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At least 235 records · Page 13Linked to original sources

PubMed2005

"Blogs" and "wikis" are valuable software tools for communication within research groups.

Appropriate software tools may improve communication and ease access to knowledge for research groups. A weblog is a website which contains periodic, chronologically ordered posts on a common webpage, whereas a wiki is hypertext-based collaborative software that enables documents to be authored collectively using a web browser. Although not primarily intended for use as an intranet-based collaborative knowledge warehouse, both blogs and wikis have the potential to offer all the features of complex and expensive IT solutions. These tools enable the team members to share knowledge simply and quickly-the collective knowledge base of the group can be efficiently managed and navigated.

Communication↗

PubMed2002

The development of a computerised equipment and drug calculator for use in resuscitation.

OBJECTIVES: To design a computerised system of calculating resuscitation requirements and to test this system to ensure that it gives accurate and fast results, so that it could potentially be used in the resuscitation of patients in a accident and emergency (A&E) department. METHODS: Using internet based technology we have developed a program that runs inside most web browsers and can be used to calculate several parameters (including endotracheal tube dimensions and drug doses). The only value that is required is the age of the patient. The weight is calculated and can be adjusted if known. The resuscitation requirement calculations are made from the weight. The program was then tested on staff members in the department to calculate theoretical resuscitation requirements for paediatric and adult patients. Accuracy and speed of the computerised calculator was compared with the conventional paper based calculation methods. RESULTS: Subjects performed better using the computerised calculator. On average they made significantly fewer errors (21.4% more accurate than using conventional methods) and were three times faster. CONCLUSION: The computerised calculator has proved, in a controlled setting, to be a more accurate and faster way of calculating resuscitation requirements than conventional methods.

Humans↗

PubMedDate not supplied

A voice-enabled, structured medical reporting system.

Kurzweil Applied Intelligence received a research grant from the National Institute of Standards and Technology (NIST) Advanced Technology Program to develop a prototype voice-enabled, structured medical reporting system. In typical usage, the physician dictates to the system, which then uses automatic speech recognition and medical knowledge bases to produce a structured report. This report can then be formatted and viewed on a computer screen, stored in databases of patient information, transmitted to other systems, used to support outcome studies, or viewed on a Web browser. The output reports are structured according to two standard, platform-independent formats: SGML and CORBA. These formats represent the data in a way that can be read by both computers and humans, and efficiently communicated to a wide range of databases and communications protocols.

Information Storage and Retrieval↗

PubMedDate not supplied

Plug-and-play XML: a health care perspective.

The application of XML (Extensible Markup Language) is still costly. The authors present an approach to ease the development of XML applications. They have developed a Web-based framework that combines existing XML resources into a comprehensive XML application. The XML framework is model-driven, i.e., the authors primarily design XML document models (XML schema, document type definition), and users can enter, search, and view related XML documents using a Web browser. The XML model itself is flexible and might be composed of existing model standards. The second part of the paper relates the approach of the authors to some problems frequently encountered in the clinical documentation process.

Documentation↗

PubMed1997

Genitourinary medicine and The Internet No. 4.

The Internet provides a rapid facility for accessing a large amount of information which, once found, can be manipulated in a variety of ways. For example, with the authors' permission, Web pages can be retrieved, converted into text files and edited to produce patient leaflets of sexually-transmitted conditions, prescribing information leaflets, clinical guidelines and protocols, etc. Collections of relevant Web sites placed in bookmarks on a Web browser for students to refer to could also form the basis for self-directed learning, and tutorials and small group teaching on specific subjects.

Computer Communication Networks↗

PubMedDate not supplied

Hyperad: augmenting and visualizing free text radiology reports.

Hyperad is an automated computer system designed to extract key concepts from thoracic radiology reports and give physicians access to a large database containing the reports and key concepts. The concepts are extracted from textual documents with natural language processing techniques, then stored with the original documents in the database, which can be queried in terms of findings or associated attributes from an intuitive and easily accessible interface. The extracted concepts are represented both textually in a coded hypertext format and graphically on a coronal cross-sectional anatomy atlas, an idealized graphical model of human anatomy. To facilitate implementation, the communication protocols and standards of the World Wide Web (Web) were adopted. The reports and associated forms are encoded in standard hypertext markup language, which makes it possible to use hypermedia links to navigate the Hyperad database with any graphical Web browser. In the future, Hyperad may prove useful for other applications.

Computer Systems↗

PubMedDate not supplied

Image file formats: past, present, and future.

Despite the rapid growth of the Internet for storage and display of World Wide Web-based teaching files, the available image file formats have remained relatively limited. The recently developed portable networks graphics (PNG) format is versatile and offers several advantages over the older Internet standard image file formats that make it an attractive option for digital teaching files. With the PNG format, it is possible to repeatedly open, edit, and save files with lossless compression along with gamma and chromicity correction. The two-dimensional interlacing capabilities of PNG allow an image to fill in from top to bottom and from right to left, making retrieval faster than with other formats. In addition, images can be viewed closer to the original settings, and metadata (ie, information about data) can be incorporated into files. The PNG format provides a network-friendly, patent-free, lossless compression scheme that is truly cross-platform and has many new features that are useful for multimedia and Web-based radiologic teaching. The widespread acceptance of PNG by the World Wide Web Consortium and by the most popular Web browsers and graphic manipulation software companies suggests an expanding role in the future of multimedia teaching file development.

Computer-Assisted Instruction↗

PubMed2005

Personal computer versus workstation display: observer performance in detection of wrist fractures on digital radiographs.

PURPOSE: To retrospectively compare the accuracy of observer performance with personal computer (PC) compared with that with dedicated picture archiving and communication system (PACS) workstation display in the detection of wrist fractures on computed radiographs. MATERIALS AND METHODS: This study was conducted according to the principles of the Declaration of Helsinki (2002 version) of the World Medical Association. The institutional clinical board approved the study; informed consent was not required. Seven observers independently assessed randomized anonymous digital radiographs of the wrist from 259 subjects; 146 had fractures, and 113 were healthy control subjects (151 male and 108 female subjects; average age, 33 years). Follow-up radiographs and/or computed tomographic scans were used as the reference standard for patients with fractures, and follow-up radiographs and/or clinical history data were used as the reference standard for controls. The PC was a standard hospital machine with a 17-inch (43-cm) color monitor with which Web browser display software was used. The PACS workstation had two portrait 21-inch (53-cm) monochrome monitors that displayed 2300 lines. The observers assigned scores to the radiographs on a scale of 1 (no fracture) to 5 (definite fracture). Receiver operating characteristic (ROC) curves, sensitivity, specificity, and accuracy were compared. RESULTS: The areas under the ROC curves were almost identical for the PC and workstation (0.910 vs 0.918, respectively; difference, 0.008; 95% confidence interval: -0.029, 0.013). The average sensitivity with the PC was almost identical to that with the workstation (85% vs 84%, respectively), as was the average specificity (82% vs 81%, respectively). The average accuracy (83%) was the same for both. CONCLUSION: The results of this study showed that there was no difference in accuracy of observer performance for detection of wrist fractures with a PC compared with that with a PACS workstation.

Adult↗

PubMedDate not supplied

Informatics in Radiology (infoRAD): mobile wireless DICOM server system and PDA with high-resolution display: feasibility of group work for radiologists.

A novel mobile system has been developed for use by radiologists in managing Digital Imaging and Communications in Medicine (DICOM) image data. The system consists of a mobile DICOM server (MDS) and personal digital assistants (PDAs), including a Linux PDA with a video graphics array (VGA) display (307,200 pixels, 3.7 inches). The MDS weighs 410 g, has a 60-GB hard disk drive and a built-in wireless local area network (LAN) access point, and supports a DICOM server (Central Test Node). The Linux-based MDS can be accessed with personal computers (PCs) and PDAs by means of a wireless or wired LAN, and client-server communications can be established at any time. DICOM images can be displayed by using any PDA or PC by means of a Web browser. Simultaneous access to the MDS is possible for multiple authenticated users. With most PDAs, image compression is necessary for complete display of DICOM images; however, the VGA screen can display a 512 x 512-pixel DICOM image almost in its entirety. This wireless system allows efficient management of heavy loads of lossless DICOM image data and will be useful for collaborative work by radiologists in education, conferences, and research.

Computers, Handheld↗

PubMed2005

Quality and efficacy of a telecolposcopy programme.

We tested the performance of telecolposcopy in the diagnosis of various squamous intraepithelial lesions. There were three groups of physicians: Group 1 consisted of 15 gynaecologists who were not trained in colposcopy; Group 2 consisted of six experienced colposcopists (specialists); Group 3 was a supervising team consisting of three experts (colposcopists with more than 15 years of colposcopy experience). The first group took colpophotographs during gynaecological examinations and used a Web browser to compare them with examples from a database of colposcopy findings. Group 2 made their own diagnoses independently. Then the supervising team examined the findings from all 250 patients and made diagnoses that could be considered the 'gold standard'. The findings were identical for Groups 1 and 2 in 219 cases, i.e. an inter-observer agreement of 88%; Cohen's kappa was 0.81. The findings were identical for Groups 1 and 3 in 208 cases, i.e. an inter-observer agreement of 83%; Cohen's kappa was 0.74. The findings were identical for Groups 2 and 3 in 239 cases, i.e. an inter-observer agreement of 96%; Cohen's kappa was 0.93. There was high inter-observer agreement between all participants. However, there were also significant differences in some cases. In the cases of suspected invasive carcinoma, the results showed a significant difference (chi2=4.8, P< 0.005) because gynaecologists from Group 1 were not sure of their diagnosis and they wanted to obtain a second opinion by referring the decision to a higher level.

Colposcopy↗

PubMed2006

Neural internet: Web surfing with brain potentials for the completely paralyzed.

Neural Internet is a new technological advancement in brain-computer interface research, which enables locked-in patients to operate a Web browser directly with their brain potentials. Neural Internet was successfully tested with a locked-in patient diagnosed with amyotrophic lateral sclerosis rendering him the first paralyzed person to surf the Internet solely by regulating his electrical brain activity. The functioning of Neural Internet and its clinical implications for motor-impaired patients are highlighted.

Amyotrophic Lateral Sclerosis↗

PubMed2001

FOUNTAIN: a JAVA open-source package to assist large sequencing projects.

BACKGROUND: Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences. RESULTS: We describe here a new program, named FOUNTAIN, for the management of large sequencing projects http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html. FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented. CONCLUSIONS: A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort.

Algorithms↗

PubMed2004

A database for G proteins and their interaction with GPCRs.

BACKGROUND: G protein-coupled receptors (GPCRs) transduce signals from extracellular space into the cell, through their interaction with G proteins, which act as switches forming hetero-trimers composed of different subunits (alpha,beta,gamma). The alpha subunit of the G protein is responsible for the recognition of a given GPCR. Whereas specialised resources for GPCRs, and other groups of receptors, are already available, currently, there is no publicly available database focusing on G Proteins and containing information about their coupling specificity with their respective receptors. DESCRIPTION: gpDB is a publicly accessible G proteins/GPCRs relational database. Including species homologs, the database contains detailed information for 418 G protein monomers (272 Galpha, 87 Gbeta and 59 Ggamma) and 2782 GPCRs sequences belonging to families with known coupling to G proteins. The GPCRs and the G proteins are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature searchs. The main innovation besides the classification of both G proteins and GPCRs is the relational model of the database, describing the known coupling specificity of the GPCRs to their respective alpha subunit of G proteins, a unique feature not available in any other database. There is full sequence information with cross-references to publicly available databases, references to the literature concerning the coupling specificity and the dimerization of GPCRs and the user may submit advanced queries for text search. Furthermore, we provide a pattern search tool, an interface for running BLAST against the database and interconnectivity with PRED-TMR, PRED-GPCR and TMRPres2D. CONCLUSIONS: The database will be very useful, for both experimentalists and bioinformaticians, for the study of G protein/GPCR interactions and for future development of predictive algorithms. It is available for academics, via a web browser at the URL: http://bioinformatics.biol.uoa.gr/gpDB.

Databases, Protein↗

PubMed2006

GenomeBlast: a web tool for small genome comparison.

BACKGROUND: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes. RESULTS: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny. We demonstrated the functions in GenomeBlast with an example of multiple herpesviral genome analysis and illustrated how GenomeBlast is useful for small genome comparison. CONCLUSION: We developed a Web tool for comparative analysis of small genomes, which allows the user not only to identify unique genes and homologous gene candidates among multiple genomes, but also to view their graphical distributions on genomes, and to reconstruct genome phylogeny. GenomeBlast runs on a Linux server with 4 CPUs and 4 GB memory. The online version of GenomeBlast is available to public by using a Web browser with the URL http://bioinfo-srv1.awh.unomaha.edu/genomeblast/.

Algorithms↗

PubMed2006

The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research.

BACKGROUND: Viroids, satellite RNAs, satellites viruses and the human hepatitis delta virus form the 'brotherhood' of the smallest known infectious RNA agents, known as the subviral RNAs. For most of these species, it is generally accepted that characteristics such as cell movement, replication, host specificity and pathogenicity are encoded in their RNA sequences and their resulting RNA structures. Although many sequences are indexed in publicly available databases, these sequence annotation databases do not provide the advanced searches and data manipulation capability for identifying and characterizing subviral RNA motifs. DESCRIPTION: The Subviral RNA database is a web-based environment that facilitates the research and analysis of viroids, satellite RNAs, satellites viruses, the human hepatitis delta virus, and related RNA sequences. It integrates a large number of Subviral RNA sequences, their respective RNA motifs, analysis tools, related publication links and additional pertinent information (ex. links, conferences, announcements), allowing users to efficiently retrieve and analyze relevant information about these small RNA agents. CONCLUSION: With its design, the Subviral RNA Database could be considered as a fundamental building block for the study of these related RNAs. It is freely available via a web browser at the URL: http://subviral.med.uottawa.ca.

Base Sequence↗

PubMed2005

Development and preliminary evaluation of the VPS ReplaySuite: a virtual double-headed microscope for pathology.

BACKGROUND: Advances in computing and telecommunications have resulted in the availability of a range of online tools for use in pathology training and quality assurance. The majority focus on either enabling pathologists to examine and diagnose cases, or providing image archives that serve as reference material. Limited emphasis has been placed on analysing the diagnostic process used by pathologists to reach a diagnosis and using this as a resource for improving diagnostic performance. METHODS: The ReplaySuite is an online pathology software tool that presents archived virtual slide examinations to pathologists in an accessible video-like format, similar to observing examinations with a double-headed microscope. Delivered through a customized web browser, it utilises PHP (Hypertext PreProcessor) to interact with a remote database and retrieve data describing virtual slide examinations, performed using the Virtual Pathology Slide (VPS). To demonstrate the technology and conduct a preliminary evaluation of pathologists opinions on its potential application in pathology training and quality assurance, 70 pathologists were invited to use the application to review their own and other pathologists examinations of 10 needle-core breast biopsies and complete an electronic survey. 9 pathologists participated, and all subsequently completed an exit survey. RESULTS: Of those who replayed an examination by another pathologist, 83.3% (5/6) agreed that replays provided an insight into the examining pathologists diagnosis and 33.3% (2/6) reconsidered their own diagnosis for at least one case. Of those who reconsidered their original diagnosis, all re-classified either concordant with group consensus or original glass slide diagnosis. 77.7% (7/9) of all participants, and all 3 participants who replayed more than 10 examinations stated the ReplaySuite to be of some or great benefit in pathology training and quality assurance. CONCLUSION: Participants conclude the ReplaySuite to be of some or of great potential benefit to pathology training and quality assurance and consider the ReplaySuite to be beneficial in evaluating the diagnostic trace of an examination. The ReplaySuite removes temporal and spatial issues that surround the use of double-headed microscopes by allowing examinations to be reviewed at different times and in different locations to the original examination. While the evaluation set was limited and potentially subject to bias, the response of participants was favourable. Further work is planned to determine whether use of the ReplaySuite can result in improved diagnostic ability.

Archives↗

PubMed2003

THoR: a tool for domain discovery and curation of multiple alignments.

We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family. The entire process is designed for use via a web-browser, with simple links and cross-references to relevant information, to assist the assessment of biological significance. THoR has been benchmarked for accuracy using the SMART and pufferfish genome databases.

Algorithms↗

PubMed2000

Human membrane transporter database: a Web-accessible relational database for drug transport studies and pharmacogenomics.

The human genome contains numerous genes that encode membrane transporters and related proteins. For drug discovery, development, and targeting, one needs to know which transporters play a role in drug disposition and effects. Moreover, genetic polymorphisms in human membrane transporters may contribute to interindividual differences in the response to drugs. Pharmacogenetics, and, on a genome-wide basis, pharmacogenomics, address the effect of genetic variants on an individual's response to drugs and xenobiotics. However, our knowledge of the relevant transporters is limited at present. To facilitate the study of drug transporters on a broad scale, including the use of microarray technology, we have constructed a human membrane transporter database (HMTD). Even though it is still largely incomplete, the database contains information on more than 250 human membrane transporters, such as sequence, gene family, structure, function, substrate, tissue distribution, and genetic disorders associated with transporter polymorphisms. Readers are invited to submit additional data. Implemented as a relational database, HMTD supports complex biological queries. Accessible through a Web browser user interface via Common Gateway Interface (CGI) and Java Database Connection (JDBC), HMTD also provides useful links and references, allowing interactive searching and downloading of data. Taking advantage of the features of an electronic journal, this paper serves as an interactive tutorial for using the database, which we expect to develop into a research tool.

Databases, Protein↗