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PubMed1987

[Use of a computer program for statistical calculation of various research data in anesthesia].

A software package for statistical data analysis will be discussed. The program "Test" help also in the computer entry and storage of data. This database package is available for small Personal Computer with a capacity of 512 kB, working with a Disk Operating System (DOS). "Test" is a very simple and very fast working statistical package. The most important advantages of this system are: (1) Simple to work and to learn, (2) Simple data collection and processing, (3) Very fast data analysis and calculation, (4) Checking of test assumptions, (5) Detailed demonstrations of results both with a matrix printer and computer display.

Algorithms↗
PubMed1991

Computer-programmed instruction: The relation of required interaction to practical application.

Computers were used to evaluate the effects of supplying answers to programmed instruction frames. A group experimental design compared passive reading, covert responding to frame blanks, and actively typing answers to blanks with and without immediate confirmation of correctness. Effects of a 315-frame program, teaching elements of programmed instruction design, were evaluated by analyzing answers to posttest generalization questions and an application test. Results strongly supported the effectiveness of requiring the student to supply fragments of a terminal repertoire while working through a program. Students who could either covertly respond to frame blanks or who were required to type frame answers performed significantly better on the frame generalization posttest and, more importantly, carefully followed program rules when preparing elements of a new instructional program.

Journal Article↗
PubMed1989

RECPAM: a computer program for recursive partition amalgamation for censored survival data and other situations frequently occurring in biostatistics. II. Applications to data on small cell carcinoma of the lung (SCCL).

The RECPAM methodology previously presented in part I (A. Ciampi et al., Comput. Methods Programs Biomed. 26 (1988) 239-256) is applied to the analysis of survival data on small cell carcinoma of the lung (SCCL). It is shown how RECPAM can help answer the following questions which occur frequently in the analysis of clinical data: Is it possible to find a classification of patients with a certain disease into distinct prognostic groups? Given a covariate of special interest, does it have an independent prognostic significance even after confounding is taken into account? Does the prognostic significance of a covariate of special interest vary across patient subgroups? For the SCCL data, a prognostic classification is obtained and the tumor marker LDH is treated as a variable of special interest. Many features of RECPAM are illustrated, including, among others, Forward and Backward (Pruning) Stopping Rules, treatment of missing data, and use of several dissimilarity measures.

Biomarkers, Tumor↗
PubMed2004

Assessment of the sensitivity of the computational programs DEREK, TOPKAT, and MCASE in the prediction of the genotoxicity of pharmaceutical molecules.

Computational models are currently being used by regulatory agencies and within the pharmaceutical industry to predict the mutagenic potential of new chemical entities. These models rely heavily, although not exclusively, on bacterial mutagenicity data of nonpharmaceutical-type molecules as the primary knowledge base. To what extent, if any, this has limited the ability of these programs to predict genotoxicity of pharmaceuticals is not clear. In order to address this question, a panel of 394 marketed pharmaceuticals with Ames Salmonella reversion assay and other genetic toxicology findings was extracted from the 2000-2002 Physicians' Desk Reference and evaluated using MCASE, TOPKAT, and DEREK, the three most commonly used computational databases. These evaluations indicate a generally poor sensitivity of all systems for predicting Ames positivity (43.4-51.9% sensitivity) and even poorer sensitivity in prediction of other genotoxicities (e.g., in vitro cytogenetics positive; 21.3-31.9%). As might be expected, all three programs were more highly predictive for molecules containing carcinogenicity structural alerts (i.e., the so-called Ashby alerts; 61% +/- 14% sensitivity) than for those without such alerts (12% +/- 6% sensitivity). Taking all genotoxicity assay findings into consideration, there were 84 instances in which positive genotoxicity results could not be explained in terms of structural alerts, suggesting the possibility of alternative mechanisms of genotoxicity not relating to covalent drug-DNA interaction. These observations suggest that the current computational systems when applied in a traditional global sense do not provide sufficient predictivity of bacterial mutagenicity (and are even less accurate at predicting genotoxicity in tests other than the Salmonella reversion assay) to be of significant value in routine drug safety applications. This relative inability of all three programs to predict the genotoxicity of drugs not carrying obvious DNA-reactive moieties is discussed with respect to the nature of the drugs whose positive responses were not predicted and to expectations of improving the predictivity of these programs. Limitations are primarily a consequence of incomplete understanding of the fundamental genotoxic mechanisms of nonstructurally alerting drugs rather than inherent deficiencies in the computational programs. Irrespective of their predictive power, however, these programs are valuable repositories of structure-activity relationship mutagenicity data that can be useful in directing chemical synthesis in early drug discovery.

Computer Simulation↗
PubMed1976

A computer program to derive the rate equations of enzyme catalysed reactions with up to ten enzyme-containing intermediates in the reaction mechanism.

The paper describes a program, designed for a desk-top computer, which can be used to derive the rate equations of enzyme catalysed reactions with up to ten enzyme-containing intermediates included in the mechanism. The program allows the rate equation to be presented in simplified forms of practical use and in a variety of formats.

Catalysis↗
PubMedDate not supplied

Robustness of biological activity spectra predicting by computer program PASS for noncongeneric sets of chemical compounds.

The computer system PASS provides simultaneous prediction of several hundreds of biological activity types for any drug-like compound. The prediction is based on the analysis of structure-activity relationships of the training set including more than 30000 known biologically active compounds. In this paper we investigate the influence on the accuracy of predicting the types of activity with PASS by (a) reduction of the number of structures in the training set and (b) reduction of the number of known activities in the training set. The compounds from the MDDR database are used to create heterogeneous training and evaluation sets. We demonstrate that predictions are robust despite the exclusion of up to 60% of information.

Chemistry, Pharmaceutical↗
PubMed2003

Qualitative analysis of the overhand throw by undergraduates in education using a distance learning computer program.

The purpose was to (a) examine whether computer-based distance learning could enhance the qualitative analysis skills (error detection in the overhand throw) of undergraduates in education and (b) examine the effectiveness of several methods of information presentation (video file and text) on distance learning. Participants were randomly assigned to 1 of 4 groups, to detect errors in an incorrect throwing motion of a model on the computer screen. Group 1 (n=13) was the control; Group 2 (n=13) viewed a video of the appropriate throwing mechanics; Group 3 (n=13) viewed text information describing the appropriate mechanics of the overhand throw; and Group 4 (n=16) received a combination of video and text information. On Day 1 participants took a pretest. Treatment and testing occurred on Days 2 through 8. Then 5 days later participants took a retention test. One-way analysis of variance confirmed no significant differences between groups at Pretest (Day 1). An analysis of variance with repeated measures indicated learning over practice. Paired-sample t tests between Days 1 and 8 showed the video plus text group without significant change.

Adolescent↗
PubMed1989

[A catalog of computer programs for dosimetric irradiation planning].

A catalogue of computer-based programmes for dosimetric irradiation planning is described, that was elaborated according to the programme of the joint research of the CMEA-countries on field of radiotherapy of malignant tumors in the years 1983-1985. The catalogue includes 55 programmes from 11 research-centres in Hungary, the GDR, Poland, the USSR, and the CSSR: 23 programmes are determined for dosimetric planning of distant irradiation, 13 for intracavitary, 7 for interstitial, 6 for combined irradiation, and 6 for radiobiological planning. 26 programmes are used to optimize the dose fields by selection of adequate irradiation conditions. The catalogue includes 42 tables, which in details inform on possibilities of the programmes, on radiotherapeutic equipments, which were these programmes elaborated for, and on their clinical use. The problem is discussed to procure the catalogue.

Catalogs as Topic↗
PubMed1994

RhoScope: a highly portable computer program for visualization of the zero-flux atomic surfaces.

Atomic boundaries are defined within the topological theory of atoms in molecules as zero-flux surfaces in the gradient of electron density. The so-defined atomic surfaces often have quite complicated shapes that reflect the local characteristics of the electron distribution. A highly portable computer visualization program, called RhoScope, that displays the zero-flux atomic surfaces is described in this article. Examples of atomic surfaces in the C60 cluster and the C2H2LiCl carbenoid, rendered with the help of RhoScope, are presented.

Carbon↗
PubMed1994

Computer programs for calculation of median effective dose (LD50 or ED50) using the method of moving average interpolation.

Over the past 40 years, toxicologists and pharmacologists have used tables published by Weil for the determination of LD50 (or ED50) values and their associated 95% confidence intervals. With the advances in computer technology, it is now common for investigators to have personal computers in their laboratories. Therefore, two identical programs were developed for determination of the LD50 (or ED50) which may be run on a personal computer. One of these programs was written in BASIC, and the other in FORTRAN. The programs are easy and rapid to use, requiring minimum computer hardware and little, if any, knowledge of programming. They also offer more user flexibility than the previously published tables of Weil, in that there are fewer restrictions on the number of animals and number of dosage levels used in an experiment. The output of the programs may be typed on the screen of a computer monitor, and may be sent to a printer. The two programs calculate the LD50 and 95% confidence intervals for the LD50. These programs should be valuable for many investigators.

Dose-Response Relationship, Drug↗
PubMed1993

A computer program for motion analysis of single cardiac myocytes.

Single adult cardiac ventricular cells were prepared by collagenase perfusion of a rat heart. They were stimulated electrically in a perfusion chamber and their length changes were followed under a microscope. The motion was followed via a video camera and by a TV-line counting device and was recorded on-line by a personal computer. The program RECORD was used to calculate peak amplitude, base line drift and peak width at different peak heights allowing the determination of a number of variables of the cellular motion. The method was applied to drugs affecting the amplitude of contractions and the speed of relaxation. Results of beta-adrenergic stimulation, muscarinic inhibition and of the Ca(2+)-ATPase inhibitor cyclopiazonic acid (CPA) are shown. Besides its stimulatory effect on length, the beta-adrenergic agonist isoprenaline concentration-dependently shortened relaxation time. Carbachol reversed the increase in cellular shortening caused by isoprenaline in a concentration-dependent manner without fully reversing the shortened relaxation. CPA prolonged the return to diastole, presumably due to its inhibition of Ca(2+)-reuptake into the sarcoplasmatic reticulum.

Animals↗
PubMed1985

Computer program for prediction of the optimal and suboptimal secondary structures of long RNA molecules.

We present an algorithm for prediction of RNA secondary structures. The program consists of three parts: the first computes location and free energy of every possible stem-loop structure, the second computes probability of its formation, and the third lists the positions and free energies of all the stem-loops in the order of their probability sizes. The circular RNA molecule of chrysanthemum stunt viroid was used as an input data for demonstrating the operation of the program.

Algorithms↗
PubMed1981

Modular computer programs for flow cytometry and sorting: the LACEL system.

A computer-based data acquisition, display and processing system for flow cytometers has been developed. The Los Alamos Cell Analysis (LACEL) programs and electronic hardware provide the capability to acquire list mode or histogram data for up to eight parameters and control bidirectional sorting based on up to four parameters for each direction. The programs described in this paper also enable the display of single parameter and bivariate histograms and the graphical manipulation of the list mode data. The electronic hardware is described in a companion paper.

Cell Separation↗
PubMed1991

Procedures and computer program for deriving the Ferguson plot from electrophoresis in a single pore gradient gel: application to agarose gel and a polystyrene particle.

This study presents a computerized evaluation of pore gradient gel electrophoretograms to arrive at estimates for both the particle-free mobility and retardation coefficient, which is related to particle size. Agarose pore gradient gels ranging from 0.2 to 1.1% agarose were formed. Gel gradients were stabilized during their formation by a density gradient of 0-20% 5-(N-2,3-dihydroxypropylacetamido)- 2,4,6-triiodo-N,N'bis-(2,3-dihydroxypropyl)-isophthalamide (Nycodenz). Densitometry of gelled-in Bromophenol Blue showed that these pore gradients exhibited a linear central segment and were reproducible. Migration distances of polystyrene sulfate microspheres (36.5 nm radius) in agarose pore gradient gel electrophoresis were determined by time-lapse photography at several durations of electrophoresis. These migration distances were evaluated as a function of migration time as previously reported (D. Tietz, Adv. Electrophoresis 1988, 2, 109-169). Although this is not necessarily required, the mathematical approach used in this study assumed linearity of both the pore gradient and the Ferguson plot for reasons of simplicity. The data evaluation on the basis of the extended Ogston model is incorporated in a user-friendly program, GRADFIT, which is designed for personal computers (Macintosh). The results obtained are compared with (1) conventional electrophoresis using several gels of single concentration with and without Nycodenz, and (ii) a different mathematical approach for the analysis of gradient gels (Rodbard et al., Anal. Biochem. 1971, 40, 135-157). Moreover, a simple procedure for evaluating linear pore gradient gels using linear regression analysis is presented. It is concluded that the values of particle-free mobility and retardation coefficient derived from pore gradient gel electrophoresis using the different mathematical methods are statistically indistinguishable from each other. However, these values are different, albeit close, to those obtained from conventional Ferguson plots. One of the possible reasons for this relatively minor discrepancy is that the particle-free mobility changed slightly during electrophoresis, which has a different effect on electrophoresis in homogeneous gels (single time measurement) and pore gradient gels (multiple time measurements). The characterization of particles according to size and charge by pore gradient electrophoresis provides a significant operational simplification and sample economy compared to that requiring the use of several gel concentrations, although at the price of increased requirements of instrumentation.

Confidence Intervals↗
PubMed1992

[Investigation of algorithm for the calculation of probability of paternity likelihood using personal computer program, including the application to parentage testing in the decreased party].

Algorithm for the computerized calculation of probability of paternity likelihood was investigated. The probability is calculated by Essen-Möller's formula as W = X/(X+Y) = 1/(1 + Y/X). The X value is also given as X = Hl, m, n/Kl, m, where kl, m and Hl, m, n are the probabilities of mother-child and mother-child-father combinations, respectively. In this study, four functions as F(PQ) = [1-(P not equal to Q)] x p x q, Z(RS) = (1- (R = S)), K(PQ,RS) = 1/2([(R = P) + (R = Q)].s + [(S = P) + (S = Q)].r).F (PQ)/Z(RS) and H(PQ, RS, TU) = 1/4([(R = P) + (R = Q)] [(S = T) + (S = U)] + [(S = P) + (S = Q)] [(R = T) + (R = U)]) x F(PQ).F(TU)/Z(RS) were created, where PQ, RS and TU were the genotypes of mother, child and the alleged father, P, Q, R, S, T and U were their alleles, and p, q, r, s, t and u were the allele frequencies. The equality or inequality in parenthesis was the relation operator which gave -1 or 0 when the expression was true of false, respectively. Then, three formulae as Y = n sigma k = l F([TU]k), Kl, m = 1 sigma i = l m sigma j = l K ([PQ]i, [RS]j) and Hl, m, n = l sigma i = l m sigma j = l n sigma k = l H([PQ]i, [RS]j, [TU]k) were obtained, where [PQ]i, [RS]j and [TU]k were one of the mother's, one of the child's and one of the putative father's genotypes considered from their phenotypes, respectively. Using these formulae, the probability of paternity likelihood could be calculated in every case. These formulae were programmed in BASIC language using a personal computer. Algorithm for the calculation of the probability in the deceased party was also investigated.

Algorithms↗