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Graphical and stereolithographic models of the developing human heart lumen.

Scaled physical models can be useful in analyzing stage-specific hemodynamics in the embryonic human heart to address correlations between early physical stressors and myocardial wall responses. We generated models of the cardiac blood space from reconstructions of four digitized human embryo images from Carnegie Collection at the Armed Forces Institute of Pathology. From physical scale models manufactured by stereolithography, compliant sleeves can be created for flow dynamics studies. This novel use of Carnegie collection images and graphical modeling software provides tools for broadening our understanding of normal and aberrant heart formation.

Embryonic and Fetal Development↗

New approaches to virtual environment surgery.

This research focused on two main problems: 1) low cost, high fidelity stereoscopic imaging of complex tissues and organs; and 2) virtual cutting of tissue. A further objective was to develop these images and virtual tissue cutting methods for use in a telemedicine project that would connect remote sites using the Next Generation Internet. For goal one we used a CT scan of a human heart, a desktop PC with an OpenGL graphics accelerator card, and LCD stereoscopic glasses. Use of multiresolution meshes ranging from approximately 1,000,000 to 20,000 polygons speeded interactive rendering rates enormously while retaining general topography of the dataset. For goal two, we used a CT scan of an infant skull with premature closure of the right coronal suture, a Silicon Graphics Onyx workstation, a Fakespace Immersive WorkBench and CrystalEyes LCD glasses. The high fidelity mesh of the skull was reduced from one million to 50,000 polygons. The cut path was automatically calculated as the shortest distance along the mesh between a small number of hand selected vertices. The region outlined by the cut path was then separated from the skull and translated/rotated to assume a new position. The results indicate that widespread high fidelity imaging in virtual environment is possible using ordinary PC capabilities if appropriate mesh reduction methods are employed. The software cutting tool is applicable to heart and other organs for surgery planning, for training surgeons in a virtual environment, and for telemedicine purposes.

Computer Simulation↗

Solving the forward problem in electrical impedance tomography for the human head using IDEAS (integrated design engineering analysis software), a finite element modelling tool.

If electrical impedance tomography is to be used as a clinical tool, the image reconstruction algorithms must yield accurate images of impedance changes. One of the keys to producing an accurate reconstructed image is the inclusion of prior information regarding the physical geometry of the object. To achieve this, many researchers have created tools for solving the forward problem by means of finite element methods (FEMs). These tools are limited, allowing only a set number of meshes to be produced from the geometric information of the object. There is a clear need for geometrical accurate FEM models to improve the quality of the reconstructed images. We present a commercial tool called IDEAS, which can be used to create FEM meshes for these models. The application of this tool is demonstrated by using segmented data from the human head to model impedance changes inside the head.

Algorithms↗

An affordable approach to interactive desktop molecular modeling.

The amazing revolution in computer hardware performance and cost reduction has yet to be carried over to computer software. In fact, application software today is often more expensive and less reliable than the hardware. New enhancements in software development techniques, such as object oriented programming and interactive graphics based user interface design, finally may be having a significant impact on the time-to-market and reliability of these application programs. We discuss our experiences using one such set of software development tools available on the NeXT workstation and describe the effort required to port our MidasPlus molecular modeling package to the NeXT work-station.

Computer Graphics↗

How changes in computer technology are revolutionizing the practice of chemistry.

During the early 1980s, two major developments in computer technology changed the way chemists approached their science. The advent of the micropressor and then the PC changed experimental chemistry, while the availability of two classes of computer, the superminicomputer and supercomputer, greatly influenced computational chemistry. In the past two years, graphics workstation computers have begun to affect the practice of chemistry by combining fast, high-resolution, multiwindow graphics with superminicomputer power. In 1988, the advent of a new class of computer--the graphics supercomputer--offers extraordinary promise to both theoretician and experimentalist. In these systems, near-Cray compute power is combined with ultrahigh-speed 3-dimensional graphics for unparalleled visualization of molecular processes and other complex events. This is made practical not just by computing and graphics power but by use of ultrahigh internal bandwidths inside the graphics supercomputers. Another major development in scientific computing is the evolving concept of the laboratory computer network. Current network designs include hierarchical configurations incorporating various levels of computers--through supercomputers--either locally or via national or regional networks. New software methods are also having impact on chemical research, allowing, for example, the scientist to better abstract information from noisy or incomplete experimental data. Use of parallelism (multiple CPUs) in new design workstation computers will extend their power, by the early 1990s, past that of current supercomputer mainframes. Within five years the chemist will have $10 million of 1985 computer power on his desk, for considerably less than $100,000, along with visualization tools and software only dreamed of in 1985.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical Phenomena↗

Effects of rigid fixation device composition on three-dimensional computed axial tomography imaging: direct measurements on a pig model.

OBJECTIVE: To compare the amount of scatter produced by titanium plates versus Vitallium (Howmedica, Rutherford, NJ) plates. Software was also evaluated to determine its effectiveness in removing the scatter and clarifying the underlying anatomy. MATERIALS AND METHODS: Miniplating and microplating systems composed of Vitallium or titanium were placed on the nasal and frontal bones of three adult pig heads. A computerized axial tomography (CAT) scan was then performed and a three-dimensional CAT scan was reconstructed using MediCad software (MediCad Inc, Cedar Knolls, NJ). The amount of scatter for each plating system was quantitated using the MediCad software measuring tool. The scatter was removed and the three-dimensional CAT scan was reconstructed to assess the clarification of the underlying anatomy. RESULTS: No scatter was found with either the miniplating or the microplating system composed of titanium. The Vitallium plates did show significant amount of scatter with the mini, micro, and micromesh system. Removal of the scatter resulted in slight improvement in the anatomic detail. CONCLUSION: Titanium plating systems do not cause any radiation scatter. The MediCad software system allows removal of the scatter found with the Vitallium plates, which helps clarify the underlying anatomy.

Animals↗

Measuring and developing suturing technique with a virtual reality surgical simulator.

BACKGROUND: We have developed an interactive virtual reality (VR) surgical simulator for the training and assessment of suturing technique. The surgical simulator is comprised of surgical tools with force feedback, a 3-dimensional graphics visual display of the simulated surgical field, physics-based computer simulations of the tissues and tools, and software to measure and evaluate the trainee's performance. STUDY DESIGN: This study uses the simulator to measure and compare the skills of 8 experienced vascular surgeons versus 12 medical students when performing a virtual reality suturing task. Eight parameters of the suturing task were measured: total tissue damage, accuracy of needle puncture, peak tissue tearing force, time to complete the task, damage to the surface of the tissue, angular error in needle technique, total distance traveled by the tool tip, and a measure of overall error. Three test conditions (dominant hand, nondominant hand, and 3-dimensional needle guide) were tested. Statistical significance was defined as a univariate two-sided p value < or = 0.05. RESULTS: The surgeons' average performance was significantly better than the students' average performance for three of the measured parameters (total tissue damage, time to complete the task, and total distance traveled by the tool tip) for each of the test conditions. For the test condition most similar to surgery (using the dominant hand to suture) one additional parameter was also significantly different (the measure of overall error). The medical students showed improvements for 6 of the 7 parameters for which the users received feedback during the training process. The surgeons also had significant improvement for 4 of the 7 parameters. The students had a larger improvement than the surgeons for 6 of the parameters, but these differences were not statistically significant. CONCLUSIONS: Data indicate differences between surgeon and nonsurgeon performance and in improvement in performance with training. One possible explanation for the superior performance of the surgeons is that their suturing skills applied well to the simulated suturing task. Additional research is required to confirm or deny the similarity between actual and simulated surgical tasks and the relevance of virtual reality surgical simulation to surgical skill assessment and training.

Computer Simulation↗

Protein databases and software on BIONET.

BIONET provides databases, software, and networking/communications tools to over 2500 molecular biologists worldwide. Software for the analysis of nucleic acid and protein sequence data is provided by both IntelliGenetics and academic contributors. BIONET is currently implementing dedicated high speed servers for searching protein databases, as well as providing more flexible tools for protein structure recognition and prediction. In this review, protein databases and analysis software available on the BIONET resource are described, and progress in providing new tools for structure prediction, comparative sequence analysis, and pattern recognition using Artificial Intelligence (AI) techniques are summarized.

Amino Acid Sequence↗

Using Lab On-line to Clone and Identify the Esophageal Cancer Related Gene 4.

Using Internet as platform, databases as materials and software as tools to assemble a lab on-line is revolutionizing in bioscience research. The major works of lab on-line are cloning, identification, localization of genes, and the structural and functional analysis of proteins. In this report, the esophageal cancer related gene 4(ECRG-4)(accession number AF325503) was successfully isolated. The 97 bp ECRG-4 EST was initiallyusedto fish the human EST databases. Five pieces of ESTs showed strong homology to it, and they were assembled to one 772 bp cDNA sequence by DNASTAR software. Then the 447 bp full open reading frame of ECRG-4 was determined by ORF FINDER to encode 148 amino acids. Sequence of ECRG-4 did not reveal remarkable similarity to the known sequences in a homology analysis with the public database of GenBank, showing that it is a new gene. Homology analysis of protein coding by ECRG-4 showed a 31% homology with mouse IgG V region. ECRG-4 gene is expressed in normal esophagus, bladder and brain tissues, but its expression was significantly down-regulated in prostate tumors and tumor cell lines. ECRG-4 gene was located in 2q14.1--4.3 by HTGS and STS, and was conformed by radiation hybrid (RH) method. We propose that this purely lab on-line cloning approach can be used by modestly sized laboratories to rapidly and accurately characterize human genes without wasting too much money and time.

Journal Article↗

Radiation biodosimetry: applications for spaceflight.

The multiparametric dosimetry system that we are developing for medical radiological defense applications could be adapted for spaceflight environments. The system complements the internationally accepted personnel dosimeters and cytogenetic analysis of chromosome aberrations, considered the best means of documenting radiation doses for health records. Our system consists of a portable hematology analyzer, molecular biodosimetry using nucleic acid and antigen-based diagnostic equipment, and a dose assessment management software application. A dry-capillary tube reagent-based centrifuge blood cell counter (QBC Autoread Plus, Becton [correction of Beckon] Dickinson Bioscience) measures peripheral blood lymphocytes and monocytes, which could determine radiation dose based on the kinetics of blood cell depletion. Molecular biomarkers for ionizing radiation exposure (gene expression changes, blood proteins) can be measured in real time using such diagnostic detection technologies as miniaturized nucleic acid sequences and antigen-based biosensors, but they require validation of dose-dependent targets and development of optimized protocols and analysis systems. The Biodosimetry Assessment Tool, a software application, calculates radiation dose based on a patient's physical signs and symptoms and blood cell count analysis. It also annotates location of personnel dosimeters, displays a summary of a patient's dosimetric information to healthcare professionals, and archives the data for further use. These radiation assessment diagnostic technologies can have dual-use applications supporting general medical-related care.

Animals↗

Flixborough revisited - an explosion simulation approach.

A literature study of explosion estimation reports from the Flixborough accident was performed and commented. The results from this survey were compared to the results obtained from explosion simulations. The simulations were done with a computer model of the Flixborough plant using the EXSIM software simulation tool. The comparison showed that explosion magnitude estimates in the literature based on visual inspection are much lower than the simulated results, while the estimates based on calculations to a large degree conform with the simulations. The simulations also showed that the exact location of the ignition source does not seem to be significant for the magnitude of the explosion.

Accidents, Occupational↗

[The role of 3-D imaging and computer-based postprocessing for surgery of the liver and pancreas].

Cross-sectional imaging based on navigation and virtual reality planning tools are well-established in the surgical routine in orthopedic surgery and neurosurgery. In various procedures, they have achieved a significant clinical relevance and efficacy and have enhanced the discipline's resection capabilities. In abdominal surgery, however, these tools have gained little attraction so far. Even with the advantage of fast and high resolution cross-sectional liver and pancreas imaging, it remains unclear whether 3D planning and interactive planning tools might increase precision and safety of liver and pancreas surgery. The inability to simply transfer the methodology from orthopedic or neurosurgery is mainly a result of intraoperative organ movements and shifting and corresponding technical difficulties in the on-line applicability of presurgical cross sectional imaging data. For the interactive planning of liver surgery, three systems partly exist in daily routine: HepaVision2 (MeVis GmbH, Bremen), LiverLive (Navidez Ltd, Slovenia) and OrgaNicer (German Cancer Research Center, Heidelberg). All these systems have realized a half- or full-automatic liver-segmentation procedure to visualize liver segments, vessel trees, resected volumes or critical residual organ volumes, either for preoperative planning or intraoperative visualization. Acquisition of data is mainly based on computed tomography. Three-dimensional navigation for intraoperative surgical guidance with ultrasound is part of the clinical testing. There are only few reports about the transfer of the visualization of the pancreas, probably caused by the difficulties with the segmentation routine due to inflammation or organ-exceeding tumor growth. With this paper, we like to evaluate and demonstrate the present status of software planning tools and pathways for future pre- and intraoperative resection planning in liver and pancreas surgery.

Hepatectomy↗

HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data.

BACKGROUND: Human immunodeficiency virus (HIV) research involves ongoing, repetitious sequencing of the HIV genome and the massive accumulation of associated investigational data. As a result, the storage of annotated DNA and/or protein sequences, as well as information retrieval, have become increasingly difficult tasks, with scientists extracting less information from their collected data than they should. OBJECTIVES: Our objective was to design and develop a software package to aid researchers in the storage, analysis and exploration of their HIV-associated data. RESULTS: HIVbase contains familiar, easy-to-use interfaces and functionality for integrating many types of disparate data. The software contains tools that allow for the mass import of raw genetic data, eliminate repetitious sequence translations, have the ability to identify automatically and store HIV regions of interest from nucleic acid or protein sequences, allow for the export of data in commonly used analysis-ready formats, and for unique querying approaches.

Algorithms↗

Verification of ophthalmic brachytherapy treatment planning.

Ophthalmic brachytherapy dose calculations were performed as an independent verification of commercial dosimetry software (BEBIG Plaque Simulator). Excel spreadsheets were constructed to follow the formalism of the AAPM Task Group No. 43. As a software commissioning tool, TG43 seed-based coordinates were reformatted to be compatible with plaque-based BEBIG dose tables for centrally positioned seeds. Plaque central axis doses were also calculated for rings of seeds. Close agreement with BEBIG doses was obtained in both cases. Tailored spreadsheet versions were subsequently created to verify patient treatment plans. Treatment time and dose to a specified central-axis point are calculated for ROPES plaques fully loaded with 1-125 model 6702 seeds.

Brachytherapy↗

A simple client-server system using a personal computer as the server.

Hospital information systems have recently grown into huge, complex systems. As a result, the cost of development and maintenance of application programs has increased and become a serious problem. We have constructed an order entry system using server-client architecture as part of a hospital intranet information system in which a personal computer is used as a server. Using a commercial database management system and software development tools, an easily maintained order entry system was developed within only three months by one programmer. Since slow response when the number of clients increased was possible, we measured turn-around times when one or ten clients accessed simultaneously. Turn-around times were 8 and 10 sec, respectively. Because we expect much better performance from personal computers in the near future, application systems using personal computers as Intranet servers will be cost and time effective and easy to develop and maintain.

Computer Communication Networks↗

Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies.

We have developed a metabolic profiling scheme based on direct-infusion Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The scheme consists of: (1) reproducible data collection under optimized FT-ICR/MS analytical conditions; (2) automatic mass-error correction and multivariate analyses for metabolome characterization using a newly developed metabolomics tool (DMASS software); (3) identification of marker metabolite candidates by searching a species-metabolite relationship database, KNApSAcK; and (4) structural analyses by an MS/MS method. The scheme was applied to metabolic phenotyping of Arabidopsis (Arabidopsis thaliana) seedlings treated with different herbicidal chemical classes for pathway-specific inhibitions. Arabidopsis extracts were directly infused into an electrospray ionization source on an FT-ICR/MS system. Acquired metabolomics data were comprised of mass-to-charge ratio values with ion intensity information subjected to principal component analysis, and metabolic phenotypes from the herbicide treatments were clearly differentiated from those of the herbicide-free treatment. From each herbicide treatment, candidate metabolites representing such metabolic phenotypes were found through the KNApSAcK database search. The database search and MS/MS analyses suggested dose-dependent accumulation patterns of specific metabolites including several flavonoid glycosides. The metabolic phenotyping scheme on the basis of FT-ICR/MS coupled with the DMASS program is discussed as a general tool for high throughput metabolic phenotyping studies.

Arabidopsis↗

[The integrated management software of primary care,a tool for analysing indicators of use].

OBJECTIVES: To analyse the indicators of use in the Gran Canaria Health Area. To characterise over-users so that the primary care team can take corrective measures. To design a computer tool giving appropriate useful information to the management, that can be directly put into practice in primary care. DESIGN: Retrospective descriptive study. SATTING: Gran Canaria Health Area. Hierarchical descent in the analysis of data in the base health area and family care unit, in the year 2000. PARTICIPANTS: Users of the Canaries Health Service registered on the individual health card data base. MAIN MEASUREMENTS AND RESULTS: The activity generated by 636 270 users with 2 876 394 appointments was studied. Mean frequency of attendance in the Gran Canaria Health Area was 4.52, with a 67.3% use rate. The user causing 11 or more visits per year was defined as an over-user. 13.4% of users were over-users and caused among them 52.3% of visits. 32.7% of users registered made no visit. CONCLUSIONS: A small section of the population causes over half the consultations. The characteristics of these users need to be analysed so that programmes can be worked out to decrease their frequency of use. The integrated management software for primary care enables this information to be analysed and serves as a support for the primary care teams. Special attention needs to be paid to the population that does not use the health centres.

Ambulatory Care Information Systems↗

Computer assisted learning (CAL) of oral manifestations of HIV disease.

General dental practitioners (GDPs) in the UK may wish additional education on relevant aspects of human immunodeficiency virus (HIV) disease. The aim of the present study was to develop and assess a computer assisted learning package on the oral manifestations of HIV disease of relevance to GDPs. A package was developed using a commercially-available software development tool and assessed by a group of 75 GDPs interested in education and computers. Fifty-four (72%) of the GDPs completed a self-administered questionnaire of their opinions of the package. The majority reported the package to be easy to load and run, that it provided clear instructions and displays, and that it was a more effective educational tool than videotapes, audiotapes, professional journals and textbooks, and of similar benefit as post-graduate courses. The GDPs often commented favourably on the effectiveness of the clinical images and use of questions and answers, although some had criticisms of these and other aspects of the package. As a consequence of this investigation the package has been modified and distributed to GDPs in England and Wales.

Adult↗