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At least 397 records · Page 22Linked to original sources

Web-based visualisation of the transcriptional control network of Escherichia coli.

Transcription is one of the basic processes of gene expression, controlled by a complex network of biochemical reactions. Despite its importance, most work on the visualisation of biochemical networks focuses on the representation of metabolic pathways. The visualisation of the complex networks controlling transcription requires the implementation of a hierarchical approach that allows the display of the structure of each regulatory region with its transcription factors and regulated operons. This paper presents a web-based application for the visualisation of transcriptional control networks. It takes as case study the organism Escherichia coli. The definition of the visual components implemented is mainly based on those proposed by Shen-Orr et al., 2002, slightly extended to visualise complex networks.

Computational Biology↗

An implementation of automated individual matching for observational studies.

OBJECTIVES: Individual matching is frequently used in observational studies. Its main purpose lies in efficiency of study conduct and parameter estimation. Ideally, an individually matched index subject differs from the reference subject(s) only by the factor(s) of interest. Matching is used to select comparable subgroups on which further data analysis can then concentrate. Finding optimal subsets is then a closed problem, which may include a lot of guesswork. It is a task that begs an algorithmic solution that can be obtained automatically. METHODS: The problem can be formalized as a minimization of a global loss function that summarizes the deviation from perfect agreement over different variables. Through the representation by a network formed by a bipartite graph of index and reference subjects, one can obtain a solution by finding a minimum cost flow in a certain network. We have implemented a Web-based application using the efficient CS2 algorithm. RESULTS: Variations of the individual matching procedures that have been implemented comprise 1:N matching and matching with a variable number of controls. The user can upload own data, view the proposed result in a list and finally download the matching plan. Representation of quality of individual matches as background colors allows rapid checks for overall matching accuracy. CONCLUSIONS: The computer-assisted variation reduces the human interaction to the tuning of a few parameters, rather than individual decisions on forming separate matches. This not only saves a lot of work but also simplifies communicating the matching process. The program addresses a general class of matching problems. The use of this tool for special cases of matching, as caliper matching or exact category matching, is highlighted.

Algorithms↗

Development of the Diabetes Indicators and Data Sources Internet Tool (DIDIT).

Developing a Web-based tool that involves the input, buy-in, and collaboration of multiple stakeholders and contractors is a complex process. Several elements facilitated the development of the Web-based Diabetes Indicators and Data Sources Internet Tool (DIDIT). The DIDIT is designed to enhance the ability of staff within the state-based Diabetes Prevention and Control Programs (DPCPs) and the Centers for Disease Control and Prevention (CDC) to perform diabetes surveillance. It contains information on 38 diabetes indicators (measures of health or factors associated with health) and 12 national- and state-level data sources. Developing the DIDIT required one contractor to conduct research on content for diabetes indicators and data sources and another contractor to develop the Web-based application to house and manage the information. During 3 years, a work group composed of representatives from the DPCPs and the Division of Diabetes Translation (DDT) at the CDC guided the development process by 1) gathering information on and communicating the needs of users and their vision for the DIDIT, 2) reviewing and approving content, and 3) providing input into the design and system functions. Strong leadership and vision of the project lead, clear communication and collaboration among all team members, and a commitment from the management of the DDT were essential elements in developing and implementing the DIDIT. Expertise in diabetes surveillance and software development, enthusiasm, and dedication were also instrumental in developing the DIDIT.

Diabetes Mellitus, Type 2↗

Planning, modelling and assessing source control concepts on catchment scale.

Today's water management practice was identified often not to be consistently structured. Usually the decision space is not clearly depicted and then systematically explored. Often stakeholders are involved too late and many objectives are neglected. An adaptive DSS is being developed to help overcoming these problems. Core of the DSS is a "decision matrix", which has been implemented as a web based application (www.wsm300.de). The management objectives are represented by the indicators labelling the rows. They will be the result of a discussion of the objectives and problems in the specific sub-basin, which is supported by the catalogue of indicators. The columns of the matrix are specified by the scenarios whose development is supported by the database of measures and a Geographical Information System (GIS). The matrix, once the labels are defined, serves as a plot for the planning process, defining clearly which objectives have to be considered and which indicator-values have to be calculated. The DSS further includes a concept and tools for the combination of existing software components and supports the processing of model-outputs to indicator-values. Filled with the indicator-values the matrix allows a comparison of the scenarios and provides a good base for a decision. Multi-criteria decision aid methods can (if desired) further help to find the optimal scenario and to mediate between stakeholders. Finding the optimal scenario will likely be an iterative process.

Databases, Factual↗

Changing academic roles--new approaches to teaching and distance learning in Australia.

OBJECTIVES: A primary objective of this study was to identify a valid method for academic workload allocation. This required the identification of significant variables that may be used to indicate and measure academic workload. A supporting objective was to illustrate how the adoption of a flexible learning mode and supporting technologies across one university with multiple campuses and an international student cohort has impacted upon academic roles and teaching delivery methods. METHODS: An extensive literature review focusing primarily on the teaching aspects of academic roles was undertaken. These roles were defined as teaching, including curriculum development, undertaking research, provide professional and community services and undertake some administrative work. This review was followed by the documentation of a case study. RESULTS: Significant changes to the roles and responsibilities of academics working in higher education are now discernable. The adoption of Web-based applications and other communication technologies have made it possible to not only extend traditional distance education offerings but also to teach large multicultural classes across multiple campuses simultaneously. This in turn necessitates a review of teaching strategies and of organization-wide student and staff support infrastructures to ensure that the teaching quality is maintained or improved whilst meeting individual student learning needs. CONCLUSIONS: Changes to academics' roles are occurring due to the globalisation of higher education as well as the adoption of new educational delivery methods and the use of new technologies. The resulting complexity of academic workload measurement and the need to equitably allocate this workload to individual academics has become more challenging than ever. More traditional universities can learn from such experiences to better prepare for these inevitable changes.

Australia↗

An open source model for open access journal publication.

We describe an electronic journal publication infrastructure that allows a flexible publication workflow, academic exchange around different forms of user submissions, and the exchange of articles between publishers and archives using a common XML based standard. This web-based application is implemented on a freely available open source software stack. This publication demonstrates the Dermatology Online Journal's use of the platform for non-biased independent open access publication.

Access to Information↗

The evaluation criteria of internet health information.

The Internet has great powerful forces for health information and education. This describes the development of a web-based evaluation criteria for internet health information. The purpose of this study was to explore the evaluation criteria (tool) of internet health information for Korean. This utilized a cross-sectional design with four sections: (1) CAHPS (Consumer assessment of health plans studies); (2) Health consumer terminology and understanding review; (3) web based interactive tool construction; (4) semantic web technology application. The findings showed follows; (1) literature review related quality evaluation tool for internet health information; (2) case study; (3) development of evaluation prototype; (4) validity assessment of tool; (5) Evaluation system information strategic planning.

Cross-Sectional Studies↗

Design of a Web interface for anatomical images.

Interactive documents for use with the World Wide Web have been developed for viewing multi-dimensional radiographic and visual images of human anatomy, derived from the Visible Human Project. Emphasis has been placed on user-controlled features and selections. The purpose was to develop an interface which was independent of host operating system and browser software which would allow viewing of information by multiple users. The interfaces were implemented using HyperText Markup Language (HTML) forms, C programming language and Perl scripting language. Images were pre-processed using ANALYZE and stored on a Web server in CompuServe GIF format. Viewing options were included in the document design, such as interactive thresholding and two-dimensional slice direction. The interface is an example of what may be achieved using the World Wide Web. Key applications envisaged for such software include education, research and accessing of information through internal databases and simultaneous sharing of images by remote computers by health personnel for diagnostic purposes.

Anatomy, Cross-Sectional↗

Using the extensible markup language (XML) in automated clinical practice guidelines.

Much work has been done in the area of web-based clinical practice guidelines. Issues such as representation, description, architectures, and implementation have been explored previously. Most if not all of these web-based applications rely exclusively on HTML, the HyperText Markup Language. In the process of prototyping a guideline service to be used in a diabetes operations improvement project, we developed a model for a guideline engine that makes use of the Extensible Markup Language (XML), both as an interface to the engine and as a vehicle for delivering structured guideline content. We feel that XML may offer advantages in implementing guideline services that are difficult (if not impossible) to accomplish with HTML alone.

Computer Systems↗

Sulfur stable isotopes separate producers in marine food-web analysis.

Ecological applications of stable isotope analysis rely on different producers having distinct isotopic ratios to trace energy and nutrient transfer to consumers. Carbon (C) and nitrogen (N) are the usual elements analysed. We tested the hypothesis that producers unable to be separated using C and N would be separated by sulphur (S), by reviewing estuarine and marine food web studies using all three elements (total of 836 pairwise comparisons between producers). S had a wider range of values across all producers than C and N (S: 34.4, C: 23.3, N: 18.7 per thousand ), and a higher mean difference among producers (S: 9.3, C: 6.5, N: 3.3 per thousand ). We varied from 1 to 10 per thousand the distance producers must be apart to be considered separate. For each of these gap distances, S-separated producers tied on C and N in 40% or more of cases. Comparing the three elements individually, S had fewer tied pairs of producers for any gap distance than C or N. However, S also has higher within-producer variability. Statistical tests on simulated data showed that this higher variability caused S to be less effective than C for analysing differences among mean producer values, yet mixing models showed that S had the smallest confidence intervals around mean estimates of source contributions to consumers. We also examined the spatial and temporal scales over which S isotope signatures of the saltmarsh plant Spartina alterniflora varied. Differences between samples taken within tens of metres were smallest, but between samples hundreds of metres apart were as different as samples thousands of kilometres apart. The time between samples being taken did not influence S signatures. Overall, the use of S is recommended because it has a high probability of distinguishing the contribution of different producers to aquatic food webs. When two elements are employed, the combination of S and C separates more producers than any other combination.

Animals↗

Abdominal aortic aneurysms: virtual imaging and analysis through a remote web server.

The study describes the application of a web-based software in the planning of the endovascular treatment of abdominal aortic aneurysms (AAA). The software has been developed in the framework of a 2-year research project called Aneurysm QUAntification Through an Internet Collaborative System (AQUATICS); it allows to manage remotely Virtual Reality Modeling Language (VRML) models of the abdominal aorta, derived from multirow computed tomography angiography (CTA) data sets, and to obtain measurements of diameters, angles and centerline lengths. To test the reliability of measurements, two radiologists performed a detailed analysis of multiple 3D models generated from a synthetic phantom, mimicking an AAA. The system was tested on 30 patients with AAA; CTA data sets were mailed and the time required for segmentation and measurement were collected for each case. The Bland-Altman plot analysis showed that the mean intra- and inter-observer differences in measures on phantoms were clinically acceptable. The mean time required for segmentation was 1 h (range 45-120 min). The mean time required for measurements on the web was 7 min (range 4-11 min). The AQUATICS web server may provide a rapid, standardized and accurate tool for the evaluation of AAA prior to the endovascular treatment.

Angiography↗

Learning and cognitive styles in web-based learning: theory, evidence, and application.

Cognitive and learning styles (CLS) have long been investigated as a basis to adapt instruction and enhance learning. Web-based learning (WBL) can reach large, heterogenous audiences, and adaptation to CLS may increase its effectiveness. Adaptation is only useful if some learners (with a defined trait) do better with one method and other learners (with a complementary trait) do better with another method (aptitude-treatment interaction). A comprehensive search of health professions education literature found 12 articles on CLS in computer-assisted learning and WBL. Because so few reports were found, research from non-medical education was also included. Among all the reports, four CLS predominated. Each CLS construct was used to predict relationships between CLS and WBL. Evidence was then reviewed to support or refute these predictions. The wholist-analytic construct shows consistent aptitude-treatment interactions consonant with predictions (wholists need structure, a broad-before-deep approach, and social interaction, while analytics need less structure and a deep-before-broad approach). Limited evidence for the active-reflective construct suggests aptitude-treatment interaction, with active learners doing better with interactive learning and reflective learners doing better with methods to promote reflection. As predicted, no consistent interaction between the concrete-abstract construct and computer format was found, but one study suggests that there is interaction with instructional method. Contrary to predictions, no interaction was found for the verbal-imager construct. Teachers developing WBL activities should consider assessing and adapting to accommodate learners defined by the wholist-analytic and active-reflective constructs. Other adaptations should be considered experimental. Further WBL research could clarify the feasibility and effectiveness of assessing and adapting to CLS.

Aptitude↗

Use and utility of Web-based residency program information: a survey of residency applicants.

BACKGROUND: The Internet has become essential to the residency application process. In recent years, applicants and residency programs have used the Internet-based tools of the National Residency Matching Program (NRMP, the Match) and the Electronic Residency Application Service (ERAS) to process and manage application and Match information. In addition, many residency programs have moved their recruitment information from printed brochures to Web sites. Despite this change, little is known about how applicants use residency program Web sites and what constitutes optimal residency Web site content, information that is critical to developing and maintaining such sites. OBJECTIVE: To study the use and perceived utility of Web-based residency program information by surveying applicants to an internal medicine program. METHODS: Our sample population was the applicants to the Oregon Health & Science University Internal Medicine Residency Program who were invited for an interview. We solicited participation using the group e-mail feature available through the Electronic Residency Application Service Post-Office application. To minimize the possibility for biased responses, the study was confined to the period between submission of National Residency Matching Program rank-order lists and release of Match results. Applicants could respond using an anonymous Web-based form or by reply to the e-mail solicitation. We tabulated responses, calculated percentages for each, and performed a qualitative analysis of comments. RESULTS: Of the 431 potential participants, 218 responded (51%) during the study period. Ninety-nine percent reported comfort browsing the Web; 52% accessed the Web primarily from home. Sixty-nine percent learned about residency Web sites primarily from residency-specific directories while 19% relied on general directories. Eighty percent found these sites helpful when deciding where to apply, 69% when deciding where to interview, and 36% when deciding how to rank order programs for the Match. Forty-nine percent found sites most useful in deciding where to apply, while 40% found them most useful while preparing for their interviews. Seventy-two percent felt that a "complete" Web site could substitute for a mailed printed brochure. Qualitative analysis identified additional important information needs. CONCLUSIONS: Applicants are turning to residency Web sites for information during critical phases of the application process. Though usually helpful, many of these sites are felt to be incomplete and may not be meeting important applicant information needs. These findings should be useful to those involved in residency recruitment efforts and in counseling applicants.

Attitude to Computers↗

A Web link management tool for optimizing utilization of distributed knowledge in health care applications.

The number of health-related Web sites on the Internet is increasing. Incorporating these sites into clinical decision support systems and other health care applications can significantly enhance the educational and instructional value of such systems. While search engines exist for finding sites and criteria are available for assessing site quality, few tools are available for managing Web-based health care information. Management of Web-based information is particularly challenging because the information is continually changing and new resources are continually being added. In this paper, we describe the development and use of a Web-link manager for health care applications. This system retains search strategies for repeated use, catalogues search results in a search results database, accommodates tracking of site review and use status, and provides periodic checking of link integrity for sites that are used in local applications. The Web-link manager is currently in use to manage the links used in a clinical decision support system that presents clinical practice guidelines interactively to clinicians at the point of care.

Computer Communication Networks↗

Flows of dioxins and furans in coastal food webs: inverse modeling, sensitivity analysis, and applications of linear system theory.

Rate constant bioaccumulation models are applied to simulate the flow of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in the coastal marine food web of Frierfjorden, a contaminated fjord in southern Norway. We apply two different ways to parameterize the rate constants in the model, global sensitivity analysis of the models using Extended Fourier Amplitude Sensitivity Test (Extended FAST) method, as well as results from general linear system theory, in order to obtain a more thorough insight to the system's behavior and to the flow pathways of the PCDD/Fs. We calibrate our models against observed body concentrations of PCDD/Fs in the food web of Frierfjorden. Differences between the predictions from the two models (using the same forcing and parameter values) are of the same magnitude as their individual deviations from observations, and the models can be said to perform about equally well in our case. Sensitivity analysis indicates that the success or failure of the models in predicting the PCDD/F concentrations in the food web organisms highly depends on the adequate estimation of the truly dissolved concentrations in water and sediment pore water. We discuss the pros and cons of such models in understanding and estimating the present and future concentrations and bioaccumulation of persistent organic pollutants in aquatic food webs.

Animals↗

Designing web services in health information systems: from process to application level.

Service-oriented architectures (SOAs) and web service technologies have been proposed to respond to some central interoperability challenges of heterogeneous health information systems (HIS). We propose a model which we are using to define services and solutions for healthcare applications from the requirements in the healthcare processes. Focusing on the transition from the process level of the model to the application level, we also present some central design considerations, which can be used to guide the design of service-based interoperability. We illustrate these aspects with examples from our current work from the service-enabled HIS.

Computer Security↗

Designing web services in health information systems: from process to application level.

Service-oriented architectures (SOA) and web service technologies have been proposed to respond to some central interoperability challenges of heterogeneous health information systems (HIS). We propose a model, which we are using to define services and solutions for healthcare applications from the requirements in the healthcare processes. Focusing on the transition from the process level of the model to the application level, we also present some central design considerations, which can be used to guide the design of service-based interoperability and illustrate these aspects with examples from our current work in service-enabled HIS.

Computer Systems↗

An interactive Web site providing major histocompatibility ligand predictions: application to HIV research.

EpiMatrix/HIV, a tool that is currently available on the World Wide Web, enables researchers to screen HIV proteins for potential MHC ligands. We have performed a comparison of EpiMatrix predictions to 158 published allotype-specific HLA-associated peptides (MHC ligands) derived from 133 proteins. The top 10 ranked EpiMatrix predictions for each of the 158 HLA allotype-protein pairs were selected for comparison with these published ligands. EpiMatrix correctly identified 134 of 158 published ligands (85%). The algorithm is now available for use by the HIV research community at the URL http:/(/)www.EpiMatrix.com/HIV.

Computer Communication Networks↗