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MIC-III--an integrated software package to support experiments using the radioactive microsphere technique.

MIC-III is a versatile program system to support gamma spectrometry data management and data collection for experiments using the radioactive microsphere technique. It is mainly written in PASCAL and running on a minicomputer. Hierarchical organ dissection schemes are used for unique classification and identification of samples. For each series of experiments, up to 12 different nuclides and up to 20 different organ dissection schemes can be handled simultaneously. Sample weights are collected on-line and sample radioactivities are measured automatically by gamma spectrometry under process control. The spectra with a resolution of 1022 channels are analyzed using a modified linear regression technique and a strategy to compensate for global spectrum shifts. The spectrum deconvolution algorithm was evaluated by calculating the recovery indices for known nuclide mixtures and compared to the stripping method, matrix method and a linear regression technique using window counts. Recovery values produced by MIC-III are better balanced than those of the other methods. MIC-III showed the smallest dispersion of the recovery index and exhibited least error accumulation in case of spectrum shift. MIC-III computes regional blood flow and arterio-venous shunt, and provides interfaces to customized programs or statistical software packages for further analysis. It has successfully been employed in more than 140 experiments.

Animals↗

A new software for initiating and optimising insulin treatment of out-patients.

Two computer programs were developed, program I to optimise insulin treatment using six injections per day, and program II to convert these insulin profiles into less frequent injections of mixtures of regular and NPH insulin. The first software in an HP 41 CV pocket computer uses iterative adjustments during the day and on subsequent days to determine the optimal timing and dosage of insulin. Six self-monitored glucose values at 3 h intervals, insulin doses, and the effects of insulin on plasma glucose are memorised for calculations. The calculated insulin doses were applied by Optipen as five s.c. injections of regular insulin and one bedside injection of NPH insulin. After 5 days the optimised individual insulin profiles with six daily injections were processed by program II. It applies the pharmacokinetics of regular and NPH insulin to make suggestions for a more conventional insulin therapy with one, two, three or four daily injections of regular insulin, NPH insulin, or varying mixtures of both insulins. The procedure was well tolerated in eight insulin-dependent diabetes mellitus out-patients. Insulin therapy with two or three injections, fitted by the second program and selected according to the quality score, produced plasma glucose profiles as satisfactory as those obtained with six injections. The system allows the fine tuning of insulin therapy to out-patients with their individual diets and physical activities.

Adult↗

DREAM: a shell-like software system for medical data analysis and decision support.

A software system was designed whose aim is to support everyday scientific research of physicians in different fields of medicine. DREAM is a shell-like tool which can be customized embedding in it the desirable structure of a particular medical problem. Various basic statistical analyses are provided along with the decision support capabilities. The decision aid is proposed in two steps--feature selection and classifier design. Genetic algorithm is implemented as the feature selection procedure. The classifier design option includes crisp and fuzzy k-Nearest Neighbors rule and a two-level classification scheme based on majority rule on the votes of several first-level k-Nearest Neighbors classifiers. The system's performance is illustrated with a database from aviation medicine.

Aerospace Medicine↗

DECIDE: a software for computer-assisted evaluation of diagnostic test performance.

The evaluation of the performance of clinical tests is a complex problem involving different steps and many statistical tools, not always structured in an organic and rational system. This paper presents a software which provides an organic system of statistical tools helping evaluation of clinical test performance. The program allows (a) the building and the organization of a working database, (b) the selection of the minimal set of tests with the maximum information content, (c) the search of the model best fitting the distribution of the test values, (d) the selection of optimal diagnostic cut-off value of the test for every positive/negative situation, (e) the evaluation of performance of the combinations of correlated and uncorrelated tests. The uncertainty associated with all the variables involved is evaluated. The program works in a MS-DOS environment with EGA or higher performing graphic card.

Clinical Laboratory Techniques↗

OoClamp: an IBM-compatible software system for electrophysiologic receptor studies in Xenopus oocytes.

A software system for IBM-compatible microcomputers running MS-DOS or Microsoft Windows 3.1 is described which facilitates the acquisition, analysis and storage of data from electrophysiologic studies of receptors expressed in Xenopus laevis oocytes. The system is designed to provide standardization of test conditions, automation of all routine functions, rapid, on-line analysis of data, and self-documentation and compact storage of data files. All system settings are optimized for use with the Xenopus expression system, but can be adapted to other large cells. An example application, expression of muscarinic acetylcholine receptors in Xenopus oocytes, is described.

Animals↗

PC software library for the production of auditory stimuli in cognitive event-related potential experiments.

Software which provides an interface to the features of the Sound Blaster Pro card for the IBM PC using MS-DOS is described. The library may be called from a Turbo Pascal version 6 program. It permits tones of specified frequency (500 Hz-8 kHz in increments of 500Hz) and aversive noise to be turned on and off by a controlling program, during cognitive event-related potential paradigms. Tones are synthesized by hardware and noise is replayed from memory using the digital sound processor. The library provides the appropriate level of abstraction for the programmer designing such paradigms, by hiding the detail of the register level. It provides a model for programming the card in other high level languages and may be augmented to provide more complex stimuli, such as short segments of speech or music. The card when controlled by the library provides a versatile and cost effective alternative to an audiometer in the electrophysiological laboratory.

Cognition↗

The image related services of the HELIOS software engineering environment.

This paper describes the approach of the European HELIOS project to integrate image processing tools into ward information systems. The image processing tools are the result of the basic research in image analysis in the Department Medical and Biological Informatics at the German Cancer Research Center. These tools for the analysis of two-dimensional images and three-dimensional data volumes with 3D reconstruction and visualization ae part of the Image Related Services of HELIOS. The HELIOS software engineering environment allows to use the image processing functionality in integrated applications.

Computer Communication Networks↗

PACS for radiology conferences--improvement of application software.

The introduction of PACS in a radiology department means that most functions that are available in the film-based system must be included. One important function is the radiology conference. The handling and application programs of digital workstations are normally not developed for demonstrations of many images in a limited time. This paper describes a workstation with specially designed software for radiology conferences. The application is separated in preparation and presentation of the cases to be demonstrated. Very fast image handling is achieved during the conference because the function is based on the principle of prefetching of the selected images. The images are presented on a large screen with high resolution. The experiences of digital radiology conferences are good. However, reference films from previous examinations create extra work because they have to be shown on the conventional lightbox.

Computer Terminals↗

CBA--an atlas-based software tool used to facilitate the interpretation of neuroimaging data.

CBA, a software tool used to improve quantification and evaluation of neuroimaging data has been developed. It uses a detailed 3-dimensional brain atlas that can be adapted to fit the brain of an individual patient represented by a series of displayed images. Anatomical information from the atlas can then be introduced into the images. If the patient has been imaged in different modalities, adaptation of the atlas to the different images will provide the transformation that brings the images into registration. CBA can thus be used as a tool for fusing multimodality information from the same patient. Furthermore, by applying the inverse atlas transformation, images from a patient can be transformed to conform to the anatomy of the atlas brain. This anatomical standardization, where the atlas brain itself serves as the anatomy standard, brings data from different individuals into a compatible form providing possibilities to perform individual-group and group-by-group comparisons between patients and normal controls.

Animals↗

A software oscilloscope for DOS computers with an integrated remote control for a video tape recorder. The assignment of acoustic events to behavioural observations.

With only a little knowledge of programming IBM compatible computers in Basic, it is possible to create a digital software oscilloscope with sampling rates up to 17 kHz (depending on the CPU- and bus-speed). The only additional hardware requirement is a common sound card compatible with the Soundblaster. The system presented in this paper is built to analyse the direction a flying bat is facing during sound emission. For this reason the system works with some additional hardware devices, in order to monitor video sequences at the computer screen, overlaid by an online oscillogram. Using an RS232-interface for a Panasonic video tape recorder both the oscillogram and the video tape recorder can be controlled simultaneously and moreover be analysed frame by frame. Not only acoustical events, but also APs, myograms, EEGs and other physiological data can be digitized and analysed in combination with the behavioural data of an experimental subject.

Animals↗

ENZEDUC 1.0: a user-friendly software package for computation of hyperbolic enzyme kinetic data in biochemical education.

ENZEDUC 1.0 is a software package developed in Microsoft QuickBASIC v7.1 for computation of hyperbolic enzyme kinetics. The educational focus of the package is laboratory practical teaching. The program can manage a maximum of 18 substrate concentration values and 72 reaction rate values for each substrate concentration (1296 pairs of values). Samples can also be of unequal sizes. More than one reaction rate value for each substrate concentration can be handled. Real-time screen plots are obtained for the Michaelis-Menten function and the most popular linear transformations. Printer outputs are available. Hardware requirements are minimum 640 Kb RAM, EGA graphics card and 80286 processor.

Algorithms↗

Symmetry and crystallography: new facilities in the graphic software MANOSK.

The new routine SYMCRY of the graphics program MANOSK is described in this paper. It is designed to analyze interactions between molecular structures related by crystalline symmetry. The symetric objects can be described in the same referential, to be manipulated as an entity, or in a referential of their own, to undergo correlative real-time movements (via the dials), given the symmetry constraints. Crystal packing can be observed, and any command of the main software MANOSK is available for the symmetric objects, including storage of the coordinates of symmetrics in the final orientation.

Computer Graphics↗

Personal computer-based visualization of molecular models by available ray-tracing software.

Developed primarily for the graphic arts, ray-tracing algorithms offer a high level of flexibility with reference to photorealistic and surrealistic image rendering. The utility of these programs is further enhanced by portability (i.e., compatibility with a number of operating systems), accessibility through various sources, and low cost. This report documents, through the use of existing software, the application of these ray-tracing attributes to molecular graphics on a desktop computer. This application is especially pertinent in view of rapid speed enhancements in personal computers (PCs), which have enabled molecular modeling and dynamics on these systems. In this regard, ray tracing on a PC provides enhanced capabilities for molecular graphics rendering that are potentially equivalent to those achieved by workstations.

Algorithms↗

The Electronic View Box: a software tool for radiation therapy treatment verification.

PURPOSE: We have developed a software tool for interactively verifying treatment plan implementation. The Electronic View Box (EVB) tool copies the paradigm of current practice but does so electronically. A portal image (online portal image or digitized port film) is displayed side by side with a prescription image (digitized simulator film or digitally reconstructed radiograph). The user can measure distances between features in prescription and portal images and "write" on the display, either to approve the image or to indicate required corrective actions. The EVB tool also provides several features not available in conventional verification practice using a light box. METHODS AND MATERIALS: The EVB tool has been written in ANSI C using the X window system. The tool makes use of the Virtual Machine Platform and Foundation Library specifications of the NCI-sponsored Radiation Therapy Planning Tools Collaborative Working Group for portability into an arbitrary treatment planning system that conforms to these specifications. The present EVB tool is based on an earlier Verification Image Review tool, but with a substantial redesign of the user interface. A graphical user interface prototyping system was used in iteratively refining the tool layout to allow rapid modifications of the interface in response to user comments. RESULTS: Features of the EVB tool include 1) hierarchical selection of digital portal images based on physician name, patient name, and field identifier; 2) side-by-side presentation of prescription and portal images at equal magnification and orientation, and with independent grayscale controls; 3) "trace" facility for outlining anatomical structures; 4) "ruler" facility for measuring distances; 5) zoomed display of corresponding regions in both images; 6) image contrast enhancement; and 7) communication of portal image evaluation results (approval, block modification, repeat image acquisition, etc.). CONCLUSION: The EVB tool facilitates the rapid comparison of prescription and portal images and permits electronic communication of corrections in port shape and positioning.

Hospital Records↗

An analysis of the costs of a hospital-wide Picture Archiving and Communication System with the software package CAPACITY.

Within the scope of the Dutch PACS project, the costs of a hospital wide PACS in the Utrecht University Hospital were estimated, with the help of the software package CAPACITY. The cost analysis was based on the most recent specifications of the costs of the equipment, on extrapolations, and on the experience acquired with a PACS prototype in the Utrecht University Hospital. Savings due to a possible reduction in the length of stay, or due to logistic improvements were not taken into account. The results indicate that the extra costs of a hospital wide PACS would amount to 3.2% of the total hospital budget. By taking into account the expected price movements, it is predicted that a hospital wide PACS may allow enough savings to pay itself back, when installed near the turn of the century. The result of this cost analysis depends on a large number of assumptions. Therefore two sensitivity analyses are carried out, i.e., concerning the number of workstations required and concerning the organizational impact of PACS.

Computer Systems↗

Solubility and acid-base behaviour of midazolam in media of different pH, studied by ultraviolet spectrophotometry with multicomponent software.

The solubility of midazolam is less than 0.1 mg ml-1 at neutral pH and it increases considerably in acidic media. A pKa value of 6.04 at 24 +/- 1 degree C was calculated from the solubility data. In acidic media midazolam is reversibly converted to the corresponding benzophenone (open-ring form). The extent of this reaction was investigated by assaying the two compounds simultaneously by UV spectrophotometry with multicomponent software. The structure of the benzophenone derivative was verified by IR, MS and 1H and 13C NMR spectrometry.

Chromatography, Thin Layer↗

CLONEPLACER: a software tool for simulating contig formation for ordered shotgun sequencing.

This communication describes a software tool that enables one to simulate large-scale regional mapping using an ordered shotgun sequencing approach. The analysis routines that are provided yield an estimate of the depth of coverage of the physical map, the largest contig formed, and the number of gaps remaining at any given juncture in the project. A detailed listing describing the span of each contig within the physical map is also presented. This provides an a priori means of estimating the resources that will be required to undertake any megabase mapping or sequencing project. CLONEPLACER provides the much needed guide to deriving the optimal strategy.

Chromosome Mapping↗