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ORDMKV: a computer program fitting proportional odds model for multi-state Markov process.

ORDMKV is a computer program designed to fit a multi-state discrete-time Markov model for k-stages disease processes having an ordinal structure. The model consists of k transient states representing the increasing severity of the disease process, and the final state can be optionally chosen to be an absorbing state in cases such as death. The ordinal structure of the stages of the disease is modelled by using ordinal response models. Each row of the one-step transition probability matrix is modelled using a proportional odds model based on the cumulative transition probabilities. By using these ordinal response models, the number of parameters used to model the disease process can be reduced significantly not only with respect to a general discrete-time model, but also compared with a parsimonuos continuous-time model. A restricted model can be fitted by assuming that the effect of the covariables in the cumulative probability has common regression coefficients in all stages of the disease process. This assumption, if it holds, reduces the number of regression coefficients associated with each covariate to only one. The regression coefficients of this model are estimated via the method of maximum likelihood, using a quasi-Newton optimization algorithm. When the last state is considered as an absorbing state, it is possible to compute survival curves from the transient states of the process. The program was written in standard FORTRAN 77 and is illustrated using a four-state model to determine factors influencing diabetic retinopathy in young subjects with insulin-dependent diabetes mellitus.

Diabetes Mellitus, Type 1↗

CombiTool--a new computer program for analyzing combination experiments with biologically active agents.

CombiTool is a new computer program for the analysis of combination effects of biologically active agents. It performs model calculations and an analysis of experimental combination effects for two or three agents according to both the Bliss independence and the Loewe additivity criteria. Zero interaction response surfaces are calculated from single-agent dose-response relations and compared to experimental combination data. The calculation of response surfaces for Loewe additivity is based on a new approach which combines the implicit definition equation in terms of doses alone with single-agent dose-response relations. The simultaneous analysis of experimental data according to both Loewe additivity and Bliss independence within one program can hopefully contribute to a better understanding of the meaning and limits of the two criteria. CombiTool has a built-in graphics facility which allows the direct visualization of the response surfaces or the corresponding contour plots and the experimental data.

Algorithms↗

A computer program for many-beam image simulation of amplitude-contrast images.

A computer program for the simulation of amplitude-contrast electron micrographs is described. The program is based on the n-beam dynamical theory of diffraction contrast as described by Howie and Whelan (see Howie, A., and Whelan, M.J. (1961) Proc. R. Soc. Lond. [Biol]). The displacement fields associated with crystal lattice defects are calculated using linear anisotropic elasticity. The program can be used to simulate images of crystals containing line or planar defects or combinations of these defects. The line defects can be oriented freely within the foil, and are not restricted to being mutually parallel, but must be straight. Different techniques available for solving the diffraction problem, with or without the column approximation, are discussed.

Crystallization↗

OPT: a package of computer programs for parameter optimisation in clinical pharmacokinetics.

1 OPT is a series of computer programs designed to assist dose optimisation for individual patients. It is based on Bayesian Statistical Theory and Maximum Likelihood Estimation. 2 OPT uses prior information on the distribution of population pharmacokinetic parameters and plasma drug concentration measurements to obtain the "most likely' set of parameters for the individual. 3 Complex dosage regimes and non-steady state conditions can be handled. 4 OPT is designed for use in a Clinical Pharmacokinetics Laboratory where informed interpretation of results is essential. 5 The drugs for which the system is currently available include theophylline, digoxin, lignocaine, disopyramide, gentamicin and phenytoin (steady state data only).

Administration, Oral↗

QC Validator 2.0: a computer program for automatic selection of statistical QC procedures for applications in healthcare laboratories.

A computer program has been developed to help healthcare laboratories select statistical control rules and numbers of control measurements that will assure the quality required by clinical decision interval criteria or analytical total error criteria. The program (QC Validator 2.0 (QC Validator and OPSpecs are registered trademarks of Westgard Quality Corporation, which has applied for a patent for this automatic QC selection process. Windows is a registered trademark of Microsoft Corporation)) runs on IBM compatible personal computers operating under Windows. The user enters information about the method imprecision, inaccuracy, and expected frequency of errors, defines the quality required in terms of a medically important change (clinical decision interval) or an analytical allowable total error, then initiates automatic selection by indicating the number of control materials that are to be analyzed (1, 2, or 3). The program returns with a chart of operating specifications (OPSpecs chart) that displays the selected control rules and numbers of control measurements. The automatic QC selection process is based on user editable criteria for the types of control rules that can be implemented by the laboratory, total numbers of control measurements that are practical, maximum levels of false rejections that can be tolerated and minimum levels of error detection that are acceptable for detection of medically important systematic or random errors.

Biometry↗

[A computer program for the support of the treatment-diagnosis process for patients with benign prostatic hyperplasia].

The computer program "Prostate" (Windows, 1.0 version) is designed to assist the urologist in: objective assessment of the lower urinary tract in benign prostatic hyperplasia (BPH), accumulation and storage of information on the patients (data file), comparison (text, graphics) with previous data to control the course of the disease, treatment efficacy, to refer to international recommendations and recent advances in the treatment of both BPH and its complications. The status of the lower urinary tract is to be described basing on the IPSS and QOL tables, PSA findings, rhythm of spontaneous uresis, uroflowmetry, residual urine, prostate size, laboratory and microbiological urinalysis. The program "Prostate" is a new step in medical recording and efficacy of BPH treatment assessment in urology.

Diagnosis, Computer-Assisted↗

Computer program for evaluating the thermal environment.

The calculations required to evaluate the thermal environment can be tedious and time consuming. To reduce this effort to a minimum, a computer program is presented that requires only five basic measurements to calculate and print out a complete evaluation of the thermal environment at a specific location. These are the dry bulb, natural wet bulb, psychrometric wet bulb and black globe temperatures, and the air velocity. Any reference to charts, tables and nomographs is unnecessary, since all other quantities are contained within, or computed by, the program.

Computers↗

A computer program to aid the sequencing of peptides in collision-activated decomposition experiments.

A computer program named MSEQ, based on graph theory has been implemented to aid the sequencing of peptides from collision-activated decomposition (CAD) spectra. Input data required by this program are: the molecular weight of the peptide, the list of the masses of the daughter ions and the masses of the N- and C-terminal groups. The output comprises a list of the most likely sequences with their respective scores and the assignments of the daughter ions. A set of probabilities for each fragment ion was computed from hundreds of CAD spectra obtained from our mass spectrometer. To date many peptides have been sequenced in our laboratory with the help of this program, and in most of them the real sequence ranks among the five top sequences. The program is able to differentiate isobaric amino acids such as leucine and isoleucine when the side-chain fragmentation appears in the spectrum. A criterion is used to discard those sequences that match the spectrum poorly from the earliest steps. The program is fast and consumes no memory.

Algorithms↗

MKVPCI: a computer program for Markov models with piecewise constant intensities and covariates.

We present a computer program for fitting Markov models with piecewise constant intensities and for estimating the effect of covariates on transition intensities. The basic idea of the proposed approach is to introduce artificial time-dependent covariates in the data to represent the time dependence of the transition intensities, and to use a modified time-homogeneous Markov model to estimate the baseline transition intensities and the regression coefficients. The program provides the maximum likelihood estimates of the parameters together with their estimated standard errors, and allows testing various statistical hypotheses. To illustrate the use of the program, we present a three-state model for analyzing the smoking habits of school children.

Child↗

RTS, a computer program for the experimental set-up and interpretation of ruggedness tests.

A computer program is described for the experimental set-up and interpretation of ruggedness tests. The implemented strategy was based on a number of case studies and contains both recommended designs and minimal designs. The minimal designs reduce the number of experiments, but they cannot be statistically interpreted based on the interaction or dummy factor effects. The use of randomization tests as an alternative statistical interpretation method for the significance of the effects was examined. Some of the minimal designs are expandable to designs with characteristics similar to those of the recommended designs. The program is designed to facilitate the selection of the designs and the interpretation of the results and to prevent or detect problems such as drifting of responses.

Chemistry Techniques, Analytical↗

A computer program for the algebraic determination of control coefficients in Metabolic Control Analysis.

A computer program (MetaCon) is described for the evaluation of flux control, concentration control and branch-point distribution control coefficients of a metabolic pathway. Requiring only the reaction scheme as input, the program produces algebraic expressions for the control coefficients in terms of elasticity coefficients, metabolite concentrations and pathway fluxes. Any of these variables can be substituted by numeric or simple algebraic expressions; the expressions will then be automatically rearranged in terms of the remaining unknown variables. When all variables have been substituted, numeric values will be obtained for the control coefficients. The program is a computerized implementation of the matrix method for the determination of control coefficients. The features of MetaCon are compared with those of other programs available to workers in Metabolic Control Analysis. Potential benefits of, and methods of using, MetaCon are discussed. The mathematical background and validity of the matrix method rules are discussed, and the algorithm used by MetaCon is described. The matrix method is shown to be a specific case of a previously described general formalism for calculating control coefficients.

Metabolism↗

[A computer program that draws pedigree charts for inbred strains of animals].

We produced a computer program that draws pedigree charts for inbred strains of animals such as mice or rats. This program is composed of four subprograms, which are (1) inputting the data, (2) drawing pedigree charts, (3) listing the data which have been input, and (4) backup of the system and the data. Pedigree charts and lists of data can be displayed on a TV screen and printed out on the papers. Using this program, we drew the pedigree charts of the inbred strains of rats which we are maintaining by brother-sister inbreeding in our institute and found that there were three sublines in one of the strains, WKAH/Hkm, because of unsuitable maintenance. This program is very convenient to draw the pedigree charts and useful for checking the maintenance of inbred strains or the strains of animal models of human diseases.

Animals↗

A Macintosh computer program for designing DNA sequences that code for specific peptides and proteins.

A computer program (PINCERS) is described for use in the design of synthetic genes and mixed-probe DNA sequences. A protein sequence is reverse translated with generation of synonymous codons at each position producing a degenerate sequence. In order to locate potential restriction enzyme sites, the degenerate sequence is searched with a library of restriction enzymes for sites that utilize any combination of synonymous codons. These sites are indicated in a map so that they may be incorporated into the synthetic gene sequence. The program allows the user to select the appropriate codon usage table for the organism of interest and then to set a threshold usage frequency below which codons are not generated. PINCERS may also be used to assist in planning the synthesis of mixed-probe DNA sequences for cross-hybridization experiments. It can identify regions of specified length with the protein sequence that have the least overall degeneracy, thereby minimizing the number of probes to be synthesized and, therefore, maximizing the concentration of a given probe sequence.

DNA↗

Accuracy of computerized electrocardiographic identification of left ventricular hypertrophy as determined by echocardiographic measurements of left ventricular mass: evaluation of a widely used computer program.

The Hewlett-Packard 1000 electrocardiographic management system employs a user-interactive computer with revisable software. The diagnostic accuracy of this system in predicting left ventricular hypertrophy has been evaluated by comparing computer-predicted with anatomic left ventricular hypertrophy. The latter was defined as a left ventricular mass greater than 247 g as determined by M-mode echocardiography within 1 week of the computerized electrocardiogram. In this study, the Hewlett-Packard system was evaluated in 134 consecutive patients having anatomic left ventricular hypertrophy and 157 similarly studied patients with a normal left ventricular mass. By means of various combinations of voltage criteria, ST-T wave changes, abnormal QRS duration or ventricular activation time, left atrial enlargement and left axis deviation, the computer correctly identified 43 of 134 patients with left ventricular hypertrophy (sensitivity 32%); left ventricular hypertrophy was suggested or identified in an additional 18 patients with a normal left ventricular mass (specificity 89%). Graded probability statements (that is, the "strength" of the left ventricular hypertrophy diagnosis) increased with ventricular mass not only in patients with anatomic left ventricular hypertrophy but also in the patients with a "false positive" computerized electrocardiogram. Overall diagnostic accuracy was improved only in men by adjusting the definition of left ventricular hypertrophy for sex (at least 300 g for men and 220 g for women). Diagnostic accuracy was significantly better in patients 65 years of age and younger than in older patients (p = 0.007). It is concluded that the overall performance of this computer program (version ECLSB6) requires modification to improve its accuracy in identifying left ventricular hypertrophy.

Age Factors↗

A computer program for comparing survival experience of two groups after adjustment for relevant covariates.

A computer program is described which evaluates the difference in survival between two groups of patients based on the methods of Mantel [1] and Hankey and Myers [3]. Life table analysis is based on the stratification of prognostic variables. In addition, an adjusted survival curve is computed for one group of patients relative to the other group based on differences in the distribution of these variables. Plots of cumulative survival curves are optionally provided.

Computers↗

A computer program for on-line measurement, storage, analysis and retrieval of urodynamic data.

A computer program is presented which allows for direct connection of a minicomputer to a urodynamic set-up. The program stores measured pressure and flow data in a random access disc file with minimal intervention of the urodynamicist, and enables the direct application of a number of methods of analysis to the data. The program is modular, and other analysis methods are easily added. Results of analyses are stored in the same disc file, and both results and measured data can be quickly and easily retrieved. The program is written in FORTRAN; hardware-dependent functions (analog input, graphics display, and random access disc storage) are implemented in subroutines (partly assembler) which can easily be replaced.

Computers↗

A pocket computer program for common calculations in clinical pediatrics.

This paper describes the use of a short computer program designed for use in a pediatric hospital ward. The program performs metric conversions, obviates the need for nomograms for body surface area and base excess determinations, and rapidly and accurately computes parenteral fluid mixtures, medication dosages, creatinine clearance, erythrocyte sedimentation rate corrections, and serum osmolality.

Computers↗