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At least 127 records · Page 7Linked to original sources

PubMed2002

Group for research in pathology education online resources to facilitate pathology instruction.

BACKGROUND: The Group for Research in Pathology Education (GRIPE) is an organization of pathology educators whose purpose is to promote and facilitate excellence in pathology education. One important function of GRIPE is the maintenance of image and multiple-choice test question data banks. These resources have recently been made available online via the GRIPE Digital Library Web site. The purpose of the GRIPE Digital Library project was to develop an online searchable database that would facilitate access to the GRIPE resources for pathology education. DESIGN: The GRIPE image bank--containing approximately 3000 peer-reviewed gross and microscopic pathologic images along with textual descriptions--was linked with the GRIPE test question bank using Gossamer Thread's DBMan Web database management program. The search and display templates create a functional user interface that integrates images, image descriptions, and test questions into a single online digital library. Using any Web browser, faculty can access the GRIPE Digital Library and search for images and/or test items that can be used in teaching. RESULTS: In the first 18 months (February 2000 through July 2001), users at 40 GRIPE member institutions signed up and used the GRIPE Digital Library to perform more than 6000 individual searches and view more than 37500 images. These digital images were used to produce lectures and laboratory modules that were posted on Web pages and made available to students remotely. CONCLUSIONS: The GRIPE Digital Library provides a unique resource that can facilitate development of educational materials for pathology instruction and helps to fulfill the educational mission of GRIPE.

Computer Communication Networks↗

PubMed2003

SeqVISTA: a graphical tool for sequence feature visualization and comparison.

BACKGROUND: Many readers will sympathize with the following story. You are viewing a gene sequence in Entrez, and you want to find whether it contains a particular sequence motif. You reach for the browser's "find in page" button, but those darn spaces every 10 bp get in the way. And what if the motif is on the opposite strand? Subsequently, your favorite sequence analysis software informs you that there is an interesting feature at position 13982-14013. By painstakingly counting the 10 bp blocks, you are able to examine the sequence at this location. But now you want to see what other features have been annotated close by, and this information is buried several screenfuls higher up the web page. RESULTS: SeqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences. SeqVISTA is able to display results from diverse sequence analysis tools in an integrated fashion, and aims to provide much-needed unity to the bioinformatics resources scattered around the Internet. Our viewer may be launched on a GenBank record by a single click of a button installed in the web browser. CONCLUSION: SeqVISTA allows insights to be gained by viewing the totality of sequence annotations and predictions, which may be more revealing than the sum of their parts. SeqVISTA runs on any operating system with a Java 1.4 virtual machine. It is freely available to academic users at http://zlab.bu.edu/SeqVISTA.

Amino Acid Sequence↗

PubMed2000

[Simultaneous query and retrieve from multiple DICOM image archives using a proxy server].

PURPOSE: DICOM clients could not access more than one archive simultaneously in the previous PACS systems. We developed a proxy server which makes it possible for clients to query and retrieve images from multivendor DICOM archives simultaneously. METHODS: We used a Web server that supports the DICOM query and retrieve(Q/R) service class as a proxy server. This system consisted of two DICOM servers and six DICOM clients of different vendors in the Radiology Department. Through Web browsers on the clients, requests for Q/R were transmitted to the proxy server by hypertext transfer protocol. The proxy server communicated with DICOM servers by DICOM Q/R Service Class(C-FIND, C-MOVE), and then DICOM servers directly transmitted images to DICOM clients by DICOM Storage Service Class(C-STORE). RESULTS: DICOM clients could transmit Q/R requests to two DICOM servers simultaneously via the proxy server and receive requested images promptly. Confirmation of conformance among the proxy server, DICOM archives, and DICOM clients became much easier than previously. CONCLUSION: A Web server working as a proxy server of the DICOM Q/R Service Class is an effective solution for allowing DICOM clients to communicate with multiple DICOM archives.

Computer Communication Networks↗

PubMed2000

[A visual displayer for publishing radiologic images on the World Wide Web].

PURPOSE: To present a software suitable for publication of medical images on the World Wide Web and compatible with both the DICOM and other popular formats like GIF and JPEG. MATERIALS AND METHODS: DICOM viewer is a Java applet, written in Java 1.0. The tool offers the capability to publish medical images, to modify brightness and contrast (windowing) and to magnify the picture (magnification lens). Information related to the image is available for consultation only for DICOM images. RESULTS: The viewer was tested with many DICOM files, generated by our PACS or downloaded from Internet. It works well with the DICOM 3.0 file format, but correct functioning is not granted for previous releases. The software was compatible with all the most popular Web browsers (MS Internet Explorer 3.0 or newer, Netscape Navigator 4.5 or newer, Sun and HotJava) and it works well in Windows, Sun Solaris. Macintosh, Windows CE. A 512 kb image (a standard MR image) requires about 5 seconds to be shown on an Intel Pentium II PC with 32 Mbyte RAM connected on a 10 Mbit/s Ethernet network. About 3 seconds are needed to download the file and about 2 seconds to display the image. Windowing and zooming are quick enough. CONCLUSIONS: The applet allows to publish DICOM medical images directly on the World Wide Web, without converting them into another graphical format. Moreover, it supplies some image processing tools common in the radiological environment. The viewer characteristics make it suitable for preparing teaching radiology sites or clinical files on the Web. The viewer's performance is somewhat poor, particularly on the Internet. Better performances are achieved on local area network (intranet). To improve performance, we will introduce file compression and rewrite the software in Java 1.1. The software is available from the author free of charge.

Humans↗

PubMed1999

Virtual reality on the web: the potentials of different methodologies and visualization techniques for scientific research and medical education.

Academic and medical imaging are increasingly using computer based 3D reconstruction and/or visualization. Three-dimensional interactive models play a major role in areas such as preclinical medical education, clinical visualization and medical research. While 3D is comparably easy to do on a high end workstations, distribution and use of interactive 3D graphics necessitate the use of personal computers and the web. Several new techniques have been demonstrated providing interactive 3D via a web browser thereby allowing a limited version of VR to be experienced by a larger majority of students, medical practitioners and researchers. These techniques include QuickTimeVR2 (QTVR), VRML2, QuickDraw3D, OpenGL and Java3D. In order to test the usability of the different techniques, Mednet have initiated a number of projects designed to evaluate the potentials of 3D techniques for scientific reporting, clinical visualization and medical education. These include datasets created by manual tracing followed by triangulation, smoothing and 3D visualization, MRI or high-resolution laserscanning. Preliminary results indicate that both VRML and QTVR fulfills most of the requirements of web based, interactive 3D visualization, whereas QuickDraw3D is too limited. Presently, the JAVA 3D has not yet reached a level where in depth testing is possible. The use of high-resolution laserscanning is an important addition to 3D digitization.

Computer Graphics↗

PubMed2026

theBIGbam: compression and interactive exploration of large-scale sequencing alignments with circular mapping support.

SUMMARY: theBIGbam (github.com/bhagavadgitadu22/theBIGbam) is a genome browser and alignment viewer designed for massive metagenomic and metatranscriptomic datasets. The tool takes BAM files containing read alignments, together with genome assemblies in FASTA format or annotated genome sequences in GenBank format. Alternatively, it can start from raw FASTQ reads and generate alignments using a modified mapper that supports circular genomes, enabling seamless read mapping across genome ends. theBIGbam can compress hundreds of gigabytes of input files 10- to 100-fold into dedicated databases while retaining key per-position information, including coverage depth and recurrent mismatches, insertions, and deletions between reads and the reference. These databases can be served to a local web browser, enabling interactive exploration of any contig in any sample using DNAFeaturesViewer for genome maps and Bokeh for mapping-derived features. Contig-sample pairs available for visualization can be filtered using a range of summary metrics calculated per contig, per sample, and per contig-sample pair to guide users toward the most relevant signals. Through its interactive visualization, theBIGbam facilitates the exploration of complex datasets, while its integrated database-combining assembly features, annotated features, and mapping-derived features-provides the information needed to investigate biological hypotheses systematically. Designed to complement existing browsing tools like IGV and Anvi'o, theBIGbam is particularly suited for examining misassemblies, subpopulations, microdiversity, and contig topology in large-scale datasets. AVAILABILITY AND IMPLEMENTATION: theBIGbam is an open-source Rust/Python package that can be installed from Bioconda or PyPI. The source code and documentation are available on GitHub (github.com/bhagavadgitadu22/theBIGbam).

Software↗

PubMed2003

JVirGel: Calculation of virtual two-dimensional protein gels.

We developed JVirGel, a collection of tools for the simulation and analysis of proteomics data. The software creates and visualizes virtual two-dimensional (2D) protein gels based on the migration behaviour of proteins in dependence of their theoretical molecular weights in combination with their calculated isoelectric points. The utilization of all proteins of an organism of interest deduced from genes of the corresponding genome project in combination with the elimination of obvious membrane proteins permits the creation of an optimized calculated proteome map. The electrophoretic separation behaviour of single proteins is accessible interactively in a Java(TM) applet (small application in a web browser) by selecting a pI/MW range and an electrophoretic timescale of interest. The calculated pattern of protein spots helps to identify unknown proteins and to localize known proteins during experimental proteomics approaches. Differences between the experimentally observed and the calculated migration behaviour of certain proteins provide first indications for potential protein modification events. When possible, the protein spots are directly linked via a mouse click to the public databases SWISS-PROT and PRODORIC. Additionally, we provide tools for the serial calculation and visualization of specific protein properties like pH dependent charge curves and hydrophobicity profiles. These values are helpful for the rational establishment of protein purification procedures. The proteomics tools are available on the World Wide Web at http://prodoric.tu-bs.de/proteomics.php.

Computer Graphics↗

PubMed1999

Internet TV set-top devices for web-based projects: smooth sailing or rough surfing?

BACKGROUND: The explosion of projects utilizing the World Wide Web in the home environment offer a select group of patients a tremendous tool for information management and health-related support. However, many patients do not have ready access to the Internet in their homes. For these patients, Internet TV set-top devices may provide a low cost alternative to PC-based web browsers. METHODS: As a part of a larger descriptive study providing adolescents with access to an on-line support group, we investigated the feasibility of using an Internet TV set-top device for those patients in need of Internet access. RESULTS: Although the devices required some configuration before being installed in the home environment, they required a minimum of support and were well accepted by these patients. However, these patients used the Internet less frequently than their peers with home personal computers--most likely due to a lack of easy availability of the telephone or television at all times. CONCLUSION: Internet TV set-top devices represent a feasible alternative access to the World Wide Web for some patients. Any attempt to use these devices should, however, be coupled with education to all family members, and an attempt at providing a dedicated television and phone line.

Adolescent↗

PubMed2006

Let's reach all of the market for health administration education: design, development, and delivery issues in distance delivery.

Web-based distance learning is an up and coming form of education. Web-based education delivered via a Web browser through the Internet has been found to be less expensive, more efficient, and sometimes more effective than classroom training. In the distance learning environment, the traditional "lecture and chalkboard" classroom pedagogy is completely absent. The virtual classroom becomes an "active learning" environment in which students, while utilizing technology, are able to discuss health administration concepts, analyze cases, work exercises, and discuss and share these interactively with both the instructor and fellow classmates. This method of Health Administration Education encourages students to learn from each other and promotes the open exchange of ideas and experiences. It does not require working students to put their careers on hold while they continue their studies. In this paper, we explore the opportunities and challenges of delivering web-based Health Administration courses via the Internet. Included is a discussion of the design, development, and delivery of a distance learning, web-based Health Administration Education system.

Adult↗

PubMed2000

Multimedia-based courseware in the Virtual Learning Center at the Hannover Medical School.

The commercial use of the World Wide Web causes an extensive change in information technology. Web browser are becoming the universal front-end for all kinds of client-server applications. The possibilities of telematics offer a base for multimedia applications, for instance telelearning. Learning is not limited by geography and does not cause pressure of time by the user. The development of such multimedia information and communication systems demands cooperative working teams of authors, who are able to master several areas of medical knowledge as well as the presentation of these using different multimedia facilities. A very important part of graphic design in the context of multimedia applications is the creation and interactive use of images (still, moving). The growth and the complexity of medical knowledge as well as the need for continuous, fast, and economically feasible maintenance impose requirements on the media used for medical education and training. Web-based courseware in the Virtual Learning Center at the Hannover Medical School is an innovative education resource for medical students and professionals.

Computer-Assisted Instruction↗

PubMed2002

[Necessary prerequisites for the function of an oncological competence center. Information technology, documentation of findings and telecommunication].

INTRODUCTION: The organisation of an interdisciplinary cancer center, especially the establishment of a daily tumorboard requires adequate hardware and intelligent software, which is not available in most hospitals and described here with concepts, realisation and first clinical results. MATERIALS AND METHODS: Based on a TCP/IP network and several inhomogeneous department subsystems we developed an intranet-based oncological documentation- and conference software (oncofile), which can be easily operated and administered in a web browser. Common digital media can be imported and the concept allows for paperless organisation of the daily tumor board. The expert decisions are documented online during tumor board runtime together with selected clinical images and the consensus of the decisionmakers. Local therapeutic guidelines as well as trial information can be accessed over the intranet, and interfaces for internet- and telecommunication are used for second opinion and integration of external expertise. RESULTS: Between 10/99 and 2/2002 3298 presentations of 2438 cases were made in the daily tumor board. 74% of the patients had a curative oncological treatment concept, and 24% of the patients received neoadjuvant treatment. 49% of the patients were scheduled for primary resection. Six patients can be effectively handled in a 30 minute tumorboard. CONCLUSION: The establishment of a daily tumorboard is possible by help of intranet-technology, a central database with web clients and moderate hardware investments. The composition of the patient cohort as well as all decisions ever made to a particular patient are transparent at all times. Prospective quality control studies are under way.

Cancer Care Facilities↗

PubMed2002

Internet programs for drawing moth pheromone analogs and searching literature database.

An Internet web page is described for organizing and analyzing information about lepidopteran sex pheromone components. Hypertext markup language (HTML) with JavaScript program code is used to draw moth pheromone analogs by combining GIF bitmap images for viewing by web browsers such as Netscape or Microsoft Intemet Explorer. Straight-chain hydrocarbons of 5-22 carbons with epoxides or unsaturated positions of E or Z geometrical configuration with several altemative functional groups can be drawn by simply checking menu bars or checkboxes representing chain length, E/Z unsaturation points, epoxide position and chirality, and optional functional groups. The functional group can be an aldehyde, alcohol, or ester of formate, acetate, propionate, or butyrate. The program is capable of drawing several million structures and naming them [e.g., (E,E)-8,10-dodecadien-1-ol and abbreviated as E8E10-12:OH]. A Java applet program run from the same page searches forthe presently drawn structure in an intemal database compiled from the Pherolist, and if the component is found, provides a textarea display of the families and species using the component. Links are automatically specified for drawn components if found in the Pherolist web site (maintained by H. Am). Windowed links can also be made to two other JavaScript programs that allow searches of a web site database with over 5900 research citations on lepidopteran semiochemicals and a calculator of vapor pressures of some moth sex pheromone analogs at a specified temperature. Various evolutionary and biosynthetic aspects are discussed in regard to the diversity of moth sex pheromone components.

Animals↗

PubMed2000

Telepathology by the Internet.

A new concept for telemicroscopy has recently been introduced using the Internet and conventional web browser, with Java support for microscope remote control as well as image transfer and discussion (http://amba.charite.de/telemic/). The system has two major components: the telemicroscopy server, which is a computer with Internet access connected to the automatic microscope, and the telemicroscopy client, who remotely operates the microscope. This simplified telemicroscopy system allows any Internet user to become a consultant for telepathology without the acquisition of specialized hardware or software. For the inquirer seeking advice, however, this solution is still very expensive, since it requires a fully automated microscope. The present study describes a system that can be used for conventional microscopes. A video camera mounted on a microscope with a photo tube is connected to the frame grabber of a PC. Java-based telemicroscopy software transforms the computer into an Internet server, which automatically distributes new microscope images, after manual operations, to all connected clients. Any Internet user can access the web page of the server to become a telemicroscopy client. A Chat function allows for the online exchange of written text and a Discuss function enables the mouse button to display an arrow to all connected clients, which highlights distinct structures of the images. The system was optimized for simplicity, while presenting all features that are necessary to show and discuss difficult cases with any expert in the field who has Internet access. It offers new perspectives for telepathology and it is envisaged that many pathologists and scientists will use this facility to connect their personal microscopes to the Internet, forming a network for teleconsultation. To foster this development, the software described in this paper is being made freely available. Hopefully, this development will promote communication between pathologists and may thus increase the quality of diagnosis. Information on inquiry and installation of the software is available at the website mentioned above. Telemicroscopy sessions using the Telemic version for conventional microscopes can be scheduled by contacting the authors by e-mail (iver. petersen@charite.de).

Communication↗

PubMed1998

Telematic system for monitoring of asthma severity in patients' homes.

Despite advances in the treatment of asthma the morbidity and mortality of this disease has increased significantly in the past several years. Recent studies have shown that monitoring of asthma severity in the patient home especially combined with patient education can reduce incidence of asthma exacerbation and subsequent hospitalization. The existing methods for home asthma monitoring are limited by four factors; they completely rely on a patient's ability to document and to evaluate test results; there is no easy way for a physician to review data in a timely manner; they use imprecise tools for evaluation of asthma severity and they don't provide clinical decision support tools. The goal of this study is to develop and to evaluate a telematic system for asthma severity monitoring which will minimize patients' efforts in performing self-testing at their homes and allow prompt reciprocal exchange of all relevant information between patients and health care providers. In our setting, patients use portable spirometer and pocket-sized palmtop computer for data exchange. Our system allows daily serial monitoring of asthma severity at patients' homes using Forced Vital Capacity test and symptom diary. The results of the tests become available for physicians review immediately after completion of self-testing procedures via Web browser. The results can be transmitted from patients' homes (or any other remote location) to the medical records database via landline or wireless networks in several minutes. Each time the remote server receives patient's results, it invokes the application which tests the validity of data, analyzes parameters trends and dispatches corresponding messages for the patient and, if necessary, for physicians. Such an approach provides constant feedback loop between asthma patient and physician. The system has been tested in 10 healthy volunteers and asthma patients. Patients participated in the study from two to 21 days. The test results showed that the system provides reliable reciprocal exchange of all relevant information between a physician and asthma patient in home settings. Average transmission time from the patient's palmtop to the remote central data repository was about 1 minute for 14.4 Kbps landline modem, 6 minutes for cellular network and 8 minutes for RAM Mobile network. After transmission, the test results were immediately available for review at our web site.

Asthma↗

PubMed2024

GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information.

High-throughput intact glycopeptide analysis is crucial for elucidating the physiological and pathological status of the glycans attached to each glycoprotein. Mass spectrometry-based glycoproteomic methods are challenging because of the diversity and heterogeneity of glycan structures. Therefore, we developed an MS1-based site-specific glycoform analysis method named "Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile (Glyco-RIDGE)" for a more comprehensive analysis. This method detects glycopeptide signals as a cluster based on the mass and chromatographic properties of glycopeptides and then searches for each combination of core peptides and glycan compositions by matching their mass and retention time differences. Here, we developed a novel browser-based software named GRable for semi-automated Glyco-RIDGE analysis with significant improvements in glycopeptide detection algorithms, including "parallel clustering." This unique function improved the comprehensiveness of glycopeptide detection and allowed the analysis to focus on specific glycan structures, such as pauci-mannose. The other notable improvement is evaluating the "confidence level" of the GRable results, especially using MS2 information. This function facilitated reduced misassignment of the core peptide and glycan composition and improved the interpretation of the results. Additional improved points of the algorithms are "correction function" for accurate monoisotopic peak picking; one-to-one correspondence of clusters and core peptides even for multiply sialylated glycopeptides; and "inter-cluster analysis" function for understanding the reason for detected but unmatched clusters. The significance of these improvements was demonstrated using purified and crude glycoprotein samples, showing that GRable allowed site-specific glycoform analysis of intact sialylated glycoproteins on a large-scale and in-depth. Therefore, this software will help us analyze the status and changes in glycans to obtain biological and clinical insights into protein glycosylation by complementing the comprehensiveness of MS2-based glycoproteomics. GRable can be freely run online using a web browser via the GlyCosmos Portal (https://glycosmos.org/grable).

Glycopeptides↗

PubMed2000

Going virtual with quicktime VR: new methods and standardized tools for interactive dynamic visualization of anatomical structures.

Continuing evolution of computer-based multimedia technologies has produced QuickTime, a multiplatform digital media standard that is supported by stand-alone commercial programs and World Wide Web browsers. While its core functions might be most commonly employed for production and delivery of conventional video programs (e.g., lecture videos), additional QuickTime VR "virtual reality" features can be used to produce photorealistic, interactive "non-linear movies" of anatomical structures ranging in size from microscopic through gross anatomic. But what is really included in QuickTime VR and how can it be easily used to produce novel and innovative visualizations for education and research? This tutorial introduces the QuickTime multimedia environment, its QuickTime VR extensions, basic linear and non-linear digital video technologies, image acquisition, and other specialized QuickTime VR production methods. Four separate practical applications are presented for light and electron microscopy, dissectable preserved specimens, and explorable functional anatomy in magnetic resonance cinegrams.

Anatomy, Cross-Sectional↗

PubMed1999

An online locus-specific mutation database for familial hypertrophic cardiomyopathy.

The aim of this locus-specific mutation database was to provide an online resource that contains summarised and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. There are 123 FHC-associated mutations catalogued along with ancillary information. By implementing the cgi/http method, remote users can query the database via the HTML interface on the Web browser and obtain data of relevance to them. The online service is available on http://www.angis.org.au/Databases/Heart.

Alternative Splicing↗

PubMed2001

Comparison of a virtual microscope laboratory to a regular microscope laboratory for teaching histology.

Emerging technology now exists to digitize a gigabyte of information from a glass slide, save it in a highly compressed file format, and deliver it over the web. By accessing these images with a standard web browser and viewer plug-in, a computer can emulate a real microscope and glass slide. Using this new technology, the immediate aims of our project were to digitize the glass slides from urinary tract, male genital, and endocrine units and implement them in the Spring 2000 Histology course at the University of Iowa, and to carry out a formative evaluation of the virtual slides of these three units in a side-by-side comparison with the regular microscope laboratory. The methods and results of this paper will describe the technology employed to create the virtual slides, and the formative evaluation carried out in the course. Anat Rec (New Anat) 265:10-14, 2001.

Computer-Assisted Instruction↗