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Administrative Personnel↗
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Results for “Web application”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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[Gastric mucosa islands in the cervical esophagus. Their potential pathogenetic significance].
Islands of gastric mucosa were sought in non-selected in- and out-patients undergoing endoscopy. Mucosal islands were found in 40 patients (out of approximately 1000 oesopho-gastroduodenoscopies), mostly a few centimetres below the mouth of the oesophagus. Histology showed "pure" corpus mucosa in 24 cases, a combination of fundus glands (with zymogenic and parietal cells) and mucoid glands were shown in 9 cases; the rest had only mucoid glands (3 cases) or surface elements of gastric mucosa (two cases). In two cases the islands were missed in the biopsy. In one case the demonstration of HCl secretion from a corpus mucosal island could be achieved by local application of congo red via endoscope after stimulation with pentagastrin. The pathogenetic significance of HCl-producing gastric mucosal islands in the cervical oesophagus is due to their ability to induce peptic lesions with subsequent web or membrane formation.
Adenocarcinoma↗
LARaLink 2.0: a comprehensive aid to basic and clinical cytogenetic research.
LARaLink 2.0 (Loci Analysis for Rearrangement Link) is an enabling web technology that permits the rapid retrieval of clinical cytogenetic and molecular data. New data mining capabilities have been incorporated into version 2.0, building upon LARaLink 1.0, to extend the utility of the system for applications in both the clinical and basic sciences. These include access to the Chromosomal Variation in Man database and the GEO database. Together these new resources enhance the user's ability to associate genotype with phenotype to identify potential gene candidates. Unlimited access for researchers exploring disease-gene relationships and for clinicians extending practice in patient care is available at LARaLink.bioinformatics.wayne.edu:8080/ unigene.
Chromosome Aberrations↗
Phylogenetic web profiler.
SUMMARY: Phylogenetic Web Profiler (PWP) is a web-based service designed to perform phylogenetic profiling of proteins against genomes. The current version offers a selection of 63 completed genomes and available plasmids as annotated in the PEDANT genome database. Unlike currently available applications, this tool offers several choices of ortholog prediction parameters including E-value cutoff, percent length difference tolerance, and annotation similarity. Additional features include tight integration with the PEDANT database and tools to analyze properties of predicted proteins. PWP should prove very useful for the analysis of functional-linkage between proteins.
Amino Acid Sequence↗
ConSeq: the identification of functionally and structurally important residues in protein sequences.
MOTIVATION: ConSeq is a web server for the identification of biologically important residues in protein sequences. Functionally important residues that take part, e.g. in ligand binding and protein-protein interactions, are often evolutionarily conserved and are most likely to be solvent-accessible, whereas conserved residues within the protein core most probably have an important structural role in maintaining the protein's fold. Thus, estimated evolutionary rates, as well as relative solvent accessibility predictions, are assigned to each amino acid in the sequence; both are subsequently used to indicate residues that have potential structural or functional importance. AVAILABILITY: The ConSeq web server is available at http://conseq.bioinfo.tau.ac.il/ SUPPLEMENTARY INFORMATION: The ConSeq methodology, a description of its performance in a set of five well-documented proteins, a comparison to other methods, and the outcome of its application to a set of 111 proteins of unknown function, are presented at http://conseq.bioinfo.tau.ac.il/ under 'OVERVIEW', 'VALIDATION', 'COMPARISON' and 'PREDICTIONS', respectively.
Algorithms↗
Taverna: a tool for the composition and enactment of bioinformatics workflows.
MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.
Computational Biology↗
LINKER: a program to generate linker sequences for fusion proteins.
The construction of functional fusion proteins often requires a linker sequence that adopts an extended conformation to allow for maximal flexibility. Linker sequences are generally selected based on intuition. Without a reliable selection criterion, the design of such linkers is often difficult, particularly in situations where longer linker sequences are required. Here we describe a program called LINKER which can automatically generate a set of linker sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. The only required input to the program is the desired linker sequence length. The program is specifically designed to assist in fusion protein construction. A number of optional input parameters have been incorporated so that users are able to enhance sequence selection based on specific applications. The program output simply contains a set of sequences with a specified length. This program should be a useful tool in both the biotechnology industry and biomedical research. It can be accessed through the Web page http://www.fccc. edu/research/labs/feng/linker.html.
Amino Acid Sequence↗
Hierarchical scaffolding with Bambus.
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information. For example, the sequence of a completed genome can be used to guide the scaffolding of a related organism. We present several applications of Bambus: support for finishing, comparative genomics, analysis of the haplotype structure of genomes, and scaffolding of a mammalian genome at low coverage. Bambus is available as an open-source package from our Web site.
Algorithms↗
Ontology driven dynamic linking of biology resources.
Biologists were early adopters of the Web and continue to use it as the primary means of delivering data, tools and knowledge to their community. The Web is made by the links between pages, yet these links have many limitations: they are static and maintained by hand; they can only link one lexical item to another single resource; ownership is necessary for the placement of link anchors and the link mechanism is essentially inflexible. Dynamic linking services, supported by ontologies, offer a mechanism to overcome such restrictions. The Conceptual Open Hypermedia Service (COHSE) system enhances web resources through the dynamic addition of hypertext links. These links are derived through the use of an ontology and associated lexicon along with a mapping from concepts to possible link targets. We describe an application of COHSE to Bioinformatics, using the Gene Ontology (GO) as an ontology and associated keyword mappings and GO associations as link targets. The resulting demonstrator (referred to here as GOHSE) provides both glossary functionality and the possibility of building knowledge based hypertext structures linking bioinformatics resources.
Animals↗
High performance workflow implementation for protein surface characterization using grid technology.
BACKGROUND: This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. METHODS: Workflows are very common in Bioinformatics because they allow to process large quantities of data by delegating the management of resources to the information streaming. Grid technology optimizes the computational load during the different workflow steps, dividing the more expensive tasks into a set of small jobs. RESULTS: Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications. The proposed workflow is implemented to integrate huge amounts of data and the results themselves must be stored into a relational database, which results as the added value to the global knowledge. CONCLUSION: A web interface has been developed to make this technology accessible to grid users. Once the workflow has started, by means of the simplified interface, it is possible to follow all the different steps throughout the data processing. Eventually, when the workflow has been terminated, the different features of the protein, like the amino acids exposed on the protein surface, can be compared with the data present in the output database.
Automation↗
Pharmacogenomics and its potential impact on drug and formulation development.
Recent advances in genomic research have provided the basis for new insights into the importance of genetic and genomic markers during the different stages of drug development. A new field of research, pharmacogenomics, which studies the relationship between drug effects and the genome, has emerged. Structural pharmacogenomics maps the complete DNA sequences of whole genomes (genotypes) including individual variations, and functional pharmacogenomics assesses the expression levels of thousands of genes in one single experiment. Together, these two areas of pharmacogenomics have generated massive databases, which have become a challenge for the research field of informatics and have fostered a new branch of research, bioinformatics. If skillfully used, the databases generated by pharmacogenomics together with data mining on the Web promise to improve the drug development process in a variety of areas: identification of drug targets, evaluation of toxicity, classification of diseases, evaluation of formulations, assessment of drug response and treatment, post-marketing applications, and development of personalized medicines.
Animals↗
Ligand.Info small-molecule Meta-Database.
Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.
Databases, Genetic↗
[Development and application of an online alternative therapy and health promotion class].
PURPOSE: This study was to develop an online "alternative therapy and health promotion" class for university students and to evaluate its changes. METHOD: The online class was developed based on the Instructional Systems Development (ISD) model and model of Web-Based Instruction (WBI) developmental process. This was a quasi- experimental, one group pretest-posttest design. The subjects of this study were 130 students in 3 universities, and they were provided the cyber class for 16 weeks. Data was analyzed by descriptive and plural answer statistics, and paired t-test. RESULTS: The cyber class was developed in five steps: analysis, design, data collection and reconstruction, programming and publishing, and evaluation. The results of program evaluation were positive, which included learning 3.47, system 3.57, and learning satisfaction 3.64 on the scale of 5. The posttest scores of cognition and reliability of alternative therapy were higher than pretest scores. The posttest scores of health promoting lifestyle (t=-5.051, p=.000) and perceived health status (t=2.979, p=.003) were significantly higher than those of the pretest. CONCLUSION: These results suggest that the cyber class is a positive method in increasing a cognition, reliability of alternative therapy, and is effective to improve a health promotion lifestyle and perceived health status for the university students.
Complementary Therapies↗
ENN-ICS--implementation and evaluation of a multilingual learning management system for sleep medicine in Europe.
A new web based network aims at the improvement of health care in Europe by integrating advanced e-learning and e-publishing technologies for the training of medical doctors, nurses, and students. The field of application is sleep physiology and sleep medicine. Based on a multilingual, multimedia communication system, ENN-ICS Centre offers direct access to medical information for users, i.e healthcare professionals and citizens, in Europe and worldwide. The use of XML supports the development of media independent contents for multiple target groups. Editorial and distributive processes are supported by customized central editorial, content management and learning management systems (CMS, LMS). ENN-ICS e-health services are evaluated by selected user groups in North, Middle and Southern Europe using reliable and scientifically accepted validation instruments. The compliance with essential quality requirements and criteria is tested and verified by using online questionnaires based on the DISCERN questionnaire for evaluating patient information, the HON principles for health-related websites and the GMDS catalogue of quality criteria for electronic publications in medicine. The system architecture and its exemplary applications can be used as a model for future e-health services dealing with neurological and other medical topics.
Europe↗
Collaborative medical informatics research using the Internet and the World Wide Web.
The InterMed Collaboratory is an interdisciplinary project involving six participating medical institutions. There are two broad mandates for the effort. The first is to further the development, sharing, and demonstration of numerous software and system components, data sets, procedures and tools that will facilitate the collaborations and support the application goals of these projects. The second is to provide a distributed suite of clinical applications, guidelines, and knowledge-bases for clinical, educational, and administrative purposes. To define the interactions among the components, datasets, procedures, and tools that we are producing and sharing, we have identified a model composed of seven tiers, each of which supports the levels above it. In this paper we briefly describe those tiers and the nature of the collaborative process with which we have experimented.
Computer Communication Networks↗
Implications of the Java language on computer-based patient records.
The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.
Computer Communication Networks↗
VATAM: developing consensus in validation of health telematics applications.
VATAM (Validation of Telematics Applications in Medicine) is an EU supported project in the Health care sector of the Telematics Application Programme. Its objective is to assist other health telematics projects by providing a platform for discussion on validation, eventually resulting in 'guidelines for validation of telematics applications in medicine'. The VATAM work can be subdivided into three phases: the inventory phase (1996) in which information is collected on validation approaches in the Telematics Application Programme, previous efforts and expertise. The dissemination phase (1997) will be used to extend and adapt the framework developed in the inventory phase, through cooperation with other projects The experiences phase (1998) in which the projects are actually applying validation, will be used by VATAM to validate the VATAM methodology. VATAM has finished the inventory phase successfully and is now working on the dissemination phase by--among others--establishing contacts with other projects, and providing information on the inventory through the World Wide Web (URL: http:(/)/www-vatam.unimaas.nl). This paper discusses the approach adopted and the proposed VATAM framework to structure the large variety of validation approaches.
Computer Communication Networks↗
Application of different types of free foot flaps in hand surgery.
From 1987, nine types of free vascularized flaps or combined flaps from the foot were used to treat 26 cases of hand injury with tissue loss. They were: (1) combined flap of 4 toe dorsums, big toe pulp, first toe web, and dorsalis pedis flap with long extensor tendons of the toes, (2) composite skin flap with the second metatarsophalangeal joint, (3) wrap-around flap from the great toe, (4) first toe web flap, (5) toe pulp flap with only an artery and a nerve, (6) wrap-around flap of the great toe with a dorsalis pedis flap, (7) second toe with dorsalis pedis flap, (8) dorsalis pedis flap, and (9) first toe web flap with second metatarsal bone. All flaps survived. All the patients have used their reconstructed hand. Of the final motor functions of the reconstructed hands, 68.8% are excellent, 27.3% are good, 3.9% are fair. Of the final cosmetic results of the reconstructed hands, 76.9% are excellent, 15.3% are good, 7.8% are acceptable. Of the patients, 64.9% are satisfied with the final results of the donor sites, 31.2% feel it is acceptable, and 3.9% feel it is unsatisfactory. The selection, indication, merits and demerits of vascularized foot flaps and attentive points in the operations are discussed in this paper.
Adolescent↗