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PubMed1989

BOOMER, a simulation and modeling program for pharmacokinetic and pharmacodynamic data analysis.

BOOMER is an improved version of an earlier non-linear regression program, MULTI-FORTE. Rather than the user writing a FORTRAN subroutine, models are defined by means of the parameters which make up the model. Models based on differential equations are specified by means of zero-order, first-order, or Michaelis-Menten-type rate constants. Doses (in units of mass) are translated into the usually observed concentration units by a reciprocal volume parameter. Integrated equation models are specified in terms of baseline terms, exponential terms, or the emax function with slope term as described by the Hill equation. Time points can be specified as parameters to specify dose times, infusion start/stop times, or lag times. With careful selection of parameters quite complex models can be specified. The user has a choice of differential equation solvers and fitting algorithms.

Computer Simulation↗
PubMedDate not supplied

Evaluation of Monte Carlo generation of long-tailed symmetric and contaminated symmetric distributions.

Generating random variables from a specific distribution, whether symmetric or asymmetric, is a concern of investigators involved in Monte Carlo studies. Of particular interest to those concerned with robustness is the generation of contaminated symmetric distributions such as those used in the Princeton Robustness Study. A reliable composite uniform U(0,1) generator is described and algorithms for transforming U(0,1) to symmetric long-tailed and contaminated symmetric distributions are given. Goodness-of-fit tests and graphical illustrations demonstrate the adequacy of the empirical distributions.

Algorithms↗
PubMed1990

An application of the D-optimal criterion to define the experimental design for a particular class of semi-parametric models.

An updated version of the computer program EXCAD [1] allows the user to optimize experimental design to estimate parameters of particular semi-parametric models. The semi-parametric models take the general form of a function of time (t): Y(t) = NL (c(t,alpha),beta). The function NL(C(t,alpha),beta), is, in general, a non-linear transformation of a function, C(t,alpha), that in turn is the convolution of two others. One of these two functions is expressed in a non-parametric form, and is not of direct interest to the experimenter. The other is of direct interest: it is a parametric function depending on a set of parameters alpha. This semi-parametric model applies to numerous kinds of biological experiments, such as pharmacokinetic/pharmacodynamic, physiological, circulatory flow experiments. This paper presents a new method for determining an optimal experimental design to estimate the parameters alpha and beta. The new approach adopts the D-optimal criterion, and is illustrated using real thiopental data.

Animals↗
PubMed1994

A knowledge acquisition tool in analytical pathology based on multi-media relational database.

The need for a knowledge based expert system for efficient decision making in the field of pathology has been well accepted. To build the knowledge-base for such an expert system is a painstaking task. This work is an attempt to provide the pathologists a powerful and user-friendly tool that will help them in the process of building the knowledge-base for medical diagnosis by closely looking at the specimen images and their extracted feature values. The tool is based on multi-media relational database and software like VAX Rally (4GL), ILIAD and SAS to provide a wide-range comparative study between feature data and image data; and also their statistical analysis.

Artificial Intelligence↗
PubMed1989

Correlation artifacts in speed of sound estimation in scattering media.

A recently described method for speed of sound estimation in tissues in pulse-echo mode involves reception of echoes generated by an ultrasonic pulse by means of a linearly tracking transducer. When the peaks of echo amplitudes are used as markers of arrival time, stairstep-like artifacts appear in the echo arrival time vs. transducer position plots. We postulate that these artifacts are a consequence of the speckle phenomenon commonly encountered in ultrasonic imaging. To test this hypothesis, we report computer simulations and water tank experiments which demonstrate similarities between the behavior of the stairsteps and the properties of ultrasonic speckle. Additionally, equations describing the precision of the speed of sound estimation in terms of the second order statistical properties of the stairstep artifact are derived.

Computer Simulation↗
PubMed1992

Processing images of helical structures: a new twist.

Helical macromolecular assemblies are particularly difficult to study by X-ray diffraction but are quite well suited to analysis by electron microscopy. Most of our information about helical macromolecular assemblies has come from the electron microscope but has been limited to about 25 A resolution. With the use of low-dose electron cryomicroscopy, one can obtain structural data to near atomic resolution on two-dimensional crystals, but the problem is to extract the information from the noise. In this paper we present methods to extract signal from low-dose electron cryomicrographs of helically symmetric structures. We apply these methods to extract 10 A data from the bacterial flagellar filament.

Algorithms↗
PubMedDate not supplied

Morphometric analysis of sonographic images by spatial geometric modeling.

A methodology able to derive spatial geometric models from input sequences of sonographic slices is proposed. The developed modeling procedure can be utilized to perform computer-assisted anatomic 3D analysis both on all echo space and selected subregions. The modeling procedure is mainly composed of three sequential phases: a) automatic acquisition and preprocessing of time sequences of 2D echotomograms; b) 3D reconstruction of images and computing of discrete distance maps of selected echoes according to predefined projective laws; and c) generation of a spatial geometric model of the examined object starting from the previously computed maps.

Algorithms↗
PubMed1997

Determination of mean particle volume, a Monte Carlo simulation.

Either length measurements or area measurements may be made on a sample of profiles for the purpose of estimating the mean volume of a population of convex particles. Diameters of spheres, caliper diameters of ellipsoids and intercept lengths are available length measurements. Profile areas can be evaluated by planimetry or point counting. Either all the available profiles in random sections or point sampled profiles can be utilized. We have applied a Monte Carlo simulation to compare several of the stereologic methods for the estimation of the mean volumes of spheres and ellipsoids. Populations of spherical, prolate ellipsoidal and oblate ellipsoidal particles were subjected to random sectioning and measurement. Diameter, point sampled intercept length, area and point sampled area were measured in the case of the spherical particles. With the ellipsoids, the same measurement excepting diameters were performed. The measurements were converted to volumes by the appropriate equations, and the means, the standard deviations of the means and the 95% confidence intervals were determined for increasing sample sizes. All the methods provide estimates that converge on their theoretical mean volumes. The area measurements and particularly the point sampled area measurement show some advantage over the length measurements, but differences among the methods are small, not entirely consistent over the different cases and unlikely to be significant in most real applications.

Algorithms↗
PubMed1991

Degenerate Hopf bifurcation and isolated periodic solutions of the Hodgkin-Huxley model with varying sodium ion concentration.

Points of degenerate Hopf bifurcation in the Hodgkin-Huxley model are found as parameters temperature T and voltage level of sodium VNa are varied. Local techniques of degenerate Hopf bifurcation analysis are used to show the existence of families of periodic solutions of the model: isolated branches of periodic solutions (i.e. branches not connected to the stationary branch) are found in addition to Hopf branches. Purely numerical techniques are used to show that the isolas persist for VNa up to a value slightly greater than 114 mV. Under some conditions there are multiple stable periodic solutions, so "jumping" between action potentials of different amplitudes might be observed.

Action Potentials↗
PubMed1990

Computerized morphonuclear cell image analyses of malignant disease in bladder tissues.

We analyzed the relationship between several morphonuclear parameters related to nuclear size, densitometry (deoxyribonucleic acid content and ploidy) and the chromatin pattern versus the histopathological grading of 46 bladder cancer samples graded according to the World Health Organization classification. We used a SAMBA 200 cell image processor with software allowing for the discrimination of 15 different parameters on Feulgen-stained imprint smears. In addition, we set up preliminary data banks that enable objective and reproducible grading of unknown cases. This approach must be validated in a large series of cases to create an expert system for bladder malignancy diagnosis.

Cell Division↗
PubMed1998

NLMEM: a new SAS/IML macro for hierarchical nonlinear models.

Analysis of longitudinal data is one of the most challenging tasks in statistical modeling. In the analysis, it is often necessary to take into account nonlinear response to a set of parameters of interest and correlation between measurements taken from the same individual. In addition, between- and within-subject variation has to be handled properly. An example of addressing these issues is the hierarchical nonlinear model, where parameter estimation can be performed using linearization method. In this paper a new NLMEM SAS/IML macro for hierarchical nonlinear models is proposed. The program uses a portion of the code developed earlier in NLINMIX. NLMEM retains all the benefits of NLINMIX while allowing the systematic part of the model structure to be specified using IML syntax. Consequently, NLMEM allows estimation of models which are not tractable using NLINMIX. In particular, it allows us to address advanced population pharmacokinetics and pharmacodynamics models specified by ordinary differential equations.

Computer Simulation↗
PubMed1998

Numerical evaluation of the production of radionuclides in a nuclear reactor (Part II).

A computer program called LAURA has been developed to predict the production rates of any member of a nuclei network undergoing spontaneous decay and/or induced neutron transformation in a nuclear reactor. The theoretical bases for the development of LAURA were discussed in Part I. In particular, in Part I, we described how an expression based on the Rubinson (1949) approach is used to evaluate the depletion function. In this paper (Part II), we describe the full simulation of radionuclide production including the decomposition of a reaction network into independent linear chains, provisions for periodic reactor shutdown and restart, and implementation of an approximate solution given by Raykin and Shlyakhter (1989) to account for the effect of feedback due to alpha decay. Also included are some examples which demonstrate possible uses for LAURA.

Computer Simulation↗
PubMed1997

Compensation for displacement of the focal point in cone beam single photon emission computed tomography reconstruction.

This study examined the effects of focal point displacement on image quality in cone beam single photon emission computed tomography (SPECT). A new image reconstruction algorithm that accounts for the focal point shift was derived and three shift geometries were investigated. The geometries included a lateral shift with a fixed focal length but off-center focusing, a linear axial shift with a variable focal length that depends linearly on the distance between a bin of the detector and the center of the detector, and a random axial shift with a randomly varying focal length. Computer simulation was conducted to evaluate the shift effects with a phantom that was composed of 118 small spherical sources. The results demonstrated that the lateral shift of the focal point was more critical to image quality than was the axial shift. With a 0.64 cm (1 pixel) lateral shift, noticeable artifacts was observed, while an axial shift resulted in minimal changes in image quality until it reached 8 cm (12.5 pixels). The derived reconstruction algorithm eliminated most of the artifacts caused by a fixed lateral shift or a linear axial shift of the focal point, but failed to do so for a random axial shift since the linear distribution assumed in image reconstruction did not match the random shift occurred in acquisition of the data.

Algorithms↗
PubMed1993

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

The microscopic interactions and mechanisms leading to nascent protein folding events are generally unknown. While such short time-scale events are difficult to study experimentally, molecular dynamics simulations of peptides can provide a useful model for studying events related to protein folding initiation. Recently, two extremely long molecular dynamics simulations (2.2 ns each) were carried out on the pentapeptide Tyr-Pro-Gly-Asp-Val [Tobias, D. J., Mertz, J. E., & Brooks, C. L., III (1991) Biochemistry 30, 6054-6058] that forms stable reverse turns in solution. Tobias et al. examined folding events in this large system (approximately 30,000 conformations) using traditional methods of trajectory analysis. The shear magnitude of this problem prompted us to develop an automated approach, based on self-organizing neural nets, to extract the key features of the molecular dynamics trajectory. The neural net is used to perform conformational clustering, which reduces the complexity of a system while minimizing the loss of information. The conformations were grouped together using distances in dihedral angle space as a measure of conformational similarity. The resulting clusters represent "conformational states", and transitions between these states were examined to identify mechanisms of conformational change. Many conformational changes involved the rotation of only a single dihedral angle, but concerted angle changes were also found. Most of the conformational information in the 30,000 samples from the full trajectories was retained in the relatively few resultant clusters, providing a powerful tool for analysis of an expanding base of large molecular simulations.

Algorithms↗
PubMed1997

Oligomerization of the amide sensor protein AmiC by x-ray and neutron scattering and molecular modeling.

AmiC is the negative regulator of the amidase operon which is involved in amide metabolism in the cytosol of Pseudomonas aeruginosa. Crystal structures show that AmiC contains two large domains that are very similar to the periplasmic leucine-isoleucine-valine binding protein (LivJ) of Escherichia coli. Synchrotron X-ray and neutron (in 100% 2H2O buffer) scattering data were obtained for AmiC in the presence of its substrate acetamide and its anti-inducer butyramide which binds more weakly to AmiC than acetamide. Guinier analyses to obtain radius of gyration RG and molecular weight Mr values showed that AmiC formed trimers whose formation was favored in the presence of acetamide and which exhibited concentration-dependent properties at concentrations between 0.4 and 2 mg/mL. Above 2 mg/mL, where trimers predominated, the RG data were identical within 0.05 nm for AmiC-acetamide and AmiC-butyramide with mean X-ray and neutron RG values of 3.35 and 3. 28 nm, respectively. Scattering curve fits constrained by the crystal structure of AmiC-acetamide were evaluated in order to describe a model for trimeric AmiC. A translational search of parallel alignments of three monomers to form a symmetric AmiC homotrimer gave a good X-ray curve fit. Combinations of calculated curves for monomeric, dimeric, trimeric, and tetrameric AmiC as seen in the crystal structure of AmiC gave reasonable but weaker X-ray curve fits which did not favor the existence of tetrameric AmiC. It is concluded that AmiC exhibits novel ligand-dependent oligomerization properties in solution when these are compared to other members of the periplasmic binding protein superfamily, where AmiC exists in monomeric and trimeric forms, the proportions of which depend on the presence of acetamide or butyramide.

Bacterial Proteins↗
PubMed1991

Mean residence times and distribution volumes for drugs undergoing linear reversible metabolism and tissue distribution and linear or nonlinear elimination from the central compartments.

Equations for the mean residence times in the body (MRT) and in the central compartment (MRTc) are derived for bolus central dosing of a drug and its metabolite which undergo linear tissue distribution and linear reversible metabolism but are eliminated either linearly or nonlinearly (Michaelis-Menten kinetics) from the central compartments. In addition, a new approach to calculate the steady-state volumes of distribution for nonlinear systems (reversible or nonreversible) is proposed based on disposition decomposition analysis. The application of these equations to a dual reversible two-compartment model is illustrated by computer simulations.

Computer Simulation↗
PubMed1996

Influence of surface free energies and cohesion parameters on pharmaceutical material interaction parameters-theoretical simulations.

PURPOSE: The aim of this study was to perform simulations of the influence of surface free energies and cohesion parameters on various interaction parameters within binary systems. METHODS: Using predictive equations derived from surface free energies and cohesion parameters originally proposed by Wu (2, 3) and by Rowe (4), values of interfacial tension, spreading and reduced spreading coefficients, interaction parameter and strength of interaction were simulated by means of a data processor. The influence of polar and disperse fractions of the two interacting materials was also examined. RESULTS: From the simulations, boundary conditions could be drawn: minimum interfacial tension, positive spreading coefficient, reduced spreading coefficient superior to unity, maximum value of the interaction parameter or of the strength of interaction. CONCLUSIONS: Simulations of the various parameters will help the formulator to select proper materials, eg. an agent that will efficiently bind some powdered substrate, a film-forming agent that will properly coat given cores or a material that will enhibit high interaction with a substrate.

Biocompatible Materials↗