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A computer program has been written which performs a stepwise selection of variables for logistic regression using maximum likelihood estimation. The selection procedure is based on likelihood ratio tests for the coefficients. These tests are used in a forward selection and a backward elimination at each step. The use of the program is illustrated by several examples.
The possibilities for reducing in Van de Geijn's computer program the original limitations for the size and the position within the field of shielding blocks are explored. New methods are presented which are based on experimental measurements as well as more theoretical approaches, without need for any change in the program itself. Two typical clinical examples are presented and the precision obtained critically investigated.
A computer program has been developed to aid in the brachytherapy of cancer of the cervix. Using a least-squares minimization algorithm, the program will optimize the source loading in intracavitary applicators so as to reproduce, as nearly as physical considerations allow, the dose distribution requested by the user. Applicator geometry and the relative positions of anatomical points of interest must be supplied to the program, as well as an inventory of available source strengths. Output from the computer includes the optimized source loading, time of application, and the resulting relative doses to the various user-selected points of interest.
Life table analysis has traditionally been the tool of choice in analyzing distribution of "survival" times when a parametric form for the survival curve could not be reasonably assumed. Chiang, in two papers [1,2] formalized the theory of life table analyses in a Markov chain framework and derived maximum likelihood estimates of the relevant parameters for the analyses. He also discussed how the techniques could be generalized to consider competing risks and follow-up studies. Although various computer programs exist for doing different types of life table analysis [3] to date, there has not been a generally available, well documented computer program to carry out multiple decrement analyses, either by Chiang's or any other method. This paper describes such a program developed by Research Triangle Institute. A user's manual is available at printing costs which supplements the contents of this paper with a discussion of the formula used in the program listing.
This article describes a computer program for analyzing bivariate flow karyotypes of human chromosomes stained with Hoechst 33258 (HO) and chromomycin A3 (CA). The karyotype first is divided into regions that contain chromosome peaks. The chromosomes that are associated with those areas are identified. The distributions in these areas then are fitted with mathematical functions of increasing complexity. The process starts by fitting a specified number of univariate Gauss functions to projections of the HO and CA distributions of each area. The final fit can include multiple bivariate Gauss functions, including a background function for debris subtraction. The results of one stage in the fitting process serve as seed values for the next, more complex step. Since the program autonomously estimates the starting values for the iterative fitting procedures, the fit results are insensitive to operator bias and the program will consistently converge to the same solutions. The resulting table of parameter values can be used to compare flow karyotypes to a reference data set.
A set of computer programs is described which has been developed for processing electron micrographs of biological structures. The programs provide facilities for efficient image storage, enhancement and display. Extensive programs are available for analysis of images of structures with translational, rotational and helical symmetry, and for performing 3-dimensional reconstruction. The considerations which went into the design of the system are listed. A description is provided of the means of control of the main program, which performs the majority of the image processing operations, and an example is given to illustrate its use. These programs are compared with other program systems also developed for micrograph image processing.
The computer program HOWBIG has been developed based on the reciprocal correlation of size to migration distance of DNA in high voltage gradient gel systems (Southern, 1979). For calculation the program automatically chooses three marker bands migrating closest to the calculated band, reducing the error down to approximately 0.5% or less (reciprocal method, local form of calculation). The big advantages of the completely menu-driven program are high accuracy, error detectability, speed and ease of data handling. Management of marker-DNA molecular weights, data and analyses as files included in the menu driven program speeds up every-day lab work.
An interactive computer program, SOLCOMP, is developed which calculates the volumes of the components that are to be added to obtain either a fresh solvent mixture or a new solvent system from the old one of required composition. The code is implemented in MicroSoft FORTRAN and GWBASIC which runs on any IBM compatible PC under MSDOS environment.
A high probability of identification of substances containing nitrogen or phosphorus in their molecules is obtained by the original gas chromatographic (GC) system. It enables the reliability of positive identification in 98.43% of cases compared with the modern GC where for the chromatographic library spectrum of 200 substances the probability of identification of unknown substances is only 28.13%. GC system is based on the parallel configuration of the two capillary columns of different polarities connected to the one-column injector and the one nitrogen-phosphorus detector as well as the original computer program developed on the qualitative-logistic approach to interpretation of chromatographic parameters using only one reference substance. The computer program can perform positive logistic identification also in the case when the unknown substance is in the closest chromatographic vicinity, with quite different reference substances on both capillary columns.
A computer program for the recording of data and calculation of results from leukapheresis and plateletpheresis procedures is described. It provides a printout of cell yields and other results for each procedure, as well as an updated list of donors and phereses. The data are kept on tape, accessible for periodic statistical analysis. While primarily set up for use with Haemonetics (intermittent-flow centrifugation) equipment, the program is adaptable for other systems.
A computer program, MOD (mixed oligo designer), which aids in planning site-directed mutagenesis experiments using highly substituted oligodeoxyribonucleotides (oligos), is described. The program calculates the relationship between the degree of oligo substitution and the mutation frequency, in order to achieve an optimal level of mutagenesis. The program can be used on a wide variety of computers and runs under a number of different operating systems.
A computer program for analysing the parameters of the acid-base status and respiratory gases has been designed. The program separates cases which are included into classical picture of certain respiratory, metabolic and mixed disorders. Out of a test series of 200 findings, 93% findings have been accurately interpreted. The program is written in BASIC, translated into machine code and occupies about 25 Kbyte computer memory. The main parts of the program use commands which do not favorize any version of BASIC increasing the program portability to other systems. The classification of respiratory gases and acid-base status was based on the already known facts.
The use of well characterized laboratory animals in biomedical research is of importance for quality securing and reproducibility of animal experiments. Therefore, breeders should not only have in mind the reproduction of their animal stocks, but they should also be interested to achieve an optimal resemblance of the animals in the main traits characterizing them as a model of human diseases. Specific software applications which helps the breeders in monitoring the main breeding parameters, selecting suitable breeding pairs and data processing are practically not available. This prompted us to develop a computer program for management of breeding and experimental data, which we called BB_RADABA. In this report we want to give a short survey on this computer program.
A simple computer program that calculates the kinetic parameters of enzyme reactions is described. Parameters are determined by nonlinear, least-squares regression using either Marquardt-Levenberg or Gauss-Newton algorithms to find the minimum sum of squares. Three types of enzyme reactions can be analyzed: single substrate reactions (Michaelis-Menten and sigmoidal kinetics), enzyme activation at a fixed substrate value or enzyme inhibition at a fixed substrate value. The user can monitor goodness of fit through nonparametric statistical tests (performed automatically by the computer) and through visual examination of the pattern of residuals. The program is unique in providing equations for activator and inhibition analysis as well as in enabling the user to fix some of the parameters before regression analysis. The simplicity of the program makes it extremely useful for quickly determining kinetic parameters during the data-gathering process.
PROPHAZ is a computer program created for the analysis of survival data using the general proportional hazards model. It was designed specifically for the situation in which the underlying hazard function may be estimated from the mortality experience of a large reference population, but may be used for other problems as well. Input for the program includes the variables of interest as well as the information necessary for estimating the hazard function (demographic and mortality data). Regression coefficients for the variables of interest are obtained iteratively using the Newton-Raphson method. Utilizing large sample asymptotic theory, x2 statistics are derived which may be used to test hypotheses of the form C beta = 0. Input format is completely flexible for the variables of interest as well as the mortality data.
A computer program is described for central axis dose calculations for 60Co and 6 MV photons. Fixed distance or isocentric calculations for regular or irregular fields can be performed. Corrections are made for wedges and blocking trays. Tissue-air ratios and percentage depth doses are calculated from scatter-air ratios eliminating the need for empirical formulas. Calculated tissue-air ratios and percentage depth doses for elongated fields agree to within 2 per cent with measured data, eliminating the need for tables of equivalent squares. Calculated values for irregular fields also agree to within 2 per cent with measured data.
A computer program has been developed to support the differential diagnosis of major rheumatic disease categories. Knowledge for the program was derived from the sensitivity and specificity of findings in a group of 1052 consecutive patients of a rheumatological outpatient clinic. Computer predictions based on two variations of Bayes's theorem were compared with 'gold standard' diagnoses in 570 test cases from the same clinic. The results demonstrate the feasibility of this approach, but also that refinements of both the method of calculation and the knowledge are required.
Computer programs for the analysis of data from techniques frequently used in nucleic acids research are described. In addition to calculating non-linear, least-squares solutions to equations describing these systems, the programs allow for data editing, normalization, plotting and storage, and are flexible and simple to use. Typical applications of the programs are described.