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At least 595 records · Page 33Linked to original sources
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↗
PubMed1996

A simple flexible program for the computational analysis of amino acyl residue distribution in proteins: application to the distribution of aromatic versus aliphatic hydrophobic amino acids in transmembrane alpha-helical spanners of integral membrane transport proteins.

We describe a simple, flexible program (AAD) with a primary function of depicting the distribution of aliphatic and aromatic amino acid residues along the linear aligned sequence of a family of homologous proteins and a secondary function of depicting the distribution of all amino acids along the same linear sequence. The program is used to examine the distribution of aromatic versus aliphatic residues in representative well-characterized families of polytopic membrane proteins. Many but not all such protein families are shown to exhibit a predominance of aliphatic residues in the central regions of their transmembrane spanners but a predominance of aromatic residues at the peripheries of their spanners. We propose that this distribution stabilizes the hydrophobic-hydrophilic interface and renders the centers of these integral membrane proteins more fluid than their peripheries.

Amino Acids↗
PubMed1998

Interaction effects of client and treatment program characteristics on retention: an exploratory analysis using hierarchical linear models.

This paper applied a hierarchical linear modeling approach to explore the interaction effects of treatment program and client characteristics on client retention in treatment for drug users. Program characteristics included services provision, funding sources, and staff-client gender congruence, and client characteristics included gender, age at admission, and drug use level prior to admission. The same model was applied separately to three modalities: residential, methadone maintenance, and outpatient drug-free programs. Data were obtained from 59 treatment programs and 3,764 of their clients who had discharge records. The most noteworthy significant interaction effect detected was program's funding source and client's gender on treatment retention in the outpatient drug-free modality. For example, female clients remained less time in the programs that accepted only public funding than in the programs that accepted both public and private funding. Male clients remained in the treatment an average of 25.3 fewer days than female clients in drug-free programs that only accepted public fund, but stayed about the same time as females if the programs received mixed funding.

Adult↗
PubMed1982

A microcomputer program for analysis of nucleic acid hybridization data.

The study of nucleic acid hybridization is facilitated by computer mediated fitting of theoretical models to experimental data. This paper describes a non-linear curve fitting program, using the 'Patternsearch' algorithm, written in BASIC for the Apple II microcomputer. The advantages and disadvantages of using a microcomputer for local data processing are discussed.

Computers↗
PubMed1987

Parametrization by non-linear regression and bayesian estimation of bentazepam in a multiple dosage regimen in humans.

The plasma levels of bentazepam were determined by an HPLC technique in a total of 10 patients receiving the drug orally in pill form who were on a dosage regimen with the drug administered every 8, 12 or 24 h. Blood samples were taken three times following the administration of the first and last dose and at times, immediately after the administration of intermediate doses. The parameters corresponding to a one-compartment kinetic model were calculated in each patient by using all the data on plasma levels still corresponding to different administrations by non-linear regression and applying programs with homoscedastic, heteroscedastic and bayesian estimation. The absorption constant had mean values of 2.33, 2.18 and 2.75 h-1. The elimination constant proved to be equal to 0.10, 0.09 and 0.22 h-1 while for the apparent distribution volume mean values of 1.89, 2.89 and 0.80 l/kg were found with each of the estimation programs employed, respectively. The values found for each of the kinetic parameters and with each of the programs were subjected to the non-parametric Kruskal-Wallis test with a view to detecting the presence or absence of statistically significant differences. The discrimination of the program that yielded the best fit was performed by linear regression between the values found for the plasma calculations and those calculated theoretically at the same time with each of the programs.

Adult↗
PubMed1986

Type 1 error and power of the linear trend test in proportions under the National Toxicology Program's modified pathology protocol.

This paper investigates the relationship between the probability of detecting a statistically significant linear trend in the proportion of animals observed to have tumors for the modified pathology protocol currently being employed by The National Toxicology Program. We considered over 300 possible dose-response relationships and tested at 5% and 1% significance levels. The results indicate that a small loss in the probability of detecting a statistically significant result will occur when the modified protocol is used instead of the previous pathology protocol. This loss varies as a function of the design of the study in terms of dose and animal allocation and as a function of the steepness of the dose-response relationship. The absolute difference between the probability of a statistically significant result for the original pathology protocol and that for the modified pathology protocol never exceeded 0.03. This difference was always less than 8% of the probability of a statistically significant result for the original pathology protocol.

Animals↗
PubMed1975

[A computer program for the implicit regression of the Hill equation].

A computer program for implicit regression of the Hill equation. The fundamentals for the regression of implicit functions following the Gauss method are dealt with. Basing on these fundamentals a program for the regression of the Hill equation is described. The binding constant, the Hill coefficient and end extinction can be estimated. The mean errors of parameters were calculated in the linear model. The program was written in ALGOL 60 for the computer Robotron 300. The program is available on request.

Computers↗
PubMed1995

Supercomputer algorithms for efficient linear octree encoding of three-dimensional brain images.

We designed and implemented algorithms for three-dimensional (3-D) reconstruction of brain images from serial sections using two important supercomputer architectures, vector and parallel. These architectures were represented by the Cray YMP and Connection Machine CM-2, respectively. The programs operated on linear octree representations of the brain data sets, and achieved 500-800 times acceleration when compared with a conventional laboratory workstation. As the need for higher resolution data sets increases, supercomputer algorithms may offer a means of performing 3-D reconstruction well above current experimental limits.

Algorithms↗
PubMed1984

Fitting physiological models to data.

Methods of fitting models to experimental data obtained from biological systems are reviewed. The Michaelis-Menten model is used as the working example of a familiar and well-studied biological model. Criteria for selecting models include goodness of fit, freedom from systematic errors, and simplicity. A given model is usually fitted and the optimal parameters determined by minimization of an objective function, usually the sum of the squared errors. Freedom from systematic errors is best judged graphically. The important mathematical methods of fitting models are derived from the calculus and include linear and quadratic programming. The latter leads to minimization of the sum of squares of errors. Optimal search procedures, which also perform this minimization, are surveyed. Other properties of models, such as the proper number of parameters and whether linearization is appropriate, are discussed. The specialized problems of biological models and data are considered.

Models, Biological↗
PubMed1982

Effect of age and sex on theophylline clearance in young subjects.

The joint effects of age and gender on theophylline plasma clearance (Clp) were assessed using an analysis of covariance technique. Data from several literature sources and from our laboratory were collated for this analysis with only non-smoking subjects aged 1.3 to 30.0 years considered. The values of Clp exhibited markedly greater variability in the younger subjects, necessitating development of a weighted linear least-squares program to fit the data. The data exhibited a linear decrease in Clp with increasing age regardless of sex. A gender influence was evident over the age range of 4 to 20 years. Male Clp values tended to be higher than those of females over this age interval [25.5 ml/hr/kg higher (31%) at 4 years and 12.5 ml/hr/kg higher (22%) at 20 years]. These differences are statistically significant, and since they represent a divergence of greater than 20%, may be clinically significant as well. The statistical technique employed may be of value in future pharmacokinetic studies for the examination of multiple effects on pharmacokinetic parameters.

Adolescent↗
PubMed1998

The effect of independent collimator misalignment on the dosimetry of abutted half-beam blocked fields for the treatment of head and neck cancer.

BACKGROUND AND PURPOSE: Independent collimation conveniently allows for the junctioning of abutting fields with non-diverging beam edges. When this technique is used at the junction of multiple fields, e.g. lateral and low anterior fields in three-field head and neck set-ups, there should be a dosimetric match with no overdose or underdose at the matchline. We set out to evaluate the actual dosimetry at the central match plane. MATERIALS AND METHODS: Independent jaws were used to mimic two half-beam blocked fields abutting at the central axis. X-Ray verification film was exposed in a water-equivalent phantom and the dose at the matchline was evaluated with laser densitometry. Collimators were then programmed to force a gap or overlap of the radiation fields to evaluate the effect of jaw misalignment within the tolerance of the manufacturer's specification. Diode measurements of the field edges were also performed. Four beam energies from four different linear accelerators were evaluated. RESULTS: Small systematic inhomogeneities were found along the matchline in all linear accelerators tested. The maximum dose on the central axis varied linearly with small programmed jaw misalignments. For a gap or overlap of 2 mm between the jaws, the matchline dose increased or decreased by 30-40%. The region of overdose or underdose around the matchline is 3-4 mm wide. The discrepancy between the width of jaw separation and the width of the region of altered dose is explained by a penumbra effect. CONCLUSION: We recommend that independent jaw alignment be evaluated routinely and provide a simple method to estimate dose inhomogeneity at the match plane. If there is a field gap or overlap resulting in a clinically significant change in dosimetry, jaw misalignment should be corrected. If it cannot be corrected, part of the benefit of asymmetric collimation is lost and other methods of field junctioning may have to be considered. We routinely use a small block over the spinal cord at the mono-isocenter set-up plane for three-field head and neck treatments to prevent an overdose.

Head and Neck Neoplasms↗
PubMed1989

Analysis of progress curves for enzyme-catalysed reactions. Automatic construction of computer programs for fitting integrated rate equations.

The computer analysis of progress curves for enzyme-catalysed reactions involves a series of mathematical and computational tasks. The three most daunting of these are the derivation of an integrated rate equation, solving this equation so that the amount of product formed by the reaction at any time can be calculated, and incorporating this solution into a non-linear-regression computer program. This paper describes the basis of a computer program that greatly simplifies the problem. The proposed mechanism is specified in the familiar kinetic constant form, which is automatically translated into a program capable of fitting this mechanism to a series of experimental progress curves. The approach is illustrated for a reversible reaction with one substrate and one product, and tested with some data obtained for the fumarase reaction. A copy of the program has been deposited as Supplementary Publication SUP 50148 (13 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1989) 257, 5.

Animals↗
PubMed1979

A program package for simulation and parameter estimation in pharmacokinetic systems.

A set of programs is presented which has been developed for parameter estimation and simulation of models arising from pharmacokinetic applications. The programs can accommodate linear and nonlinear models with multiple inputs and multiple outputs. When the model is defined by differential equations, non-uniform repetitive dosage regimens can be handled. The model may also be entered in integrated form when single dose studies or uniform multiple dose studies are being considered. The programs employ a variable-step, variable-order integration routine to solve the model differential equations, and the Nelder-Mead simplex procedure to determine the parameter values which minimize a weighted least squares criterion. The programs have been written for an interactive time-sharing environment with the experimental data and model equations stored in files for future use.

Computers↗
PubMed2003

Concept and realization of a multimedia program for veterinary physiology.

A multimedia program, a non-linear system which supplements the traditional, linear way of learning (e.g. with a text book), was developed. Non-linear systems allow the direct use of information in a free sequence. A problem of these systems is the danger that the reader becomes lost in detail. Therefore, a program was constructed which tries to combine the properties of linear and non-linear teaching systems. Student groups were continuously involved during all stages of the project. The program is organized in several levels. These are: (1) choice of chapters; (2) table of contents of one chapter; (3) summary; (4) text and (5) pictures, animations, simulations and video sequences. The program can be used in different ways. In the linear mode, the reader selects via action words different levels of the program. The user can read either only on the level of the summaries or on detailed information (text, pictures, simulations and videos). In the non-linear mode the user jumps via menu items or buttons to selected pictures, simulations or a searched term. In this way, more than 3500 screen pages are integrated into a multimedia program for veterinary physiology. The program is written in TOOLBOOK, and can be used on a personal computer with Windows 95 or higher.

Animal Population Groups↗
PubMed1999

Genetic programming as an analytical tool for non-linear dielectric spectroscopy.

By modelling the non-linear effects of membranous enzymes on an applied oscillating electromagnetic field using supervised multivariate analysis methods, Non-Linear Dielectric Spectroscopy (NLDS) has previously been shown to produce quantitative information that is indicative of the metabolic state of various organisms. The use of Genetic Programming (GP) for the multivariate analysis of NLDS data recorded from yeast fermentations is discussed, and GPs are compared with previous results using Partial Least Squares (PLS) and Artificial Neural Nets (NN). GP considerably outperforms these methods, both in terms of the precision of the predictions and their interpretability.

Computational Biology↗