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At least 217 records · Page 12Linked to original sources

WebaCGH: an interactive online tool for the analysis and display of array comparative genomic hybridisation data.

UNLABELLED: Gene copy number variations occur both in normal cells and in numerous pathologies including cancer and developmental diseases. Array comparative genomic hybridisation (aCGH) is an emerging technology that allows detection of chromosomal gains and losses in a high-resolution format. When aCGH is performed on cDNA and oligonucleotide microarrays, the impact of DNA copy number on gene transcription profiles may be directly compared. We have created an online software tool, WebaCGH, that functions to (i) upload aCGH and gene transcription results from multiple experiments; (ii) identify significant aberrant regions using a local Z-score threshold in user-selected chromosomal segments subjected to smoothing with moving averages; and (iii) display results in a graphical format with full genome and individual chromosome views. In the individual chromosome display, data can be zoomed in/out in both dimensions (i.e. ratio and physical location) and plotted features can have 'mouse over' linking to outside databases to identify loci of interest. Uploaded data can be stored indefinitely for subsequent retrieval and analysis. WebaCGH was created as a Java-based web application using the open-source database MySQL. AVAILABILITY: WebaCGH is freely accessible at http://129.43.22.27/WebaCGH/welcome.htm CONTACT: Xiaolin Wu (forestwu@mail.nih.gov) or Ulises Urzúa (uurzua@med.uchile.cl).

Animals↗

Taxonomic informatics tools for the electronic Nomenclator Zoologicus.

Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase retrieval rates for documents and to refine data recovery. Biological data have traditionally been well managed using taxonomic principles. As part of a larger initiative to build an array of names-based network services that emulate taxonomic principles for managing biological information, we undertook the digitization of a major taxonomic reference text, Nomenclator Zoologicus. The process involved replicating the text to a high level of fidelity, parsing the content for inclusion within a database, developing tools to enable expert input into the product, and integrating the metadata and factual content within taxonomic network services. The result is a high-quality and freely available web application (http://uio.mbl.edu/NomenclatorZoologicus/) capable of being exploited in an array of biological informatics services.

Animals↗

CoPreTHi: a Web tool which combines transmembrane protein segment prediction methods.

CoPreTHi is a Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces superior quality results than individual prediction schemes. The program is available at http://o2.db.uoa.gr/CoPreTHi.

Algorithms↗

CHIP TUNER: a web tool for evidence-based noise reduction in gene discovery.

The potential for gene discovery, fueled by DNA microchip technology and the sequencing of hundreds of genomes, is unprecedented. In this context, trying to discover genes that are actually of significance rather than merely appearing so due to noise is of utmost importance. We present a web application, CHIP TUNER, which assists in this gene discovery process. Our system uses evidence-based noise reduction to help delineate candidate target genes of biological importance. Specifically, CHIP TUNER learns from redundant experiments an "identity mask" that defines a region of noise inherent to biological sampling and DNA microarray processing; it then takes this into account during actual sample comparisons. The goal of CHIP TUNER is to improve the chances that newly discovered "important" genes are actually of importance before large amounts of time and resources are invested.

Computational Biology↗

Bioterrorism preparedness.

The Connecticut Department of Public Health (DPH) entered into a cooperative agreement with the Centers for Disease Control and Prevention (CDC) to establish public health preparedness and a response plan for bioterrorism. With funds from the CDC and an additional grant from the Health Resources and Services Administration (HRSA), the DPH designated Hartford Hospital as one of two Centers of Excellence that will coordinate and manage a statewide system for bioterrorism preparedness. This paper reviews the progress that Hartford Hospital has made in meeting this challenge. Highlighted are the development of a Web application to use for statewide preparedness and response, and the preparation for a smallpox vaccination program at Hartford Hospital.

Bioterrorism↗

CRC Tissue Core Management System (TCMS): integration of basic science and clinical data for translational research.

The Chronic Lymphocytic Leukemia (CLL) Research Consortium (CRC) consists of 9 geographically distributed sites conducting a program of research including both basic science and clinical components. The CRC TCMS was designed to capture and integrate basic science and clinical data sets. The system utilizes multiple data modeling methodologies and web-application platforms, and was designed with the high level objectives of providing an extensible, generalizable model for integrating data as required to conduct translational research.

Biomedical Research↗

CRC Clinical Trials Management System (CTMS): an integrated information management solution for collaborative clinical research.

The Chronic Lymphocytic Leukemia (CLL) Research Consortium (CRC) consists of 9 geographically distributed sites conducting a program of research including both basic science and clinical components. To enable the CRC's clinical research efforts, a system providing for real-time collaboration was required. CTMS provides such functionality, and demonstrates that the use of novel data modeling, web-application platforms, and management strategies provides for the deployment of an extensible, cost effective solution in such an environment.

Biomedical Research↗

Integration architecture of a mobile virtual health record for shared home care.

The coexistence of different information systems that are unable to communicate with each other is a persistent problem in health care in general, and in shared care in particular. This is especially critical when it comes to information access needed at the point of care, e.g. in the patient's home. The purpose of this paper is to present the technical architecture of a virtual health record (VHR) that both integrates information from different electronic health records (EHRs) and allows for documenting at the point of care using mobile devices. The VHR supports a seamless information and communication flow between different care providers giving them mobile access to selected patient-oriented information. A service oriented system architecture where database functionality and services are separated has been implemented. This guarantees flexibility with regard to changed functional demands and allows third party systems to interact with the platform in a standardised way. Major requirements for the VHR have been documentation support at the point of care, integrated presentation of the information from different feeder systems, and the possibility of offline access to the data on handheld devices. Therefore, publishing was chosen for the integration design. A patient centred XML schema is published as an interface for integration with the information broker. The feeder systems deliver their information in XML.-files that are mapped against the ideal schema and inserted into the mediator database. The paper describes both an online web application and an offline solution that was implemented on personal digital assistants (PDAs). The system has been introduced in a Swedish home care district with an established fiber-optical network infrastructure connecting all the locations forming the study site.

Computers, Handheld↗

An introduction to the Semantic Web for health sciences librarians.

OBJECTIVES: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. METHODOLOGY: The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. DISCUSSION AND CONCLUSIONS: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects.

Humans↗

Surveillance for foodborne-disease outbreaks--United States, 1998-2002.

PROBLEM/CONDITION: Since 1973, CDC has maintained a collaborative surveillance program for collection and periodic reporting of data on the occurrence and causes of foodborne-disease outbreaks (FBDOs) in the United States. REPORTING PERIOD COVERED: 1998-2002. DESCRIPTION OF SYSTEM: The Foodborne Disease Outbreak Surveillance System reviews data on FBDOs, defined as the occurrence of two or more cases of a similar illness resulting from the ingestion of a common food. State and local public health departments have primary responsibility for identifying and investigating FBDOs. State, local, and territorial health departments use a standard form to report these outbreaks to CDC. In 1998, CDC implemented enhanced surveillance for FBDOs by increasing communication with state, local, and territorial health departments and revising the outbreak report form. Since 2001, reports of FBDOs are submitted through a web application on the Internet called the electronic Foodborne Outbreak Reporting System (eFORS). RESULTS: During 1998-2002, a total of 6,647 outbreaks of foodborne disease were reported (1,314 in 1998, 1,343 in 1999, 1,417 in 2000, 1,243 in 2001, and 1,330 in 2002). These outbreaks caused a reported 128,370 persons to become ill. Among 2,167 (33%) outbreaks for which the etiology was determined, bacterial pathogens caused the largest percentage of outbreaks (55%) and the largest percentage of cases (55%). Among bacterial pathogens, Salmonella serotype Enteritidis accounted for the largest number of outbreaks and outbreak-related cases; Listeria monocytogenes accounted for the majority of deaths of any pathogen. Viral pathogens, predominantly norovirus, caused 33% of outbreaks and 41% of cases; the proportion of outbreaks attributed to viral agents increased from 16% in 1998 to 42% in 2002. Chemical agents caused 10% of outbreaks and 2% of cases, and parasites caused 1% of outbreaks and 1% of cases. INTERPRETATION: Following implementation of measures to enhance outbreak surveillance, the annual number of FBDOs reported to CDC increased during this period compared with previous years. Viral pathogens accounted for an increased proportion of outbreaks each year during this reporting period and a higher proportion of outbreaks of known etiology during this reporting period than preceding reporting periods, probably reflecting the increased availability of improved viral diagnostic tests. S. Enteritidis continued to be a major cause of illness and L. monocytogenes was a major cause of death. In addition, multistate outbreaks caused by contaminated produce and outbreaks caused by Escherichia coli O157:H7 remained prominent. PUBLIC HEALTH ACTIONS: Methods to detect FBDOs are improving, and several changes to improve the ease and timeliness of reporting FBDO data have been implemented (e.g., a revised form to simplify FBDO reporting by state health departments and improved electronic reporting methods). State and local health departments continue to investigate and report FBDOs as part of efforts to better understand and define the epidemiology of foodborne disease in the United States. At the regional and national levels, surveillance data provide an indication of the etiologic agents, vehicles of transmission, and contributing factors associated with FBDOs and help direct public health actions to reduce illness and death caused by FBDOs.

Disease Outbreaks↗

Emergency medical information system for transferring patients to the medical institute by triage-result.

The Objective of this study was to triage the emergency patients in a pre-hospital stage and transfer them to the appropriate medical institute by the triaged result. For this, considering the pre-hospital emergence situation, we selected the Manchester system as the triage. So we analyzed the components of the ambulance records in Korea, transformed MTS components according to analysis-results of the ambulances and applied them to the information system in using a C# web application. Then we made the emergency medical institute database with the distances of any selected places and institute-grade in the emergency medical system and connected the triage-result with the medical institute database. Through this study, the medical institute can be selected based on patient condition. In addition we also can expect the emergency medical institutes to be effectively managed.

Emergency Service, Hospital↗

Using concept maps on the World-Wide Web to access a curriculum database for problem-based learning.

Development of medical school curriculum databases continues to be challenging. Representation of the instructional unit is becoming increasingly difficult due to characteristics of the problem-based learning (PBL) curricula. Curriculum databases may be used to store materials for the PBL curricula, and also to provide a delivery mechanism for those materials. However, in order to take advantage of the curriculum database as a tool for PBL, methods for accessing the curriculum database that are better suited to the information needs of students, faculty, and administrators must be developed. Concept maps are directed graph representations of conceptual relationships, and may be used to represent the content of a curriculum database. In this paper, we describe a Web application that uses Java-based concept maps was the user interface to a curriculum database.

Computer Communication Networks↗

Stochastic webs and their applications.

The conditions for the appearance of a stochastic web in degenerate dynamic systems and typical physical problems that lead to such a web are analyzed. Examples of webs are considered, as well as their symmetry, width, and structural changes. A description is given of a change in the diffusion dynamics along the web channels as a function of the number of the degrees of freedom and the phenomenon of stochastic percolation is discussed.

Journal Article↗

Internet as clinical information system: application development using the World Wide Web.

Clinical computing application development at Columbia-Presbyterian Medical Center has been limited by the lack of a flexible programming environment that supports multiple client user platforms. The World Wide Web offers a potential solution, with its multifunction servers, multiplatform clients, and use of standard protocols for displaying information. The authors are now using the Web, coupled with their own local clinical data server and vocabulary server, to carry out rapid prototype development of clinical information systems. They have developed one such prototype system that can be run on most popular computing platforms from anywhere on the Internet. The Web paradigm allows easy integration of clinical information with other local and Internet-based information sources. The Web also simplifies many aspects of application design; for example, it includes facilities for the use of encryption to meet the authors' security and confidentiality requirements. The prototype currently runs on only the Web server in the Department of Medical Informatics at Columbia University, but it could be run on other Web servers that access the authors' clinical data and vocabulary servers. It could also be adapted to access clinical information from other systems with similar server capabilities. This approach may be adaptable for use in developing institution-independent standards for data and application sharing.

Computer Communication Networks↗

Development of a web based electronic patient record extending accessibility to clinical information and integrating ancillary applications.

Web-technology offers a powerful mechanism for providing access to clinic information. Applications need no longer to be tied to a specific client operating system. The Johns Hopkins Hospital has designed a web based electronic patient record system which seamlessly incorporates multiple web sites. This paper will discuss the motivations for building the system, the architecture, and the challenges faced in designing the architecture.

Academic Medical Centers↗

Building messaging substrates for Web and Grid applications.

Grid application frameworks have increasingly aligned themselves with the developments in Web services. Web services are currently the most popular infrastructure based on service-oriented architecture (SOA) paradigm. There are three core areas within the SOA framework: (i) a set of capabilities that are remotely accessible, (ii) communications using messages and (iii) metadata pertaining to the aforementioned capabilities. In this paper, we focus on issues related to the messaging substrate hosting these services; we base these discussions on the NARADABROKERING system. We outline strategies to leverage capabilities available within the substrate without the need to make any changes to the service implementations themselves. We also identify the set of services needed to build Grids of Grids. Finally, we discuss another technology, HPSEARCH, which facilitates the administration of the substrate and the deployment of applications via a scripting interface. These issues have direct relevance to scientific Grid applications, which need to go beyond remote procedure calls in client-server interactions to support integrated distributed applications that couple databases, high performance computing codes and visualization codes.

Computer Simulation↗

Distributed nuclear medicine applications using World Wide Web and Java technology.

At present, medical applications applying World Wide Web (WWW) technology are mainly used to view static images and to retrieve some information. The Java platform is a relative new way of computing, especially designed for network computing and distributed applications which enables interactive connection between user and information via the WWW. The Java 2 Software Development Kit (SDK) including Java2D API, Java Remote Method Invocation (RMI) technology, Object Serialization and the Java Advanced Imaging (JAI) extension was used to achieve a robust, platform independent and network centric solution. Medical image processing software based on this technology is presented and adequate performance capability of Java is demonstrated by an iterative reconstruction algorithm for single photon emission computerized tomography (SPECT).

Image Processing, Computer-Assisted↗