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The DHAIR software system is a database-driven, web-based survey platform. It implements the delivery of survey instruments in packaged assessments, creation and editing of those assessments, researcher access to the results of the survey application, and a flexible authorization framework.
The Virtual Cell is a modular computational framework that permits construction of models, application of numerical solvers to perform simulations, and analysis of simulation results. A key feature of the Virtual Cell is that it permits the incorporation of realistic experimental geometries within full 3D spatial models. An intuitive JAVA interface allows access via a web browser and includes options for database access, geometry definition (including directly from microscope images), specification of compartment topology, species definition and assignment, chemical reaction input and computational mesh. The system is designed for cell biologists to aid both the interpretation and the planning of experiments. It also contains sophisticated modelling tools that are appropriate for the needs of mathematical biologists. Thus, communication between these traditionally separate scientific communities can be facilitated. This paper will describe the status of the project and will survey several applications to cell biological problems.
BACKGROUND: Regulatory regions that function in DNA replication and gene transcription contain specific sequences that bind proteins as well as less-specific sequences in which the double helix is often easy to unwind. Progress towards predicting and characterizing regulatory regions could be accelerated by computer programs that perform a combined analysis of specific sequences and DNA unwinding properties. RESULTS: Here we present PATTERNFINDER, a web server that searches DNA sequences for matches to specific or flexible patterns, and analyzes DNA helical stability. A batch mode of the program generates a tabular map of matches to multiple, different patterns. Regions flanking pattern matches can be targeted for helical stability analysis to identify sequences with a minimum free energy for DNA unwinding. As an example application, we analyzed a regulatory region of the human c-myc proto-oncogene consisting of a single-strand-specific protein binding site within a DNA region that unwindsin vivo. The predicted region of minimal helical stability overlapped both the protein binding site and the unwound DNA region identified experimentally. CONCLUSIONS: The PATTERNFINDER web server permits localization of known functional elements or landmarks in DNA sequences as well as prediction of potential new elements. Batch analysis of multiple patterns facilitates the annotation of DNA regulatory regions. Identifying specific pattern matches linked to DNA with low helical stability is useful in characterizing regulatory regions for transcription, replication and other processes and may predict functional DNA unwinding elements.PATTERNFINDER can be accessed freely at: http://wings.buffalo.edu/gsa/dna/dk/PFP/
Environmental toxicology is the study of the ecological effects of anthropogenic substances released into the environment. It is a relatively diverse field addressing impacts to aquatic and terrestrial organisms and communities. The determination of potential risk associated with toxic agents is of interest to government regulators, industry, researchers, private organizations and citizen groups. In assessing the ecological risk associated with a chemical stressor, it is important to establish linkages between likely exposure concentrations and adverse effects to ecological receptors. To do so requires access to reliable information resources. The proper application of such data requires familiarity with the scientific literature and keeping abreast of new and emerging issues as well as state-of-the-art research findings and methods. In addition, an understanding of government regulations as they relate to environmental issues is also of primary interest. The advent of the Web has made these tools accessible at computer desktops. This review focuses on currently available free Web resources related to environmental toxicology, specifically those which address available empirical data sources, predictive tools and publications of interest such as standard test methods, guidance documents and governmental regulations.
Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes.
OBJECTIVE: To assess the content of general surgery residency program websites, the websites' potential as tools in resident recruitment, and their "usability." DESIGN: The homepages of general surgery residency programs were evaluated for accessibility, ease-of-use, adherence to established principles of website design, and content. Investigators completed a questionnaire on aspects of their online search, including number of mouse-clicks used, number of errors encountered, and number of returns to the residency homepage. SETTING: The World Wide Web listings on the Fellowship and Residency Electronic Interactive Database (FREIDA) of the American Medical Association (AMA). PARTICIPANTS: A total of 251 ACGME-accredited general surgery residency programs. RESULTS: One hundred sixty-seven programs (67%) provided a viable link to the program's website. Evaluators found an average of 5.9 of 16 content items; 2 (1.2%) websites provided as many as 12 content items. Five of the 16 content items (program description, conference schedules, listing of faculty, caseload, and salary) were found on more than half of the sites. An average of 24 mouse-clicks was required to complete the questionnaire for each site. Forty-six sites (28%) generated at least 1 error during our search. The residency homepage was revisited an average of 5 times during each search. On average, programs adhered to 6 of the 10 design principles; only 6 (3.6%) sites adhered to all 10 design principles. Two of the 10 design principles (use of familiar fonts, absence of frames) were adhered to in more than half of the sites. Our overall success rate when searching residency websites was 38%. CONCLUSIONS: General surgery residency programs do not use the World Wide Web optimally, particularly for users who are potential residency candidates. The usability of these websites could be increased by providing relevant content, making that content easier to find, and adhering to established web design principles.
New bone for the repair or the restoration of the function of traumatized, damaged, or lost bone is a major clinical need, and bone tissue engineering has been heralded as an alternative strategy for regenerating bone. A novel web-like structured biodegradable hybrid sheet has been developed for bone tissue engineering by preparing knitted poly(DL-lactic-co-glycolic acid) sheets (PLGA sheets) with collagen microsponges in their openings. The PLGA skeleton facilitates the formation of the hybrid sheets into desired shapes, and the collagen microsponges in the pores of the PLGA sheet promote cell adhesion and uniform cell distribution throughout the sheet. A large number of osteoblasts established from marrow stroma adhere to the scaffolds and generate the desired-shaped bone in combination with these novel sheets. These results indicate that the web-like structured novel sheet shows promise for use as a tool for custom-shaped bone regeneration in basic research on osteogenesis and for the development of therapeutic applications.
BACKGROUND: "Get With The Guidelines (GWTG)" was developed and piloted by the American Heart Association (AHA), New England Affiliate; MassPRO, Inc.; and other organizations to reduce the gap in the application of secondary prevention guidelines in hospitalized cardiovascular disease patients. Collaborative learning programs and technology solutions were created for the project. THE PATIENT MANAGEMENT TOOL (PMT): The interactive Web-based patient management tool (PMT) was developed using quality measures derived from the AHA/American College of Cardiology secondary prevention guidelines. It provided data entry, embedded reminders and guideline summaries, and online reports of quality measure performance, including comparisons with the aggregate performance of all hospitals. LEARNING SESSIONS: Multidisciplinary teams from 24 hospitals participated in the 2000-2001 pilot. Four collaborative learning sessions and monthly conference calls supported team interaction. Best-practices sharing and the use of an Internet tool enabled hospitals to change systems and collect data on 1,738 patients. SUMMARY AND CONCLUSIONS: The GWTG program, a template of learning sessions with didactic presentations, best-practices sharing, and collaborative multidisciplinary team meetings supported by the Internet-based data collection and reporting system, can be extended to multiple regions without requiring additional development. Following the completion of the pilot, the AHA adopted GWTG as a national program.
Internet presentations are common tools for better medical communication and better scientific work. Meanwhile a great number of gynecological and obstetrical institutions present data via the world wide web within a wide range of quality and performance. Specific HTML editors offer quick and easy presentations, but only advanced internet techniques enable interesting multimedia presentations. N-tier applications are the future standard and we must integrate them in general informatical systems. New Concepts, actual tools and general problems will be discussed and new principles similar to actual E commerce techniques are able to solve our special medical demands.
OBJECTIVE: To systematically review and evaluate published risk prediction models for perioperative blood transfusion in patients undergoing total hip or knee arthroplasty (THA/TKA). METHODS: We systematically searched PubMed, Web of Science, the Cochrane Library, and Embase from inception to May 31, 2025. Two researchers independently screened the literature, extracted data, and assessed the risk of bias and applicability using the Prediction model Risk Of Bias Assessment Tool (PROBAST). The area under the receiver operating characteristic curve (AUC) values were pooled via a meta-analysis using Stata 18.0. RESULTS: d Fourteen studies containing 36 prediction models were included. The incidence of blood transfusion among THA/TKA patients ranged from 3.2% to 30.8%. Preoperative hemoglobin (Hb) level, tranexamic acid (TXA) use, operative duration, intraoperative blood loss, and age were the most frequently incorporated predictors. Model sensitivity ranged from 58% to 94.5%, and specificity ranged from 71.3% to 94%. Meta-analysis showed that the pooled AUC value of the 13 validated models was 0.87 (95% CI: 0.85-0.90), suggesting good discriminatory performance. All models were rated as having a high risk of bias. The applicability of four studies was rated as unclear. CONCLUSION: Although the included studies demonstrated promising discriminative ability of prediction models for blood transfusion in THA/TKA, all were assessed as having a high risk of bias using the PROBAST tool. Therefore, future research should prioritize the development of models with larger sample sizes, rigorous study designs, and multicenter external validation.
Patients rely on the Internet for medical information. It is difficult to discern which resources are accurate or appropriate for patients. The purpose of this study was to develop a quality-assessment tool for health Internet Web sites and to apply this tool to assess the quality of burn scar management information on the Internet. Between September and December 2001, we prospectively evaluated all Web sites on the Internet search engine Yahoo! containing the headings "burn scar management," "burn scar healing," "burn scar treatment," and "burn scar therapy." The quality of each Web site's medical information was evaluated using our scoring system consisting of the following two components: quality and technical characteristics. The total score for each Web site was converted to a percent grade (eg, > or =80% = excellent, 70 to 79% = very good, 60 to 69% = good, 50 to 59% = fair, and <50% = poor). The Web sites were grouped into three categories: commercial (for profit), academic (university, hospital), and organizational (nonprofit). Of 88 Web sites evaluated, the majority 68 (77%) were commercial, 7 (8%) academic, and 13 (15%) organizational. Burn scar management information on the Internet was poor in the majority (79%) of commercial Web sites and was excellent, very good, or good in the majority of academic (86%) and organizational (77%) Web sites. Using our health information evaluation, we found that the majority of burn scar management information on the internet (77%) was of fair or poor quality. Academic and organizational Web sites had the best quality of burn scar management information. Additional testing of the developed tool will be needed to analyze the reproducibility of the results and their applicability in other medical domains.
Macromolecular crystallography requires simple yet effective means of organizing and managing the large amounts of data generated by crystallization experiments. There are several freely available web-based Laboratory Information Management Systems (LIMS) that assist in these tasks. These, however, rely on the limited user interfaces allowed in HTML-based web pages. To address this limitation, a new LIMS for protein crystallization, which features a novel rich graphical user interface (GUI) to a relational database, has been developed. This application, which is called CLIMS (Crystallography LIMS), assists in all aspects of protein-crystallization projects: protein expression, handling, crystallization optimization, visualization of results and preliminary diffraction data. Extensive use of templates, particularly for commercial screens and common optimization grid screens, exploits the redundancy in experimental setups. The crystallization tray is the central focus of the graphical interface, thus facilitating rapid visualization and annotation of results. CLIMS was developed specifically to cater for the needs of individual laboratories requiring an intuitive and robust system for managing crystallization experiments and is freely available.
The objective of the medical teleconsultation system presented in this paper is to demonstrate the use of the World Wide Web (WWW) for telemedicine and interactive medical information exchange. The system, which is developed based on Java, could provide several basic Java tools to fulfill the requirements of medical applications, including a file manager, data tool, bulletin board, and digital audio tool. The digital audio tool uses point-to-point structure to enable two physicians to communicate directly through voice. The others use multipoint structure. The file manager manages the medical images stored in the WWW information server, which come from a hospital database. The data tool supports cooperative operations on the medical data between the participating physicians. The bulletin board enables the users to discuss special cases by writing text on the board, send their personal or group diagnostic reports on the cases, and reorganize the reports and store them in its report file for later use. The system provides a hardware-independent platform for physicians to interact with one another as well as to access medical information over the WWW.
The new Web Ontology Language (OWL) and its Description Logic compatible sublanguage (OWL-DL) explicitly exclude defaults and exceptions, as do all logic based formalisms for ontologies. However, many biomedical applications appear to require default reasoning, at least if they are to be engineered in a maintainable way. Default reasoning has always been one of the great strengths of Frame systems such as Protégé. Resolving this conflict requires analysis of the different uses for defaults and exceptions. In some cases, alternatives can be provided within the OWL framework; in others, it appears that hybrid reasoning about a knowledge base of contingent facts built around the core ontology is necessary. Trade-offs include both human factors and the scaling of computational performance. The analysis presented here is based on the OpenGALEN experience with large scale ontologies using a formalism, GRAIL, which explicitly incorporates constructs for hybrid reasoning, numerous experiments with OWL, and initial work on combining OWL and Protégé.
Neuroimaging plays a major role in the evaluation of patients with neurological disorders. Surveys of neurologists have revealed that most rely on their own readings of images for patient management, and a majority believe that neurologists should be allowed to officially interpret and bill for scan reviews. The importance of neuroimaging training for neurology residents has been stressed by the Association of University Professors of Neurology. Although there is a desire to promote the neuroimaging education of neurologists, no curricula have existed previously. The Neuroimaging Section of the American Academy of Neurology (AAN) developed a task force of practicing neuroimagers to provide a neuroimaging curriculum for neurological trainees and training directors. The resulting curriculum is available on the Web sites of the AAN (http://www.aan.com) and the American Society of Neuroimaging (http://www.asnweb.org/education/curriculum.shtml) and will be updated as the need arises through evolving technology or breadth of applications. This curriculum should help in the design of neurology residency and fellowship programs and subspecialty pathways in which adequate neuroimaging education and training are desired for various reasons, including certification and the demonstration of competency and proficiency.
SETTING: It has been proposed that the sensitivity of direct sputum smear microscopy can be improved if sputum is liquefied with sodium hypochlorite (NaOCl or household bleach), and concentrated by centrifugation before acid-fast staining. OBJECTIVE: To summarise the results of the studies of the bleach method for improved sensitivity of sputum microscopy and to describe the opinions and knowledge of key persons in National Tuberculosis Control Programmes (NTPs) about this method. DESIGN: We searched Medline, EMBASE and Web of Science for studies comparing the bleach method to direct sputum smear microscopy in low- or middle-income countries. Each study was assessed regarding methodology and field applicability. We also sent out questionnaires concerning the bleach method to key persons in NTPs in 85 countries. RESULTS: In 15 of the 19 studies identified there was a statistically significant improvement in the proportion of positive tests or sensitivity ranging from 7-253%. The majority (73%) of the key persons had heard of the bleach method. Forty-four per cent thought it could improve case detection in their countries, while 49% did not know; 93% of them would promote the bleach method; the most common reasons for doing so would be recommendations from the WHO or the IUATLD, or favourable studies performed in their own country. The bleach method was used routinely in only three countries. CONCLUSION: There is enough evidence to recommend the evaluation and introduction of the bleach method in most settings where mycobacterial culture is not performed routinely.
The University of New South Wales School of Rural Health, Australia, like many other rural clinical schools, relies heavily on patient-based learning which is largely serendipitous. The learning is not driven by courses of lectures but by the patients who become available in a variety of settings. Students, who, in their first 3 years have been exposed to a very structured didactic learning experience, start their rural experience in Year IV with a curriculum mainly concerned with general medicine and surgery. They have to learn to adapt to a largely self-directed model. While their rural clinical experience is very much broader than that of their city-based peers, an excellent feature, it engenders feelings of insecurity and a perceived need for students and faculty to have a method of tracking patient encounters so they can ensure the syllabus is covered. Early attempts with a paper-based system and later a Reflective Learning Diary proved unsuccessful. This article presents Syllabus Tracking (STRAC) together with a Reflective Case History Template which encourages reflective learning from patients encountered. STRAC is a web-based solution that includes a reporting function, and is easily modified to suit the needs of the curriculum. It is believed it may also prove useful for future applications. Most rural clinical schools in Australia are young, as are these tools. They are not formally evaluated but are offered to other schools as a suggestion.
Can we improve access in primary care without compromising the quality of care? The purpose of this article is to demonstrate how timely access to primary care can be achieved without compromising the quality of the care being delivered. The Veterans Health Administration (VHA) is an integrated healthcare system that has implemented change to improve primary care access to the veterans it serves, while not only maintaining but also actually improving the quality of care. Many healthcare executives are struggling with achieving desirable access to care and continuity of care. To confront this problem, many large and small practices have initiated an approach known as advanced clinic access, open access, or same-day scheduling, introduced by the Institute for Healthcare Improvement (IHI). This approach has increasingly been used to reduce waits and delays in primary care without adding resources. To measure quality of care, specific performance measures were developed to quantify the effectiveness of primary care in VHA. Although it was initially viewed with concern and suspicion and was seen as a symptom of unnecessary micromanagement, healthcare team members were encouraged to use performance feedback as an opportunity for systems improvement as well as self-assessment and performance improvement for the team. All quality data are posted quarterly on VHA's internal web site, providing visible accountability at all levels of the organization. Clinical workflow redesign leads to reduced wait times without compromising quality of care. These large system improvements are applicable to large and small organizations looking to tackle change through the use of a collaborative model.