traditional learning tools. Results showed that 88% of the respondents strongly agreed that the CAI tool was easy to navigate and overall beneficial. Eighty-four percent strongly agreed that the CAI tool was educational in structure identification and had clear images. Furthermore, 95% of the respondents thought that the CAI tool was much to somewhat better than traditional learning tools. We conclude that the design of a CAI tool, with minimal limitations, provides a useful ancillary tool for human neuroanatomy instruction.

Computer-Assisted Instruction↗

PubMedDate not supplied

PASS biological activity spectrum predictions in the enhanced open NCI database browser.

The application of the program PASS (Prediction of Activity Spectra for Substances) to about 250 000 compounds of the NCI Open Database and the incorporation of over 64 million PASS predictions in the Enhanced NCI Database Browser are described. A total of 565 different types of activity are included, encompassing general pharmacological effects, specific mechanisms of action, known toxicities, and others. Application of this Web-based service to prediction of activities of the kinds "Angiogenesis inhibitor," "Antiviral (HIV)", and a set of activities that can be associated with antineoplastic action are reported. For this latter data set, a very substantial enrichment over random selection was found in the PASS predictions. It is shown how the user can conduct complex searches by combining ranges of PASS-predicted probabilities of compounds to be active or to be inactive, respectively, with, e.g., value ranges of physicochemical parameters, presence or absence of particular substructural fragment, and other search criteria.

Antineoplastic Agents↗

PubMed2004

Design and implementation of a web-enabled haematological system.

This paper describes the design and the implementation of a web-enabled integrated haematological system, named e-HS. The proposed system runs on a set of distributed network nodes providing useful haematological services. These services include patient-oriented data management, digitized histopathological slides (DHS) acquisition, teleconsulting facilities, etc. The objective of e-HS is to supply web-enabled services according to haematological requirements, implement a distributed storage scheme for DHS, and provide a common database containing all haematological laboratory results by using eXtensible Markup Language (XML) and web technologies. Our implementation can be accessible to every authorized physician at the distributed nodes without any additional software. The only software required for the user is the widely used browser (e.g. MS Internet Explorer v 3.02 or higher). Besides, by using a self-explaining user interfaces and HTML-techniques, such as hyperlinks, the necessary amount of training at the physicians-side is reduced to a minimum. A first implementation of the e-HS, has been established at the Medical Physics Department of the University of Patras (master node of the system), and has been tested with success by the medical staff of the Hospital Departments of the University of Patras and Thessalonica that served as distributed nodes of the system.

Clinical Laboratory Information Systems↗

PubMedDate not supplied

A web-based database for diagnosis of haematologic neoplasms using immunophenotyping by flow cytometry.

The interpretation of immunophenotyping results by flow cytometry involves pattern recognition of different haematologic neoplasms that may have similar immunologic marker patterns. The numerous markers available in the flow cytometry laboratory make these patterns difficult to remember, especially for those of uncommon neoplasms. We describe the design and implementation of a Web-based database for diagnosis of haematologic neoplasms using results of immunophenotyping by flow cytometry. This database aims to assist pathology and haematology residents in interpreting flow cytometry data, and is designed to reach a wide base of users who use a variety of browsers on different computer platforms. Five modules are developed in this comprehensive program: (a) differential diagnosis: to generate a list of differential diagnoses that closely match the marker results in a given case; (b) display of disorders: typical results of markers for each disorder; (c) display of markers: relevant information of each immunologic marker; (d) display of archived cases for a disorder: marker results of cases previously diagnosed for a disorder; and (e) display of summary for archived cases: summary of marker results of all the archived cases for each disorder. Our experience with this Web-based database in teaching pathology residents has been very encouraging. Since the World Wide Web is increasingly more accessible to computer users, it has become an ideal medium for distribution of clinical decision-support software.

Antigens, CD↗

PubMed2002

OpenRIMS: an open architecture radiology informatics Management system.

The following are benefits of an integrated picture archiving and communication system/radiology information system archive built with open-source tools and methods: open source, inexpensive interfaces can be updated as needed, and reduced risk of redundant and inconsistent data. Also, wide adoption would promote standard data mining tools, reducing user needs to learn multiple methods to perform the same task. A model has been constructed capable of accepting orders, performing exam resource scheduling, providing Digital communications in Medicine (DICOM) work list information to modalities, archiving studies, and supporting DICOM query/retrieve from third-party viewing software. The multitiered architecture uses a single database communicating via an open database connectivity bridge to a Linux server with Health Level 7 (HL7), DICOM, and HTTP connections. Human interaction is supported via a browser, whereas other informatics systems communicate over the HL7 and DICOM links. The system is still under development, but the primary database schema is complete, as are key pieces of the Web user interface. Additional work is needed on the DICOM/HL7 interface broker and completion of the base DICOM service classes.

Databases as Topic↗

PubMed1997

Teaching physiology and the World Wide Web: electrochemistry and electrophysiology on the Internet.

Students seek active learning experiences that can rapidly impart relevant information in the most convenient way possible. Computer-assisted education can now use the resources of the World Wide Web to convey the important characteristics of events as elemental as the physical properties of osmotically active particles in the cell and as complex as the nerve action potential or the integrative behavior of the intact organism. We have designed laboratory exercises that introduce first-year medical students to membrane and action potentials, as well as the more complex example of integrative physiology, using the dynamic properties of computer simulations. Two specific examples are presented. The first presents the physical laws that apply to osmotic, chemical, and electrical gradients, leading to the development of the concept of membrane potentials; this module concludes with the simulation of the ability of the sodium-potassium pump to establish chemical gradients and maintain cell volume. The second module simulates the action potential according to the Hodgkin-Huxley model, illustrating the concepts of threshold, inactivation, refractory period, and accommodation. Students can access these resources during the scheduled laboratories or on their own time via our Web site on the Internet (http./(/)phys-main.umsmed.edu) by using the World Wide Web protocol. Accurate version control is possible because one valid, but easily edited, copy of the labs exists at the Web site. A common graphical interface is possible through the use of the Hypertext mark-up language. Platform independence is possible through the logical and arithmetic calculations inherent to graphical browsers and the Javascript computer language. The initial success of this program indicates that medical education can be very effective both by the use of accurate simulations and by the existence of a universally accessible Internet resource.

Computer Communication Networks↗