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At least 379 records · Page 21Linked to original sources

PubMed2006

FM-test: a fuzzy-set-theory-based approach to differential gene expression data analysis.

BACKGROUND: Microarray techniques have revolutionized genomic research by making it possible to monitor the expression of thousands of genes in parallel. As the amount of microarray data being produced is increasing at an exponential rate, there is a great demand for efficient and effective expression data analysis tools. Comparison of gene expression profiles of patients against those of normal counterpart people will enhance our understanding of a disease and identify leads for therapeutic intervention. RESULTS: In this paper, we propose an innovative approach, fuzzy membership test (FM-test), based on fuzzy set theory to identify disease associated genes from microarray gene expression profiles. A new concept of FM d-value is defined to quantify the divergence of two sets of values. We further analyze the asymptotic property of FM-test, and then establish the relationship between FM d-value and p-value. We applied FM-test to a diabetes expression dataset and a lung cancer expression dataset, respectively. Within the 10 significant genes identified in diabetes dataset, six of them have been confirmed to be associated with diabetes in the literature and one has been suggested by other researchers. Within the 10 significantly overexpressed genes identified in lung cancer data, most (eight) of them have been confirmed by the literatures which are related to the lung cancer. CONCLUSION: Our experiments on synthetic datasets show that FM-test is effective and robust. The results in diabetes and lung cancer datasets validated the effectiveness of FM-test. FM-test is implemented as a Web-based application and is available for free at http://database.cs.wayne.edu/bioinformatics.

Algorithms↗

PubMed2007

IDconverter and IDClight: conversion and annotation of gene and protein IDs.

BACKGROUND: Researchers involved in the annotation of large numbers of gene, clone or protein identifiers are usually required to perform a one-by-one conversion for each identifier. When the field of research is one such as microarray experiments, this number may be around 30,000. RESULTS: To help researchers map accession numbers and identifiers among clones, genes, proteins and chromosomal positions, we have designed and developed IDconverter and IDClight. They are two user-friendly, freely available web server applications that also provide additional functional information by mapping the identifiers on to pathways, Gene Ontology terms, and literature references. Both tools are high-throughput oriented and include identifiers for the most common genomic databases. These tools have been compared to other similar tools, showing that they are among the fastest and the most up-to-date. CONCLUSION: These tools provide a fast and intuitive way of enriching the information coming out of high-throughput experiments like microarrays. They can be valuable both to wet-lab researchers and to bioinformaticians.

Algorithms↗

PubMed2004

Quantitative evaluation of recall and precision of CAT Crawler, a search engine specialized on retrieval of Critically Appraised Topics.

BACKGROUND: Critically Appraised Topics (CATs) are a useful tool that helps physicians to make clinical decisions as the healthcare moves towards the practice of Evidence-Based Medicine (EBM). The fast growing World Wide Web has provided a place for physicians to share their appraised topics online, but an increasing amount of time is needed to find a particular topic within such a rich repository. METHODS: A web-based application, namely the CAT Crawler, was developed by Singapore's Bioinformatics Institute to allow physicians to adequately access available appraised topics on the Internet. A meta-search engine, as the core component of the application, finds relevant topics following keyword input. The primary objective of the work presented here is to evaluate the quantity and quality of search results obtained from the meta-search engine of the CAT Crawler by comparing them with those obtained from two individual CAT search engines. From the CAT libraries at these two sites, all possible keywords were extracted using a keyword extractor. Of those common to both libraries, ten were randomly chosen for evaluation. All ten were submitted to the two search engines individually, and through the meta-search engine of the CAT Crawler. Search results were evaluated for relevance both by medical amateurs and professionals, and the respective recall and precision were calculated. RESULTS: While achieving an identical recall, the meta-search engine showed a precision of 77.26% (+/-14.45) compared to the individual search engines' 52.65% (+/-12.0) (p < 0.001). CONCLUSION: The results demonstrate the validity of the CAT Crawler meta-search engine approach. The improved precision due to inherent filters underlines the practical usefulness of this tool for clinicians.

Data Collection↗

PubMed2003

Development of a Web-based event reporting system in an academic environment.

In pursuit of a strategy for patient safety and error reduction, The Ohio State University Health System developed and implemented a standardized voluntary event reporting system. The Web-based application is user friendly as well as context-sensitive and encompasses a broad range of errors, events, and near misses. A full organizational transformation was required to effectively implement the system, which involved process reengineering for event entry and for postentry automated workflows. This system serves as the foundation for efficient and consistent reporting processes, which are essential for encouraging a culture of commitment to patient safety.

Academic Medical Centers↗

PubMed2003

A Web-based approach to low-cost telemedicine.

We have developed a Web-based application for managing e-consultations. This solves some of the problems inherent in peer-to-peer email communication. Referrals were from three hospitals in Vietnam. Each hospital was provided with Internet access for up to 4 hours a day for an initial 12-month period. In the first six months, six doctors from the Vietnamese hospitals submitted a total of 30 cases. Specialists in Sydney provided their expertise on a voluntary basis. Preliminary data suggest that the Vietnamese doctors found the system benefited their diagnostic and management decision making. Challenges have included equipment failures, language barriers and the difficulty of obtaining feedback. Successes have included the relationship building between doctors in the two countries. Preliminary results were encouraging and most of the Vietnamese doctors (five of the six) reported that they were slowly incorporating use of the system into their daily practice.

Attitude of Health Personnel↗

PubMed2006

Web-based information search and retrieval: effects of strategy use and age on search success.

OBJECTIVE: The purpose of this study was to investigate the relationship between strategy use and search success on the World Wide Web (i.e., the Web) for experienced Web users. An additional goal was to extend understanding of how the age of the searcher may influence strategy use. BACKGROUND: Current investigations of information search and retrieval on the Web have provided an incomplete picture of Web strategy use because participants have not been given the opportunity to demonstrate their knowledge of Web strategies while also searching for information on the Web. METHODS: Using both behavioral and knowledge-engineering methods, we investigated searching behavior and system knowledge for 16 younger adults (M = 20.88 years of age) and 16 older adults (M = 67.88 years). RESULTS: Older adults were less successful than younger adults in finding correct answers to the search tasks. Knowledge engineering revealed that the age-related effect resulted from ineffective search strategies and amount of Web experience rather than age per se. Our analysis led to the development of a decision-action diagram representing search behavior for both age groups. CONCLUSION: Older adults had more difficulty than younger adults when searching for information on the Web. However, this difficulty was related to the selection of inefficient search strategies, which may have been attributable to a lack of knowledge about available Web search strategies. APPLICATION: Actual or potential applications of this research include training Web users to search more effectively and suggestions to improve the design of search engines.

Adult↗

PubMed2005

Faculty as a community engaged with ongoing curricular development: use of groupware and electronic resources.

This article describes how technology can facilitate faculty engagement in curriculum development, use faculty time efficiently, and ensure program quality. A plan to initiate an accelerated second-degree bachelor of science in nursing option was the impetus for use of groupware electronic strategies to support faculty as valued members of the academic community, engaged in the undergraduate program and its curriculum. This article describes the two Web-based applications (electronic-based strategies) developed: the curriculum development homepage as a collaborative communication tool, and a curricular tracking tool.

Communication↗

PubMed2006

The tissue microarray object model: a data model for storage, analysis, and exchange of tissue microarray experimental data.

CONTEXT: Tissue microarray (TMA) is an array-based technology allowing the examination of hundreds of tissue samples on a single slide. To handle, exchange, and disseminate TMA data, we need standard representations of the methods used, of the data generated, and of the clinical and histopathologic information related to TMA data analysis. OBJECTIVE: To create a comprehensive data model with flexibility that supports diverse experimental designs and with expressivity and extensibility that enables an adequate and comprehensive description of new clinical and histopathologic data elements. DESIGN: We designed a tissue microarray object model (TMA-OM). Both the array information and the experimental procedure models are created by referring to the microarray gene expression object model, minimum information specification for in situ hybridization and immunohistochemistry experiments, and the TMA data exchange specifications. The clinical and histopathologic information model is created by using College of American Pathologists cancer protocols and National Cancer Institute common data elements. Microarray Gene Expression Data Ontology, the Unified Medical Language System, and the terms extracted from College of American Pathologists cancer protocols and NCI common data elements are used to create a controlled vocabulary for unambiguous annotation. RESULT: The TMA-OM consists of 111 classes in 17 packages to represent clinical and histopathologic information as well as experimental data for any type of cancer. We implemented a Web-based application for TMA-OM, supporting data export in XML format conforming to the TMA data exchange specifications or the document type definition derived from TMA-OM. CONCLUSIONS: The TMA-OM provides a comprehensive data model for storage, analysis, and exchange of TMA data and facilitates model-level integration of other biological models.

Gene Expression Profiling↗

PubMed1996

The quest for the Holy Grail of systems.

Software agents like Edify can be used to retrieve (and store) information from most online systems, without having to access each system's database. These techniques allow information integration (display) into Windows applications or in new reference and information retrieval applications or Web pages. These techniques can be used to bridge the gap until the Holy Grail of systems is built (and works).

Delivery of Health Care, Integrated↗

PubMed1998

HIMSS/IBM survey: staffing top priority.

Finding qualified IT staff members and integrating multivendor systems are this year's main challenges. Voice recognition, wireless information appliances and Web-enabled applications are the top new technologies.

Budgets↗

PubMed1998

Technology and the business office.

Providing access to information is the key to streamlining business office operations. Because they broaden access, document imaging, data marts, EDI and Web-enabled applications are winning a back-office following.

Ambulatory Care Information Systems↗

PubMed2000

Graphically-enabled integration of bioinformatics tools allowing parallel execution.

Rapid analysis of large amounts of genomic data is of great biological as well as medical interest. This type of analysis will greatly benefit from the ability to rapidly assemble a set of related analysis programs and to exploit the power of parallel computing. TurboGenomics, which is a software package currently in its alpha-testing phase, allows integration of heterogeneous software components to be done graphically. In addition, the tool is capable of making the integrated components run in parallel. To demonstrate these abilities, we use the tool to develop a Web-based application that allows integrated access to a set of large-scale sequence data analysis programs used by a transposon-insertion based yeast genome project. We also contrast the differences in building such an application with and without using the TurboGenomics software.

Computational Biology↗

PubMed2000

Weaving the Web into legacy information systems.

For many years, client-server systems were developed as the backbone of clinical computing in leading hospitals around the country. Beth Israel Deaconess Medical Center now faces the challenge of bridging the technology gap between such systems and the Internet. While developing Web interfaces to legacy clinical systems gives a taste of the future, it is clear that complete institutional migration to the Web is not imminent. Asking clinicians to utilize two different systems, Web-based and legacy, in the interim phase is just one of the difficulties in such transition. This paper describes "Mbridge", a solution that allows legacy system users to exploit the benefits of the Internet in a fashion that does not interfere with their workflow and is both simple and affordable to implement. The service allows clinicians to work on the legacy platform while context-sensitive clinical content is streamed to the browser without their intervention. Using the system, we can gradually expose clinicians to new Web-based applications and resources without forcing them to operate two computing environments simultaneously. The service achieves these goals by means of linkage and coordination rather than by code-translation, data exchange or replication.

Computer Systems↗

PubMed2000

Using the Internet to facilitate computerized patient records.

This paper explores using the Internet to implement an electronic medical records system. It examines methods and technologies, security issues, current Web-based applications and system vendors, and describes how to implement a clinic-suitable system.

Computer Security↗

PubMed2000

Web-based virtual endoscopy.

A web-based application for computed tomography (CT) image analysis and visualization of the bronchial airways is presented in the paper. The technique used in this application provides a noninvasive way to examine the interior of the bronchial tubes. Many different properties of the tubes such as presence of the foreign objects or structure abnormalities of the tubes can be detected this way. This method can also be used for other similar structures, such as blood vessels. The application uses the CT images obtained by spiral computed tomography as input. Amplitude thresholding is used for segmentation of the airways. The medial axis of the airways has been used as the path for animation. The procedure produces a fly-through animation in the MPEG format, which is obtained by volume rendering of the original CT images along the extracted path. The user can choose the appropriate path using the Virtual Reality Modeling Language (VRML) model, which is sufficient for visualization of basic structures. The algorithms and the software have been developed on the SUN Ultra 1 workstation.

Bronchoscopy↗

PubMed2001

Developing a protocol for an educational software competition.

This project developed a protocol for the inaugural Instructional Software Competition of the American Dental Education Association (ADEA). The evaluation instrument was derived from the Guidelines for the Design of Educational Software developed by the ANSI-accredited Standards Committee for Dental Informatics. Eleven judges were calibrated in a conference call and rated a total of 30 submissions using a 66-question instrument. The maximum score was 204 points. The mean score of WWW-based programs was 106.7 points, and of CD-ROM-based programs 109.5 points. The summative review of the judging process identified several potential improvements, such as distinguishing between standalone programs and educational support material; increasing the number of answer choices on rating scales; differential weighting of criteria; and a more discriminative approach to judging formative and summative evaluations. We plan to improve the protocol by supporting the process through a Web-based application; calibrating judges with an online handbook; improving and adapting the rating instrument itself; using at least three judges for each program; and conducting a measurement study.

American Dental Association↗

PubMed2003

Patient relation management: a relevant solution to connect the links of a healthcare chain.

The USIT-tool is used to investigate the health care chain of Multiple Sclerosis (MS) in a Dutch region. The advantage of the USIT-tool is that is results in insight in the relevant problems, solutions and constraints of the caregivers both in the organisational and the information technological area. The main problem in the MS-health care chain proved to be the lack of co-ordination and the inefficient communication between caregivers. Although most caregivers were convinced of the need to improve delivered care for MS-patient, most of them also expressed that they would spend little time and energy on improving MS-care, because of the low relevance of MS-care compared to other kinds of care. To improve care, taking in account this constraint we propose to build a Patient Relation Management (PRM) System. A PRM is a simple web-based application that is based on agreement by the caregivers about the route an MS-patient should follow through health care. PRM supports routing, tracking and tracing of a patient and supplies the caregivers with professional guidelines. The PRM-concept can easily be expanded to other patient groups or diseases and can serve as a first step to a regional Electronic Patient Record. It is likely that we would have suggested a far more complicated ICT solution if we had only analysed the MS-care process as such, without specific consideration of the USIT dimensions. The USIT analysis helped us to balance the breadth of the proposed solution with the nature of the situation the future users of the system are in.

Consumer Behavior↗

PubMed2003

Mobile technology in a clinical setting.

Wireless technology can offer clinicians access to the latest patient data when they are located outside of the hospital campus. It allows physicians to be more effective with their time by enabling a new method of delivering clinical information, thus improving patient care. Imagine being stuck in traffic, or at a conference in another state, when a call comes in for the patient's latest lab results. With a wireless handheld device, and a web-based application, the physician can access this information in minutes.

Attitude of Health Personnel↗