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A computer program for the statistical analysis of disease prevalence data from survival/sacrifice experiments.

This paper presents a computer program for analyzing disease prevalence data from animal survival experiments in which there may also be some serial sacrifice. The method has been described in Biometrics 35 (1979) 221-234. The user is interrogated about the details of particular models he wishes to fit. Then a generalized EM algorithm is used to compute maximum likelihood estimates of various quantities of interest concerning the effects of treatment, time and presence of other diseases on the prevalences and lethalities of specific diseases of interest.

Animals↗
PubMed1985

A simple, low-cost computer program for Scatchard plot analysis of binding data in steroid hormone receptor assays.

This paper presents a relatively simple computer program for Scatchard plot analysis of binding data in steroid hormone receptor determination. The program is written in BASIC and adapted to a low-cost desktop calculator. The program is designed to permit data input without demanding extensive technical knowledge of either computer systems or mathematical background of receptor binding assays.

Breast Neoplasms↗
PubMed1975

VECTAN II: A computer program for the spatial analysis of the vectorcardiogram.

This paper presents the operation of a digital computer program, VECTAN II, for the spatial analysis of the vectorcardiogram (VCG). The program incorporates a unique waveform recognition algorithm based on the spatial vector length which has been shown to perform better than previous algorithms. The waveform analysis employed by the program considers the vectorcardiogram as a three dimensional entity rather than as scalar or planar representations. VECTAN II is designed chiefly to measure and quantify the VCG response of normal subjects to a controlled stress by analyzing one VCG complex every five seconds throughout a long experiment. The program has been used to analyzeom the NASA Johnson Space Center Cardiovascular Laboratory, from the pre- and postflight medical examinations of the Apollo 15, 16 and 17 crewmen, and from onboard Skylab experiments.

Aerospace Medicine↗
PubMed1985

A computer program for an illness-death process with time-dependent covariates.

This paper presents a computer program for estimating transition probabilities between states in a stochastic model for an illness-death process which incorporates time-dependent covariates. Parameters are estimated by the method of maximum likelihood using the Newton-Raphson iterative procedure. The program provides the standard normal deviate statistics as well as the value of the maximum of the likelihood function which can be used on repeated applications to test hypotheses concerning coefficients associated with covariates. Although this program is demonstrated by using a model with two 'illness' states and two 'death' states, it is also suitable for analyzing data with models involving fewer states, such as the analysis of survival time with covariates assuming a proportional hazard model.

Computers↗
PubMed1977

MASSFORM: a computer program for the assignment of elemental compositions to high resolution mass spectral data.

This paper describes a computer program which calculates all possible empirical formulas for each accurately measured mass in a high resolution mass spectrum. The program, MASSFORM, incorporates a novel mechanism for classifying the empirical formulas generated according to their empirical formula. This mechanism makes it possible to use a set of general empirical formulas to aid in the analysis of complex mixtures in much less time than most other such programs. The program is being used as an important aid to environmental studies.

Chemical Phenomena↗
PubMed1995

A computer program for the study of synaptic transmission at the neuromuscular junction.

The study of synaptic biopotentials at the neuromuscular junction has proven to be an invaluable tool in understanding the pre- and post-synaptic mechanisms underlying chemical synaptic transmission and exploring the pathogenesis of neuromuscular disorders. Computer technology has become an important part of these experiments as it increases accuracy and automates the process, allowing more data to be collected and quantitatively analysed. This paper presents a computer program for IBM PC compatible computers capable of recording and analysing the spontaneously occurring miniature end-plate potentials (MEPPs), neurally evoked end-plate potentials (EPPs) and muscle fiber action potentials (APs). The program performs its basic analysis immediately following the sampling of biopotentials from a muscle fiber, thus providing the user with immediate feedback on the status of the experiment; 45 parameters of neuromuscular transmission are computed on-line and displayed on the monitor along with the signal-averaged waveforms. After a series of fibers has been recorded, the program will compile the data into summary tables. The program is designed to provide an experimenter with an easy-to-use, comprehensive method of performing electrophysiological measurements and analysis at the neuromuscular junction.

Action Potentials↗
PubMed1988

BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability.

We have written a computer program, BIGPROBE, which facilitates the design of long nucleic acid probes from the partial or complete amino acid sequence of a protein. BIGPROBE relies upon information on codon usage, intercodon dinucleotide frequency, and potential probe self-complementarity. We have examined the accuracy with which the program predicts coding sequences using sample human and rat genes and probe lengths of 30-60 nucleotides. Rat probe sequences selected by BIGPROBE using either codon usage or dinucleotide frequency data alone averaged 86-92% homology with the known exons of the corresponding gene sequences. Predictive accuracy with rat gene probes could be improved to 89-94%, depending upon probe length, by applying codon usage and dinucleotide frequency data in combination. Similar accuracy was achieved for human genes.

Amino Acid Sequence↗
PubMed1979

A computer program for testing average partial association in three-way contingency tables (PARCAT).

PARCAT is a computer program which implements alternative tests for average partial association in three-way contingency tables within the framework of the product multiple hypergeometric probability model. Primary attention is directed at the relationship between two of the variables, controlling for the effects of a covariable. This approach is essentially a multivariate extension of the Cochran/Mantel-Haenszel test to sets of (s x r) tables. A set of scores such as uniform, ridits, or probits can be assigned to categories which are ordinally scaled. In particular, if ridit scores with midranks assigned for ties are utilized, this procedure is equivalent to a partial Kruskal-Wallis test when one variable is ordinally scaled, and is equivalent to a partial Spearman rank correlation test when both variables are ordinally scaled.

Age Factors↗
PubMed1980

Computer programs for the radioactive microsphere technique. Determination of regional blood flows and other haemodynamic variables in different experimental circumstances.

Computer programs in FORTRAN IV have been designed to calculate regional blood flow values from injections of gamma radiation-emitting radioactive microspheres. The first program PRSO constitutes a file containing the names of organs, organ groups and systemic haemodynamic variables and data about the isotopes in use. The second program PRSI transfers the data of the particular experiment concerning protocol, systemic haemodynamic variables, organ weights, number of vials belonging to each organ and the radioactivity from each vial into a data file that is subsequently analyzed by the third program PRSII. One of 5 data conditions which later directs calculations in PRSII is determined by PRSI. PRSII deducts background radioactivity, decomposes the spectrum from the mixture of up to 6 nuclides using the "stripping' method, and corrects for isotope decay during the counting period. Depending upon the data condition, PRSII calculates one or more of the following variables: (i) cardiac output (CO); (ii) the distribution of CO; (iii) regional blood flow values and tissue vascular resistances; (iv) the distribution of blood flow within an arterial bed; (v) arteriovenous anastomotic blood flow; (vi) some specified systemic haemodynamic variables; and (vii) blood flow ratios. The systemic and regional haemodynamic data belonging to experiments are saved for later statistical analyses (e.g., mean, standard error of the variables, changes from the base line, comparison between two groups of experiments) by other programs. PRSO, PRSI and PRSII can be operated by investigators with little or no special training in computer use.

Animals↗
PubMed1991

A computer program for the deconvolution of mass spectral peak abundance data from experiments using stable isotopes.

A computer program is described for deconvoluting the overlap which is often found in mass spectral peak abundance data from stable isotope experiments. Peak intensity data from calibration standards are corrected using parameters calculated from the analysis of separate external standard solutions of analytes and internal standard. If the calibration data are satisfactory, the same parameters and the slope and intercept values from the least squares analysis of the calibration data are used to correct and quantitate the mass spectral peak intensity data from the quality assurance and experimental samples. Reports and graphs appropriate to the process are produced. Applications are given for the analysis of plasma samples from stable isotope experiments with carprofen, cifenline, and midazolam.

Carbazoles↗
PubMed2005

A computer program to estimate the parameters of covariate dependent higher order Markov model.

This paper presents a computer program developed in S-plus to estimate the parameters of covariate dependent higher order Markov Chain and related tests. The program can be applied for two states Markov Chain with any order and any number of covariates depending on the PC capabilities. The program provides the maximum likelihood estimates of the parameters, together with their estimated standard error, t-value and significance level. It also produces the test results for likelihood ratio and model chi-square. To illustrate the program we have used a longitudinal data set on maternal morbidity of rural women in Bangladesh. The occurrences of haemorrhage, convulsion, or fits at different follow-ups were used as outcome variable. Economic status, wanted pregnancy, ages at marriage, and education of women were used as covariates.

Algorithms↗
PubMed1998

Development of a computer program, MDGP, for population pharmacokinetic analysis written using ANSI C language on wide platforms.

MDGP, a computer program for population pharmacokinetics, has been developed. This program is based on maximum likelihood estimation with poly-dimensional normal distribution errors, and variable metric methods, direction set methods, conjugate gradient methods and the polytope method are provided as minimizations of objective function. The source codes of MDGP are described using ANSI C language. MDGP is able to run on wide platforms equipped with an ANSI C compiler. Users can use algebraic, ordinary differential and Laplace-transformed equations as descriptions of a pharmacokinetic model. Partial differential equations for each model parameter are not needed. Comparison of the estimated parameters, the iteration counts until convergence and objective function value, using MDGP and NONMEM, revealed that the calculation performance of the two programs are comparable. The MDGP is thought to be useful for the analysis of various pharmacokinetic models, including population pharmacokinetic analysis.

Humans↗
PubMed2005

A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries.

A computer program for the generation and analysis of in silico random point mutagenesis libraries is described. The program operates by mutagenizing an input nucleic acid sequence according to mutation parameters specified by the user for each sequence position and type of point mutation. The program can mimic almost any type of random mutagenesis library, including those produced via error-prone PCR (ep-PCR), mutator Escherichia coli strains, chemical mutagenesis, and doped or random oligonucleotide synthesis. The program analyzes the generated nucleic acid sequences and/or the associated protein library to produce several estimates of library diversity (number of unique sequences, point mutations, and single point mutants) and the rate of saturation of these diversities during experimental screening or selection of clones. This information allows one to select the optimal screen size for a given mutagenesis library, necessary to efficiently obtain a certain coverage of the sequence-space. The program also reports the abundance of each specific protein mutation at each sequence position, which is useful as a measure of the level and type of mutation bias in the library. Alternatively, one can use the program to evaluate the relative merits of preexisting libraries, or to examine various hypothetical mutation schemes to determine the optimal method for creating a library that serves the screen/selection of interest. Simulated libraries of at least 10(9) sequences are accessible by the numerical algorithm with currently available personal computers; an analytical algorithm is also available which can rapidly calculate a subset of the numerical statistics in libraries of arbitrarily large size. A multi-type double-strand stochastic model of ep-PCR is developed in an appendix to demonstrate the applicability of the algorithm to amplifying mutagenesis procedures. Estimators of DNA polymerase mutation-type-specific error rates are derived using the model. Analyses of an alpha-synuclein ep-PCR library and NNS synthetic oligonucleotide libraries are given as examples.

Algorithms↗
PubMed1985

SEQ-ED: an interactive computer program for editing, analysis and storage of long DNA sequences.

The rapidly growing body of sequenced DNA demands efficient computer programs for its analysis and storage. The program described in this paper, SEQ-ED, has been designed to handle a large number of DNA sequences up to 200 kilobases [kb] long stored in a sequence library. In order to minimize the required storage space, the sequences are stored in a compressed format using three binary digits per base. In the development of this program, special care has been given to make it easy to use for molecular biologists without any previous computer experience.

Algorithms↗
PubMed1995

Development of a computer program for teaching periodontal diagnosis based on clinical epidemiological principles.

Multimedia teaching tools in dental education are still rare. This paper describes the development of an inexpensive yet powerful computer program for instruction in the principles of clinical epidemiology. The application was developed in the context of periodontal diagnostic methodologies at the third year D.D.S. level. Principles of probabilistic thinking are invoked as the student is guided from the application of raw research data to the derivation of likelihood ratios and how they affect clinical decision making. A questionnaire was used to evaluate student satisfaction with the program and the responses indicated good acceptance of the concepts presented in the program and an interest in further computer-aided instruction.

Computer-Assisted Instruction↗
PubMed1979

A computer program for the analysis of dental models.

This paper presents the details and logic of a Fortran computer program which carries out routine clinical analysis of dental models resulting from impressions of the teeth and related structures, which are subsequently cast in plaster of Paris. The program is primarily intended for use by the orthodontist who is engaged in research or clinical practice, and is useful in studies related to changes in the dentition as a result of orthodontic treatment.

Computers↗
PubMed1984

A computer program for estimating thresholds by means of Wetherill's Up-Down Transformed Response Rule (UDTR).

A Fortran IV computer program is presented which allows for automatic estimation of thresholds on an S-shaped psychometric curve by means of Wetherill's Up-Down Transformed Response Rule (UDTR). The efficiency and asymptotic properties of these rules are discussed and illustrated. The main program is in the form of a keyboard portable tutorial which calls the main decision-making subroutine. The subroutine can be detached from the tutorial. Only a single call with seven parameters is required to reach the subroutine. The program is particularly useful in forced-choice procedures.

Auditory Threshold↗