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At least 163 records · Page 9Linked to original sources
PubMed1995

Computer program for performing whole-cell voltage-clamp experiments.

This computer program was designed to be used instead of a stimulator and an oscilloscope in whole-cell voltage-clamp experiments. It runs on IBM XT-AT compatible computers under MS-DOS. The program uses drivers for specific ADC-DAC boards, which are stored in separate files. The driver to be used is loaded on start-up. Drivers for Labmaster TL-1 and CSY-10 are available and the driver for CED 1401 is now being developed. Stimulus waveforms of up to five consecutive pulses are supported. Data may be acquired from up to four input channels, using two ADC sampling rates. The acquired data are visualised on six plots which can be resized and moved independently on the screen in order to obtain a readable picture. A special mode for monitoring the giga-seal formation is supported. There are several data processing procedures, which can be used without interrupting the experiment, including I-V relationships, cursor measurements, addition and subtraction of obtained currents.

Microcomputers↗
PubMed1995

RefVal: a program implementing the recommendations of the International Federation of Clinical Chemistry on the statistical treatment of reference values.

RefVal is a computer program that implements the recommendations of the International Federation of Clinical Chemistry on the statistical treatment of reference values. The program performs the following main tasks: graphical display of the distribution of reference values, identification or elimination of outliers, testing of the fit of the distribution to Gaussian shape (coefficients of skewness and kurtosis, Anderson-Darling's test, Cramér-von Mises' test, Kolmogorov-Smirnov's test), non-parametric and parametric estimation of reference limits (fractiles, percentiles). The parametric estimation method is based on a two-stage mathematical transformation of data: (1) Manly's exponential transformation (to remove skewness) and (2) John and Draper's modulus transformation (to adjust for remaining kurtosis). The program exists in different versions. The paper describes two of these: (1) a library of FORTRAN functions and subroutines and (2) a Pascal PC program that runs under MS-DOS.

Bias↗
PubMed1995

Prediction of polypeptide secondary structures analysing the oscillation of the hydropathy profile.

The hydropathy profile of a polypeptide can reflect periodicity tightly linked, in particular, with alpha-helix and beta-strand conformations. We have developed an algorithm to detect such periodicity to predict the secondary structure of proteins. The method uses profiles constructed with the weighted average of hydropathy along the primary structure of the polypeptide and does the analysis of the variation of the profile for looking for periodic oscillations, using a variation detecting algorithm, without the definition of an empirical threshold. The independence of the method from known structures makes it particularly reliable for analysing membrane proteins.

Algorithms↗
PubMed1996

Clinical evaluation of the DIABETES expert system for decision support by multiple regimen insulin dose adjustment.

A performance evaluation of the DIABETES rule-based expert system prototype for clinical decision making is presented. The system facilitates multiple insulin regimen and dose adjustment of insulin dependent Type I or II diabetic patients. The study was performed on 600 subjects from two diabetological centres and three diabetological offices of Greek hospitals. The responses of the attendant medical doctors were compared with those of the DIABETES system, with the aid of a specifically devised valuation range (0-5 degrees, 0 indicating full agreement and 5 full disagreement). The capabilities and the weakness of the system in terms of its practicality for decision support in assisting therapy of diabetes mellitus by blood glucose monitoring and subsequent insulin dose adjustment are discussed. The potential benefits of decision support systems for diabetic patient management are seen to be the cost saving they provide in terms of man-hours of verbal instruction by medical experts, the support in terms of objective and consistent decision making, as well as the recording of medical knowledge in the ill-defined field of insulin administration, thus aiding the education and training of medical personnel.

Aged↗
PubMed1996

Implementation of OSPOP, an algorithm for the estimation of optimal sampling times in pharmacokinetics by the ED, EID and API criteria.

The most common approach to optimize the sampling schedule in parameter estimation experiments is the D-optimality criterion, which consists in maximizing the determinant of the Fisher information matrix (max det F). In order to incorporate prior parameter uncertainty in the optimal design, other criteria have been proposed: The ED = max E (det F), EID = min E (l/det F) and API = max E (log det F) criteria, where the expectation is with respect to the given prior distribution of the parameters. Previously described algorithm for the estimation of optimal sampling times according to these criteria are adaptive random search (ARS), a robust and global but slow optimizer for API, and stochastic gradient (SG), a fast but local optimizer for ED and EID. We implemented an algorithm named OSPOP 1.0, based on non-adaptive random search (RS) followed by stochastic gradient to determine optimal sampling times for parameter estimation in various pharmacokinetic models according to ED, EID and API criteria. Prior distributions are allowed to be uniform, normal or lognormal. This algorithm combines the robustness of RS and the speediness of SG (convergence is obtained in a few minutes on a microcomputer). The results of the SG algorithm have been compared to those described in the literature using the ARS algorithm on a one compartment model with first- order absorption and were very similar. Also, the CPU time needed by SG and ARS algorithms were compared and the former proved to be much faster. Then, it has been applied to a five parameters stochastic model with zero-order absorption rate and Weibull-distributed residence times which was shown to describe adequately the kinetics of metacycline in humans. Population pharmacokinetic parameters of metacycline were estimated from a six subject pilot study, by the iterative two-staged method, using ADAPT II repeatedly. Optimal sampling times were determined with each criterion (ED, EID, API) with a multivariate normal prior parameter distribution. Six to seven distinct sampling times could be estimated. Higher numbers of samples revealed coalescing of design points.

Algorithms↗
PubMed1996

Analysis of pressurized resistance vessel diameter changes with a low cost digital image processing device.

A low cost digital image processing device (frame grabber) together with a program running under MS_WINDOWS for automatic on-line analysis of diameter changes of in vitro pressurized blood vessels with an inner diameter of 80-400 microns is presented. The frame grabber is designed to receive light microscopic images either from a video camera or from a VCR and to present the digitized image on the computer monitor. The special software allows to manipulate the image, e.g. filtering, calibrating, storing of vessel images, and detects the outer and inner border of the two vessel walls with a new, simple algorithm. The inner diameter and the vessel wall thickness are calculated and the diameter is presented in a diameter versus time diagram on the monitor screen. Further, these data are stored in an ASCII-file for later import into calculation and presentation programs like MS-EXCEL.

Algorithms↗
PubMed1996

Add-in macros for rapid and versatile calculation of non-compartmental pharmacokinetic parameters on Microsoft Excel spreadsheets.

We developed a package of macro programs (named PK_MOMENT) to automatically calculate non-compartmental pharmacokinetic parameters on Microsoft Excel spreadsheets. These macros include rigorous algorithms to execute moment calculations in a comprehensive manner. An optimum number of terminal data points for infinite-time extrapolation can be calculated with one of these macros so that automatic calculation of infinite moment parameters is possible. The moment calculation with PK_MOMENT provided satisfactory results using the hybrid (mixed linear-logarithmic) trapezoidal method rather than the conventional linear trapezoidal method. The macro-aided pharmacokinetic analyses turned out to be useful in that the macro-containing cells can be easily copied and pasted to analyze other data sets and that powerful tools of Excel can be utilized. The use of our macros will be significantly time-saving for routine pharmacokinetic analyses, considering that pharmacokinetic data are usually stored in a spreadsheet format, typically with Excel.

Administration, Oral↗
PubMed1996

Implementation of a reference management system, MacRefer, under HyperCard.

We have developed a reference management system, MacRefer, using HyperTalk on Macintosh personal computers. Using this program, one can automatically acquire data from databases created by EndNote Plus and from OVID- or Medlar-formatted records downloaded via an online use of Medline. The MacRefer's capability of formatting bibliographic database in user-defined formats is comparable with the exemplified bibliography maker, EndNote Plus. Moreover, MacRefer has several competitive features, which are insufficiently equipped with EndNote Plus. For example, MacRefer is capable of (1) maintaining subsets within a database, (2) executing complex, structured searches combining up to nine keywords for any data field with the results and search conditions preserved, and (3) easily browsing (a portion of) reference database. Although MacRefer cannot be recognized as an absolute alternative of EndNote Plus because of several limitations inherent to HyperCard, the compensatory use of these two programs will expand the personal utilization of bibliographic databases.

Computers↗
PubMed1996

A computer program for comprehensive ST-segment depression/heart rate analysis of the exercise ECG test.

The ST-segment depression/heart rate (ST/HR) analysis has been found to improve the diagnostic accuracy of the exercise ECG test in detecting myocardial ischemia. Recently, three different continuous diagnostic variables based on the ST/HR analysis have been introduced; the ST/HR slope, the ST/HR index and the ST/HR hysteresis. The latter utilises both the exercise and recovery phases of the exercise ECG test, whereas the two former are based on the exercise phase only. This present article presents a computer program which not only calculates the above three diagnostic variables but also plots the full diagrams of ST-segment depression against heart rate during both exercise and recovery phases for each ECG lead from given ST/HR data. The program can be used in the exercise ECG diagnosis of daily clinical practice provided that the ST/HR data from the ECG measurement system can be linked to the program. At present, the main purpose of the program is to provide clinical and medical researchers with a practical tool for comprehensive clinical evaluation and development of the ST/HR analysis.

Exercise Test↗
PubMed1996

Mathematical model for chemically induced lipid peroxidation in precision-cut liver slices: computer simulation and experimental calibration.

A biologically based pharmacodynamic (BBPD) model was developed in order to describe and simulate chemically induced lipid peroxidation in precision cut mouse liver slices. The model was written in Advanced Continuous Simulation Language (ACSL) and simulations were performed using SIMUSOLV software on a VAX/VMS mainframe computer. The BBPD model simulated formation of lipid hydroperoxides and thiobarbituric acid reactive substances (TBARS) over time as a function of the amounts of cytochrome P450 (CYP)-activated chemical inducer and active antioxidants. The rate of peroxidation was controlled by lipid peroxidizability, destruction of CYP, autooxidation, and activity of glutathione peroxidase. The BBPD model was initially parameterized with the literature data for TBARS formation during lipid peroxidation, reported for rat liver slices induced with bromotrichloromethane and tert-butyl hydroperoxide (TBOOH). Then, the biochemical parameters were adjusted to reflect the physiology of the mouse liver, and the BBPD model was used to simulate TBARS formation during lipid peroxidation in precision cut mouse liver slices induced with TBOOH. The BBPD model predictions were in agreement with the experimental data.

Animals↗
PubMed1995

A dual approach to structural texture analysis in microscopic cell images.

The computer-based quantitative analysis of microscopic cell images provides important diagnostic information in clinical and experimental pathology. The arrangement of various cell structures can be described as texture. We developed a new approach to structural texture analysis. It assumes that texture consists of homogeneous regions (texture primitives). Texture can be regarded in a dual way--as a composition of regions or as a pattern composed of the regions' boundaries (lines). We implemented methods for the segmentation of regions and lines in grayscale images. The detection of regions is followed by a region-growing process to avoid an oversegmentation. The segmented regions and lines are stored in a uniform data structure which reflects their arrangement in the image. The presented methods were applied to study the chromatin distribution in cell nuclei and the development and differentiation of intermediate filaments in fetal liver cells.

Algorithms↗
PubMed1990

Testing a 3-D radiation therapy planning program.

This report describes a systematic effort to test all functions of a large 3-D radiation therapy planning program, including graphics and user interaction. Previous studies in quality assurance for radiation therapy programs do not adequately address the problem of programming errors. They compare dose estimates calculated by planning programs to actual doses measured in phantoms, so they cannot distinguish programming errors from measurement errors or physical unsoundness of the beam model. Moreover, they fail to exercise graphics and user interaction functions. This report describes a different methodology: test cases are derived from the program specification, results are calculated by an independent technique, and compared to program output. Derivation of test cases is described in detail. Effectiveness of testing is assessed by reporting the number of errors revealed by testing and comparing to the number of errors discovered during routine use in five successive program versions. The size of the test set is related to the total program size, and the effort devoted to deriving and performing tests is compared to the total program development effort. We conclude that systematic testing can reveal errors that are not found by informal testing, routine program use, or comparison with measurements. However, additional errors remain that are only discovered during use. This study suggests that a typical large planning system may include more than 100 errors when it is released for clinical use. Methods for increasing testing effectiveness are recommended.

Radiotherapy, Computer-Assisted↗
PubMed1990

Portal dose images. I: Quantitative treatment plan verification.

The comparison of a predicted portal dose image, calculated during treatment planning, with the measured image obtained during treatment is proposed as an approach to verify the correct implementation of a patient treatment plan. The comparison inherently verifies both the geometric alignment and the dose delivered. Feasibility studies were conducted with 60Co irradiation of a modular plastic phantom, an anthropomorphic phantom and a patient with lung cancer. Calculations were made with the 3-dimensional scatter ray-trace Delta Volume method. Calculated distributions and/or selected points of transmitted dose correction factors were compared with measurements made with TLD, scanning ionization chamber and film. For the two phantom studies, excellent agreement, usually to within 3%, was achieved when positioning of the phantoms were accurate. The patient study showed that selected point comparisons were inadequate in identifying the cause of errors when disagreement occurred. Simple subtraction of the calculated and measured images showed a 4 mm translational misalignment. The results are encouraging and demonstrate that portal dose images can be used to detect large geometric and dosimetric discrepancies between treatment plan calculations and measurements. The results also show that perfect verification is virtually impossible in the clinical situation. More work is required to use the verification information for improving the estimation of dose to the patient.

Cobalt Radioisotopes↗
PubMed1990

Portal dose images. II: Patient dose estimation.

Due to the many sources of uncertainties in radiotherapy, conventional treatment planning can only provide a nominal presentation of the dose delivered to the patient. Provided that large setup errors can be detected and corrected, we propose that measured and calculated portal dose images can be used to improve estimation of patient dose. The iterative approach described in this paper requires an accurate method of dose calculations, 3-dimensional CT data that closely represents the patient and the measured portal dose image. From the CT data, a portal dose image is calculated for comparison with the measured one. The differences are then used to modify the original CT data so that a new image can be calculated. The process is repeated until the calculated and measured images agree to satisfaction. At that point, the internal dose is calculated using the modified CT data. If the method is successful, daily portal dose images could be used to cumulatively estimate patient dose throughout the course of treatment. This manuscript describes 60Co simulation results to demonstrate the feasibility of the approach.

Cobalt Radioisotopes↗
PubMed1990

On-line radiotherapy imaging with an array of fiber-optic image reducers.

In the optical approach for on-line radiotherapy imaging, a large metal sheet-fluorescent screen combination is used to convert the radiation intensity distribution into a visible light image. Data are then captured via a mirror with a camera located out of the beam. Although usable portal images can be acquired, presence of the large mirror renders the system impractical in many treatment geometries. We have overcome this limitation by replacing the mirror with an array of 16 by 16 bundles of plastic fiber-optic image reducers. Each bundle, in turn, is made up of 16 by 16 individual optical fibers. The total of 256 by 256 fibers spans an input area of 40 cm by 40 cm with each individual fiber viewing an area of 1.6 mm by 1.6 mm. Within a height of 12 cm, each fiber is reduced to an area of 0.1 mm by 0.1 mm. The reduced portal image is then turned and "piped" to a final 3.0 cm by 3.0 cm output area. For data acquisition and digitization, the fiber output is directly coupled to the sensor of a TV camera interfaced to a small computer via a 512 by 512 frame grabber. In this initial evaluation, the imaging system has been characterized in terms of its line spread function, noise and resistance to radiation damage. Adequate phantom and patient images are presented.

Fiber Optic Technology↗
PubMed1990

Full integration of the beam's eye view concept into computerized treatment planning.

A complete set of beam's eye view (BEV) and beam portal design features have been integrated into a computerized 3-dimensional radiotherapy treatment planning system. Among the features implemented is the ability to mix BEV graphics with gray-scale images such as simulator and verification radiographs, and digital reconstructed radiographs. Image processing techniques have been developed to both enhance verification images and to detect radiation field boundaries. These portal simulation and presentation techniques are being used clinically to design and verify radiation fields with manual or automatically-designed field shaping blocks. The ability to perform computer dose calculations for planes which are parallel or perpendicular to a specified beam's central axis is available and this feature has also proven useful for treatment plan evaluation and optimization. Finally, direct comparison of computer-generated portal images with actual simulation and verification radiographs is also possible. These techniques allow the direct integration of "CT-directed treatment planning" with block design, simulator films and port films, and other Beam's Eye View-type displays.

Computer Simulation↗
PubMedDate not supplied

3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations.

In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel serial sections. It is explained how this geometrical data base is useful with the different processing approaches of a 3D shape, such as analysis and visualisation. Methods of conversion between the geometrical representations are discussed. Examples of the operation of the data base as it is embedded in a data base management system are given by illustrations of retrieval of geometrical information.

Algorithms↗
PubMedDate not supplied

A gray-level thinning method for delineation and representation of arteries.

The quantification of three dimensional (3D) properties of coronary arteries is of significant importance. The performance of the 3D analysis is critically based on low-level representation of the arterial tree for different projections. A skeletal representation of arteries can provide appropriate data structure for registration of multiple angiographic projections and it can be further utilized for 3D reconstruction of the arterial tree. This paper presents an automated method for extracting the skeletal points of an arterial tree directly from the gray-level information without determining the edges a priori. It offers the advantage of improved reliability compared to methods based on detecting dual edges of the arteries. Novel application of filtering techniques provide accurate estimates of the statistics of the background. A recursive search scheme is used to aggregate the skeletal representation at multiple resolutions. Results on a set of Digitally Subtracted Angiograms (DSA) have been presented.

Algorithms↗