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PubMed1989

BUMP: a FORTRAN program for identifying dose-response curves subject to downturns.

BUMP is a FORTRAN implementation of a modified Jonckheere-Terpstra test, proposed by Simpson and Margolin, to test nonparametrically for a dose-response curve when a downturn is possible at high doses. The Jonckheere-Terpstra statistic is commonly used to test for increasing or decreasing trends in dose-response relationships. In many experimental settings, however, a test agent has more than one effect, and a "bump"-shaped dose-response can occur. For instance, increasing the concentration of a certain nutrient on a petri dish may increase the growth rate at low doses yet decrease the growth rate at high doses because of toxicity. The modified test allows one to assess the significance of the initial increase in the dose-response curve and yet to minimize the effect on the conclusions of any downturn at higher doses. A complete system which operates directly on SYSTAT/MYSTAT files is available for the IBM-PC and compatibles; it includes a utility which converts ASCII data files to the SYSTAT/MYSTAT format. The FORTRAN 77 source code is available for those who would like to run BUMP on other machines.

Data Interpretation, Statistical↗

PubMed1989

Computer model of cardiac repolarization processes and of the recovery sequence.

A computer model simulating both excitation and recovery processes within a block of heart muscle tissue has been developed and implemented on different IBM PC AT compatible computers. The model incorporates blocks of tissue consisting of several thousand elements and introduces phenomena which are completely or partly omitted in other existing cardiac electrophysiology models. These phenomena include the electric anisotropy of the tissue, different durations of repolarization in different layers of tissue, and the different shapes of action potential which correspond to cells excited when not fully recovered. Implementation of the model on small personal computers requires the use of a special data structure management and an effective algorithmic background. The program of the model is written in PASCAL and uses dynamically allocated data structures and the asynchronous simulation technique of event planing. These techniques are described in detail. The model has been used in various experiments. Results of simulation studies are presented in the form of modeled three-lead electrocardiographic records. The experimental series which are described include basic patterns of regular activation sequences, modeling of premature beats, simulation of effects due to fast pacing, models of ischemia and infarction, simulation of reentry mechanisms with a special reference to the initiation of ventricular fibrillation, and models of late potentials. The future development of more realistic models of the cardiac recovery process is also discussed.

Action Potentials↗

PubMed1989

PROPOV-K: a FORTRAN program for computing a kappa coefficient using a proportional overlap procedure.

The computer program PROPOV-K allows the computation of an unweighted kappa coefficient for expressing interrater agreement in the general case in which multiple raters (not necessarily fixed in number) formulate a variable number of multiple diagnoses for each subject. PROPOV-K assesses agreement among lists of multiple diagnoses composed of nonordered categories. PROPOV-K calculates a kappa coefficient on the basis of estimating proportion of agreement between two diagnostic formulations as the ratio of the number of agreements between specific categories over the number of different specific categories mentioned in the two diagnostic lists. When multiple raters formulate a variable number of multiple diagnoses for each subject, the use of a kappa coefficient has been limited to researchers since there are no generally available computer programs. The purpose of this paper is to present a FORTRAN computer program allowing the computation of a kappa coefficient for the case mentioned above and to illustrate its use with examples respectively involving multiple psychiatric and multiple physical diagnoses.

Algorithms↗

PubMed1989

SESAM-DIABETE, an expert system for insulin-requiring diabetic patient education.

SESAM-DIABETE is an interactive educational expert system that provides personalized advice and therapeutic recommendations for insulin-requiring diabetic patients. Because of its sophisticated explanation facilities, this system is intended to complete the more traditional educational tools for diabetic patients. It has been developed using an original essential expert system, namely SESAM, itself implemented in an upper-layer of Lisp, MBX. Its control structure uses a top-down strategy to solve a problem; i.e., it decomposes the current problem into subproblems easier to solve, this method being recursively applied to each subproblem. All information about patients is kept in a Patient Medical Record, which allows their follow-up. This system is currently available from their home for selected patients through the French telematic network TELETEL and is under clinical evaluation.

Computer Communication Networks↗

PubMed1989

A computer program for analyses of vital statistics-based occupational mortality data.

Routinely collected vital statistics mortality data (death certificate data) on occupation and industry are useful for (1) generating hypotheses about potential occupational hazards and (2) identifying occupational mortality differentials possibly associated with socioeconomic and life-style factors. This paper presents a Fortran program that analyzes occupational mortality using vital statistics and census data. The user can form any desired grouping of age, race, occupation (or industry), and cause of death codes for analysis. The program also allows stratification on social class or other user-defined correlates of occupation such as smoking behavior. Furthermore, program output can be used for Poisson regression analysis of mortality rates.

California↗

PubMed1990

A program to estimate insulin sensitivity and pancreatic responsivity from an IVGTT using the minimal modeling technique.

A user-friendly program coded in PASCAL for the IBM PC has been developed to determine the etiology of impaired glucose tolerance using an intravenous glucose tolerance test (IVGTT). It makes use of the "minimal modeling technique," a method that has been shown to be adequate for the quantitative determination of insulin sensitivity and insulin resistance. Two models are used, the minimal model of glucose disappearance and the minimal model of insulin kinetics. The first model is described by two nonlinear ordinary differential equations (ODEs) which are solved numerically, and which yield the insulin sensitivity index SI. The second model is described by an ODE for which an explicit solution was obtained, and which yields the pancreatic responsivity parameters phi 1 and phi 2. The product SI.phi 2 can be used to segregate subjects into "good" and "low" tolerance types. The program provides best-fit plots along with numerical values of the parameters and their uncertainties, and requires little intervention from the user. The fact that it requires a noninvasive IVGTT as input and that it has been written for the ubiquitous IBM PC are added advantages.

Glucose Tolerance Test↗

PubMed1990

A computer program for estimating imprecision characteristics of immunoassays.

A reliable numerical algorithm is described, together with a computer program written in FORTRAN IV and FORTRAN 77, for estimating a three-parameter variance function by approximate conditional likelihood. The function is sufficiently flexible to provide for a several thousand-fold relative change in variance and appears to be a good model for the severely heteroscedastic results obtained from immunoassays. The computer program is primarily intended for summarizing imprecision characteristics of immunoassays in the form of imprecision profiles, but the estimated variance functions have additional application whenever further parametric analysis of immunoassay results is undertaken (e.g., as a weighting function when immunoassay results are used in a least-squares regression analysis). The flexibility of the function implies useful application in any area where heteroscedasticity is particularly severe.

Algorithms↗

PubMed1990

A Prolog knowledge base for drug interactions.

This article describes a Prolog knowledge base for drug interactions. The knowledge base combines information from two databases: one of drug interactions and the second of drug chemical names and structures. Researchers can interrogate this knowledge base to answer questions about relationships between interacting drugs and their chemical components.

Artificial Intelligence↗

PubMed1990

Interpreting chromosomal abnormalities using Prolog.

This paper describes an expert system for interpreting the standard notation used to represent human chromosomal abnormalities, namely, the International System for Human Cytogenetic Nomenclature. Written in Prolog, this program is very powerful, easy to maintain, and portable. The system can be used as a front end to any database that employs cytogenetic notation, such as a patient registry.

Chromosome Aberrations↗

PubMed1990

A method for conforming the pH dependence of the michaelis parameters of nonallosteric enzymes to four kinetic schemes.

A nonlinear regression program for the analysis of the effect of pH on enzyme activity has been developed for the IBM micro range and compatible machines. The program conforms the V and Km pH profiles to one of four commonly occurring kinetic schemes. By using multiple linear regression the program computes initial estimates for the nonlinear search which are thus not required from the user. Two nonlinear optimization methods are included in order to effectively handle the nonnegativity constraints on the parameters. The program is user-friendly and provides plots of the fit and residual plots to help the user decide on the goodness of fit obtained. The program was coded in Turbo Pascal version 4.0 and runs on IBM micros or close compatibles with four types of graphics cards.

Algorithms↗

PubMed1990

Determination of first and second derivatives of progress curves in the case of unknown experimental error.

The first and second derivatives of progress curves are obtained from the cubic spline function. The new approach is based on a development of the splining quality test which was used for estimating the precision of the splining. The proposed method is used on a computer with a FORTRAN 77 program. The method may also be applied for an approximate estimation of experimental error.

Computer Simulation↗

PubMed1991

Computations of adjusted rates and lifetime risks from occupational cohort data: a program package using FORTRAN and GLIM.

A program package using FORTRAN and GLIM is presented to compute lifetime risks of dying from a particular cause of death for a worker subjected to specific risk exposures using death rates adjusted for selected covariates (risk factors). Calculations of the exposure index and adjusted rates depend on several commonly used procedures. Tests of homogeneity and trend for adjusted rates are provided. Lifetime risks are calculated in two different ways: adjusting or ignoring competing causes of death.

Cohort Studies↗

PubMed1991

Finite dose percutaneous drug absorption: a BASIC program for the solution of the diffusion equation.

A BASIC program to obtain the solution for the diffusion equation describing the finite dose percutaneous absorption pharmacokinetics is shown. Drug amount in the solution matrix, Av, that in the skin which is regarded as a simple diffusion membrane. As, and the drug flux from the skin which is provided by the local circulation per unit area, J, and the blood drug concentration. C, expressed as functions of time are obtained using Fourier series. Usually, a small number (less than 10) of series is enough to obtain the accurate values for Av, As, J, and C. It is also shown that the solution of the diffusion equation reported previously for the specific case where both the diffusion coefficient of a drug through the vehicle and skin-capillary clearance are very large is expressed as a limit.

Administration, Cutaneous↗

PubMed1991

Heuristic determination of quantitative data for knowledge acquisition in medicine.

Knowledge acquisition for medical knowledge bases can be aided by programs that suggest possible values for portions of the data. The paper presents an experiment which was used in designing a heuristic to help the process of knowledge acquisition. The heuristic helps to determine numerical data from stylized literature excerpts in the context of knowledge acquisition for the QMR medical knowledge base. Quantitative suggestions from the heuristics are shown to agree substantially with the data incorporated in the final version of the knowledge base. The experiment shows the potential of knowledge base specific heuristics in simplifying the task of knowledge base creation.

Artificial Intelligence↗

PubMed1992

Validation of the medical expert system PNEUMON-IA.

The present study validates the expert system PNEUMON-IA. The aim of PNEUMON-IA is assessing the etiology of community-acquired pneumonias from clinical, radiological, and laboratory data obtained at the onset of the disease. Validation was performed using data from medical records of 76 patients with proven clinical diagnosis of pneumonia. The etiological diagnoses provided by PNEUMON-IA were compared to those established by five specialists unrelated to the development of the expert system. For each etiological possibility, both PNEUMON-IA and the experts provided a causal possibility, expressed as a linguistic label (i.e., "almost impossible"). Linguistic labels were then converted to numeric values. In the majority of cases, an etiological diagnosis was unavailable to be used as a gold standard. To overcome this limitation, distances between arrays of etiological possibilities given by specialists and by PNEUMON-IA were considered as an agreement measure between diagnoses. Cluster analysis based on those distances was used to classify PNEUMON-IA among experts. Results showed the same differences between specialists and PNEUMON-IA as among the specialists themselves. The method used to validate PNEUMON-IA could prove useful to assess the performance of expert systems in fields where no gold standard is available.

Adolescent↗

PubMed1992

LMSMVE: a program for least median of squares regression and robust distances.

The program LMSMVE performs robust regression analysis by using the method of the least median of squares. It also computes robust distances to locate leverage points, that is, outliers with respect to the set of independent variables. LMSMVE constructs plots of least median of squares residuals against robust distances. Both methods can tolerate up to half the data being outliers before they fail to give results that describe the bulk of the data. A complete system that operates directly on SYSTAT files is available for the IBM PC and compatibles; it includes a utility that converts ASCII files to SYSTAT format.

Animals↗

PubMed1987

A subroutine for rounding of numbers. Program in BASIC and for programmable calculators.

The present programs were developed to compensate for the poor precision of some microcomputer-BASICs, and to avoid printing of the non-significant figures of a numerical result. The program will round any number to a user defined number of significant digits. The subroutine is well suited for statistical programs. It enables the programmer to control the precision and format of numerical output. The program is given in two versions, one in BASIC and one for the programmable calculator TI-59.

Algorithms↗

PubMed1987

A microcomputer program for fitting enzyme inhibition rate equations.

This paper presents a computer program written in BASIC for fitting different enzyme inhibition kinetic models. The program, based on a nonlinear least-squares regression, can be run on any microcomputer with the CP/M operating system. Weighting of observed initial velocities is decided by the user by assessing constant variance, proportional variance or by incorporation of the variances calculated by a subroutine. The program also uses robust regression by bisquare weighting. All questions concerning data input, type of rate function, type of weight and the use of bisquare regression appear on the video display unit.

Enzyme Inhibitors↗