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PubMedDate not supplied

Digital hand atlas and web-based bone age assessment: system design and implementation.

Bone age assessment is a procedure frequently performed in pediatric patients to evaluate their growth disorder. A simple method commonly used in bone age assessment is atlas matching by a radiological examination of a left-hand radiograph against a small reference set of Greulich-Pyle atlas patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas developed in the 1950s based on middle upper class white populations, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The CAD system is built on top of existing picture archiving and communication system (PACS), as well as recent advances in Internet technology. It consists of a hand atlas database, a CAD module and a Java-based Web user interface. The digital atlas is based on a large new set of clinically normal hand images of diverse ethnic groups. A relational image database system is used to organize hand images, their extracted quantitative features and patient data. The digital atlas removes the disadvantages of the currently out-of-date Greulich-Pyle atlas and allows the bone age assessment to be computerized. The Java-based Web user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, are then extracted and compared with patterns from the atlas database to assess the bone age. The digital atlas method based on open system Internet technology provides an alternative to supplement or replace the traditional one for a quantitative, accurate and cost-effective assessment of bone age.

Adolescent↗

PubMed2004

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.

Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html.

Crystallography, X-Ray↗

PubMedDate not supplied

Hub-based simulation and graphics hardware accelerated visualization for nanotechnology applications.

The Network for Computational Nanotechnology (NCN) has developed a science gateway at nanoHUB.org for nanotechnology education and research. Remote users can browse through online seminars and courses, and launch sophisticated nanotechnology simulation tools, all within their web browser. Simulations are supported by a middleware that can route complex jobs to grid supercomputing resources. But what is truly unique about the middleware is the way that it uses hardware accelerated graphics to support both problem setup and result visualization. This paper describes the design and integration of a remote visualization framework into the nanoHUB for interactive visual analytics of nanotechnology simulations. Our services flexibly handle a variety of nanoscience simulations, render them utilizing graphics hardware acceleration in a scalable manner, and deliver them seamlessly through the middleware to the user. Rendering is done only on-demand, as needed, so each graphics hardware unit can simultaneously support many user sessions. Additionally, a novel node distribution scheme further improves our system's scalability. Our approach is not only efficient but also cost-effective. Only a half-dozen render nodes are anticipated to support hundreds of active tool sessions on the nanoHUB. Moreover, this architecture and visual analytics environment provides capabilities that can serve many areas of scientific simulation and analysis beyond nanotechnology with its ability to interactively analyze and visualize multivariate scalar and vector fields.

Computer Graphics↗

PubMedDate not supplied

Design and applications of a multimodality image data warehouse framework.

A comprehensive data warehouse framework is needed, which encompasses imaging and non-imaging information in supporting disease management and research. The authors propose such a framework, describe general design principles and system architecture, and illustrate a multimodality neuroimaging data warehouse system implemented for clinical epilepsy research. The data warehouse system is built on top of a picture archiving and communication system (PACS) environment and applies an iterative object-oriented analysis and design (OOAD) approach and recognized data interface and design standards. The implementation is based on a Java CORBA (Common Object Request Broker Architecture) and Web-based architecture that separates the graphical user interface presentation, data warehouse business services, data staging area, and backend source systems into distinct software layers. To illustrate the practicality of the data warehouse system, the authors describe two distinct biomedical applications--namely, clinical diagnostic workup of multimodality neuroimaging cases and research data analysis and decision threshold on seizure foci lateralization. The image data warehouse framework can be modified and generalized for new application domains.

Decision Making, Computer-Assisted↗

PubMed1991

Thieno-triazolo-1,4-diazepines as antagonists of platelet-activating factor: present status.

The platelet-activating factor, 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine, (PAF) antagonistic activity of thienotriazolodiazepines has recently been described. The lead compound in this series was brotizolam, which also exhibits sedative and hypnotic effects. By combination of brotizolam with the benzodiazepine receptor antagonist RO 15-1788, PAF antagonistic and central nervous system (CNS) activities could be segregated. Systematic structure variation has led to potent and selective PAF antagonists without CNS effects. WEB 2086 and its analogues WEB 2170 and STY 2108 are representative examples of this structural type and have shown a high potency and selectivity in PAF-induced and PAF-dependent in vitro tests and in experimental models. Studies in healthy volunteers have demonstrated potent pharmacological activity and good safety and tolerance of oral, intravenous or inhaled WEB 2086 in man. These agents should therefore prove useful for the further elucidation of the pathophysiological role of PAF and provide an opportunity for therapeutic applications in diseases in which the involvement of PAF has been implicated.

Animals↗

PubMed2000

XML: a lingua franca for science?

XML is a new language designed to solve one of the biggest problems of the World Wide Web: its main language, HTML, is not extensible. In this article, the authors discuss the current successes and limitations of the World Wide Web, briefly explain the basics of XML and present the benefits of using XML as a data-exchange language. Finally, they discuss real-life applications that have been developed using XML, with a focus on biology.

Internet↗

PubMed2001

Quick fuzzy backpropagation algorithm.

A modification of the fuzzy backpropagation (FBP) algorithm called QuickFBP algorithm is proposed, where the computation of the net function is significantly quicker. It is proved that the FBP algorithm is of exponential time complexity, while the QuickFBP algorithm is of polynomial time complexity. Convergence conditions of the QuickFBP, resp. the FBP algorithm are defined and proved for: (1) single output neural networks in case of training patterns with different targets; and (2) multiple output neural networks in case of training patterns with equivalued target vector. They support the automation of the weights training process (quasi-unsupervised learning) establishing the target value(s) depending on the network's input values. In these cases the simulation results confirm the convergence of both algorithms. An example with a large-sized neural network illustrates the significantly greater training speed of the QuickFBP rather than the FBP algorithm. The adaptation of an interactive web system to users on the basis of the QuickFBP algorithm is presented. Since the QuickFBP algorithm ensures quasi-unsupervised learning, this implies its broad applicability in areas of adaptive and adaptable interactive systems, data mining, etc. applications.

Algorithms↗

PubMed2001

Review of telemedicine projects in Taiwan.

Taiwan is a heavily populated country, with a small land area and many mountains and isolated islands. Because medical resources are unequally distributed, high quality accessible medical care is a major problem in rural areas. Medical personnel are unwilling to practice in rural areas because of fear of isolation from peers and lack of continuing medical education (CME) in those areas. Telemedicine provides a timeless and spaceless measure for teleconsultation and education. The development of telemedicine in Taiwan began under the National Information Infrastructure (NII) Project. Distance education and teleconsultation were the first experimental projects during the initiation research stage. The cost and effectiveness of the hardware and network bandwidth were evaluated. In the promotion research stage, applications in different medical disciplines were tested to promote multipoint videoconference, electronic journals and VOD. Investigation of user satisfaction put on more emphasis on improving application functions. In 1998, a new Cyber Medical Center (CMC) international collaboration project was begun, integrating technologies of multimedia, networking, database management, and the World Wide Web. The aim of the CMC is to create a multimedia network system for the management of electronic patient records, teleconsultation, online continuing medical education, and information services on the web. A Taiwan mirror site of Virtual Hospital and two international telemedicine trials through Next Generation Internet (NGI) were done at the end of 1998. In the future, telemedicine systems in Taiwan are expected to combine the Internet and broadband CATV, ADSL, and DBS networking to connect clinics, hospitals, insurance organizations, and public health administrations; and, finally, to extend to every household.

Databases, Factual↗

PubMed2003

The power of collaboration: using internet-based tools to facilitate networking and benchmarking within a consortium of academic health centers.

The University HealthSystem Consortium (UHC) represents a strategic alliance of 169 academic health centers and associated institutions engaged in knowledge sharing and idea-generation. The use of the Internet as a tool in the delivery of UHC's products and services has increased dramatically over the past year and will continue to increase during the foreseeable future. This paper examines the current state of UHC-member institution driven tools and services that utilize the Web as a fundamental component in their delivery. The evolution of knowledge management at UHC, its management information and reporting tools, and expansion of e-commerce provide real world examples of Internet use in health care delivery and management. Health care workers are using these Web-based tools to help manage rising costs and optimize patient outcomes. Policy, technical, and organizational issues must be resolved to facilitate rapid adoption of Internet applications.

Academic Medical Centers↗

PubMed1998

Surgical management of hands in children with recessive dystrophic epidermolysis bullosa: use of allogeneic composite cultured skin grafts.

Recessive dystrophic epidermolysis bullosa (RDEB) is characterised by progressive childhood hand syndactyly and flexion contractures, which can be managed surgically but require split thickness autografts to facilitate satisfactory postoperative healing. We report on the partial substitution, for autografts, of improved composite cultured skin (CCS) allografts. The structure and preparation of these CCSs is outlined and their application in the course of 16 operations performed on 7 RDEB children with syndactyly and flexor contractures of fingers is described. Hand contractures were released and web spaces were covered with local flaps and split thickness autografts, while adjacent sides of the digits and other areas, as well as donor sites were generally grafted with CCS. Morphologic and functional results with CCS were judged to be good to excellent, the average time to recurrence was increased approximately 2-fold and smaller autografts needed to be used. In addition, healed CCS-treated donor sites could provide superior donor sites for further surgery.

Adolescent↗

PubMed2003

The DynDom database of protein domain motions.

UNLABELLED: A relational database has been developed based on the results from the application of the DynDom program to a number of proteins for which multiple X-ray conformers are available. The database is populated via a web-based tool that allows visitors to the website to run the DynDom program server-side by selecting pairs of X-ray conformers by Protein Data Bank code and chain identifier. AVAILABILITY: The website can be found at: http://www.sys.uea.ac.uk/dyndom.

Crystallography↗

PubMed2005

MuPlex: multi-objective multiplex PCR assay design.

We have developed a web-enabled system called MuPlex that aids researchers in the design of multiplex PCR assays. Multiplex PCR is a key technology for an endless list of applications, including detecting infectious microorganisms, whole-genome sequencing and closure, forensic analysis and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR assays is computationally challenging because it involves tradeoffs among competing objectives, and extensive computational analysis is required in order to screen out primer-pair cross interactions. With MuPlex, users specify a set of DNA sequences along with primer selection criteria, interaction parameters and the target multiplexing level. MuPlex designs a set of multiplex PCR assays designed to cover as many of the input sequences as possible. MuPlex provides multiple solution alternatives that reveal tradeoffs among competing objectives. MuPlex is uniquely designed for large-scale multiplex PCR assay design in an automated high-throughput environment, where high coverage of potentially thousands of single nucleotide polymorphisms is required. The server is available at http://genomics14.bu.edu:8080/MuPlex/MuPlex.html.

Algorithms↗

PubMed2006

Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation.

Antisense oligodeoxynucleotides (oligos) are widely used for functional studies of both prokaryotic and eukaryotic genes. However, the identification of effective target sites is a major issue in antisense applications. Here, we study a number of thermodynamic and structural parameters that may affect the potency of antisense inhibition. We develop a cell-free assay for rapid oligo screening. This assay is used for measuring the expression of Escherichia coli lacZ, the antisense target for experimental testing and validation. Based on a training set of 18 oligos, we found that structural accessibility predicted by local folding of the target mRNA is the most important predictor for antisense activity. This finding was further confirmed by a direct validation study. In this study, a set of 10 oligos was designed to target accessible sites, and another set of 10 oligos was selected to target inaccessible sites. Seven of the 10 oligos for accessible sites were found to be effective (>50% inhibition), but none of the oligos for inaccessible sites was effective. The difference in the antisense activity between the two sets of oligos was statistically significant. We also found that the predictability of antisense activity by target accessibility was greatly improved for oligos targeted to the regions upstream of the end of the active domain for beta-galactosidase, the protein encoded by lacZ. The combination of the structure-based antisense design and extension of the lacZ assay to include gene fusions will be applicable to high-throughput gene functional screening, and to the identification of new drug targets in pathogenic microbes. Design tools are available through the Sfold Web server at http://sfold.wadsworth.org.

Algorithms↗

PubMedDate not supplied

Student perspectives on transitioning to new technologies for distance learning.

This article reports on students' perceptions of their learning experiences when an existing distance-learning master's program transitions to new technologies and new instructional strategies. Unique elements addressed in this article include (1) findings when a program with extensive experience delivering distance education changes to new technologies and (2) findings when a multidimensional format is used to evaluate program delivery. The technology changes involved migrating from a satellite-based technician-supported videoconferencing system to a land-based faculty-operated videoconferencing system and the addition of class Web materials and asynchronous computer conferencing to course delivery. The multidimensional evaluation format examined student experiences within the context of specific interactions among instructional activities, technology applications, and desired learning outcomes. The evaluation process involved (1) open-ended and structured items in course surveys and (2) an end-of-year student focus group discussion. A formative evaluation approach was used; this article reports on efforts to address the problems identified. Findings include (1) program planners should not assume that prior institutional experiences with distance education facilitate a smooth transition to use of different technologies and (2) a formative multidimensional approach to program evaluation is critical for understanding student experiences with technology-mediated distance education.

Adaptation, Psychological↗

PubMedDate not supplied

Molluscan and vertebrate immune responses to bird schistosomes.

There is a growing understanding of risks posed by human contact with the cercariae of bird schistosomes. In general, there are no fundamental biological differences between human and bird schistosomes in terms of their interactions with snail and vertebrate hosts. The penetration of host surfaces is accompanied by the release of penetration gland products and the shedding of highly antigenic surface components (miracidial ciliated plates and cercarial glycocalyx) which trigger host immune reactions. New surface structures are formed during transformation: the tegument of mother sporocysts and the tegumental double membrane of schistosomula. These surfaces apparently serve as protection against the host immune response. Certain parasite excretory-secretory products may contribute to immunosuppression or, on the other hand, stimulation of host immune reactions. Discovery of new species and their life cycles, the characterization of host-parasite interactions (including at the molecular level), the determination of parasite pathogenicity towards the host, the development of tools for differential diagnosis and the application of protective measures are all topical research streams of the future. Regularly updated information on bird schistosomes and cercarial dermatitis can be found at http://www.schistosomes.cz (web pages of Schistosome Group Prague).

Animals↗

PubMed1992

Measurement of marine picoplankton cell size by using a cooled, charge-coupled device camera with image-analyzed fluorescence microscopy.

Accurate measurement of the biomass and size distribution of picoplankton cells (0.2 to 2.0 microns) is paramount in characterizing their contribution to the oceanic food web and global biogeochemical cycling. Image-analyzed fluorescence microscopy, usually based on video camera technology, allows detailed measurements of individual cells to be taken. The application of an imaging system employing a cooled, slow-scan charge-coupled device (CCD) camera to automated counting and sizing of individual picoplankton cells from natural marine samples is described. A slow-scan CCD-based camera was compared to a video camera and was superior for detecting and sizing very small, dim particles such as fluorochrome-stained bacteria. Several edge detection methods for accurately measuring picoplankton cells were evaluated. Standard fluorescent microspheres and a Sargasso Sea surface water picoplankton population were used in the evaluation. Global thresholding was inappropriate for these samples. Methods used previously in image analysis of nanoplankton cells (2 to 20 microns) also did not work well with the smaller picoplankton cells. A method combining an edge detector and an adaptive edge strength operator worked best for rapidly generating accurate cell sizes. A complete sample analysis of more than 1,000 cells averages about 50 min and yields size, shape, and fluorescence data for each cell. With this system, the entire size range of picoplankton can be counted and measured.

Algorithms↗

PubMed1997

Addressing information security training and awareness within the European healthcare community.

This paper discusses the need to promote information security issues within modern healthcare establishments and the consequent need for appropriate training and awareness initiatives. Security is an area of extreme significance in healthcare information systems but, whilst the need is generally recognised, many personnel are not familiar with even basic concepts and procedures. As such, adequate promotion of security through training and awareness initiatives is viewed as a vital first step. The paper highlights a series of basic factors that healthcare establishments (HCEs) should consider in setting up a training and awareness framework. The discussion then examines a number of ways in which relevant information may be disseminated to staff, including security guidelines, training seminars and world-wide web based services. The paper is largely based upon work that is currently being conducted as part of the Health Telematics ISHTAR (Implementing Secure Healthcare Telematics Applications in euRope) project.

Awareness↗

PubMed1999

Semi-automatic scene generation using the Digital Anatomist Foundational Model.

A recent survey shows that a major impediment to more widespread use of computers in anatomy education is the inability to directly manipulate 3-D models, and to relate these to corresponding textual information. In the University of Washington Digital Anatomist Project we have developed a prototype Web-based scene generation program that combines the symbolic Foundational Model of Anatomy with 3-D models. A Web user can browse the Foundational Model (FM), then click to request that a 3-D scene be created of an object and its parts or branches. The scene is rendered by a graphics server, and a snapshot is sent to the Web client. The user can then manipulate the scene, adding new structures, deleting structures, rotating the scene, zooming, and saving the scene as a VRML file. Applications such as this, when fully realized with fast rendering and more anatomical content, have the potential to significantly change the way computers are used in anatomy education.

Anatomy↗