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PubMed1989

The effect of dependence on the performance of Bayes' theorem: an evaluation using a computer simulation.

A computer simulation is described which generates 'cases' of vaginal discharge. This simulation was used to evaluate the potential effects of dependence between clinical features on the diagnostic performance of Bayes' theorem. The following observations were made: (1) dependence between some but not all pairs of features reduced the overall diagnostic efficiency (judged by the number of true positive diagnoses); (2) the overall reduction in efficiency was never substantial; (3) the largest effects on the diagnosis of individual conditions was observed with rarer diseases, and with combinations of features which were inherently unlikely to be dependent. It is concluded that the diagnostic efficiency of Bayes' theorem will not be greatly influenced by dependence if a reasonable amount of commonsense is applied to the selection of the knowledge base.

Bayes Theorem↗
PubMed1992

Cell cycle kinetics analysis of HeLa cells exposed to aphidicolin: computer simulation.

A computer simulation model was developed and used to analyze the inhibitory effect of aphidicolin on the proliferation of Hela cells. Simulation results were compared with actual experimental results [Pedrali-Noy et al. (1980) Nuc. Acid Res. 8, 377] and were found to be in good agreement. Also, the simulation showed that aphidicolin caused cells to be accumulated at the G1/S boundary and that recruitment and synchrony occurred.

Aphidicolin↗
PubMedDate not supplied

Virtual ambulatory care. Computer simulation applications.

Computer simulation modeling has evolved during the past twenty years into an effective tool for analyzing and planning ambulatory care facilities. This article explains the use of this tool in three case-study, ambulatory care settings--a GI lab, holding beds for a cardiac catheterization laboratory, and in emergency services. These examples also illustrate the use of three software packages currently available: MedModel, Simul8, and WITNESS.

Ambulatory Care Facilities↗
PubMed1993

Electrogenic property of Na+, K(+)-ATPase through computer simulation.

A computer simulation of the electrogenic nature of the membrane-bound Na+, K(+)-ATPase is presented. The model involves coupling two simulation systems for passive and active transports, using a minimum of empirical parameters, and studies the contribution of the pump to the membrane potential. The simulation results indicate that electrogenic active transport accelerates the restoration of the resting electrochemical gradients and contributes approximately 0.44-1.1 mV to the resting potential of the membrane, depending on the Na:K coupling ratio. The effect of membrane potential and the physical positioning of the enzyme from the passive transporting channel on the enzyme function is also presented. The validity of the model is checked by comparing our results with reported literature values.

Biological Transport↗
PubMed1998

Wave propagation in cardiac tissue and effects of intracellular calcium dynamics (computer simulation study).

Computer simulation using Luo-Rudy I1 model of ventricular myocyte showed that intracellular calcium dynamics become irregular in case of high rate stimulation. This causes the transition from stationary to nonstationary spiral wave and its breakup in 2D model of cardiac tissue. Obtained results suggest how ventricular fibrillation may occur due to the abnormalities of intracellular calcium dynamics. The short review of existing cardiac cell models with calcium dynamics is presented.

Animals↗
PubMed1980

Cell proliferation in EMT6 tumours treated with single doses of X-rays or hydroxyurea. II. Computer simulations.

A computer simulation technique was used to analyse data on the proliferation of clonogenic cells in EMT6 tumours treated with 5 mg/mouse of hydroxyurea (HU) or 3.0 Gy (300 rads) X-rays. This simulation technique is able to determine the respective roles of selective killing, blocks in cell progression and recruitment of the treated population. When the technique was applied to tumours treated with HU, it was possible to prove that both a G1/S block and recruitment occurred. These phenomena could not have been demonstrated quantitatively, or even qualitatively, without the use of the simulation. After irradiation, blocks in cell progression and differences in the proliferative patterns of the surviving clonogenic cells and the total tumour cell population were found.

Animals↗
PubMed1979

Dependence of refractory period measurements on conduction distance: a computer simulation analysis.

Computer simulations were used to study the recovery of conduction velocity in the temporal and spatial domains during the relative refractory period. The impulse exhibits increased duration and reduced amplitude during the relative refractory period as well as a reduced conduction velocity. Changes in conduction velocity are reflected by a deviation from linearity in the plots of latency variation versus interstimulus interval and of interval-between-impulses versus intersimulus interval. The latency increase for the second impulse is monotonically related to interstimulus interval, and is maximal at the beginning of relative refractory period. The magnitude of the latency increase is also related monotonically, but not in a linear manner, to conduction distance. The distance-dependence of latency variation during the relative refractory period is most marked close to the site of impulse initiation. These findings may be relevant to relative refractory period measurements in clinical neurophysiology.

Action Potentials↗
PubMed1985

Escherichia coli DNA distributions measured by flow cytometry and compared with theoretical computer simulations.

A computer simulation routine has been made to calculate the DNA distributions of exponentially growing cultures of Escherichia coli. Calculations were based on a previously published model (S. Cooper and C.E. Helmstetter, J. Mol. Biol. 31:519-540, 1968). Simulated distributions were compared with experimental DNA distributions (histograms) recorded by flow cytometry. Cell cycle parameters were determined by varying the parameters to find the best fit of theoretical to experimental histograms. A culture of E. coli B/r A with a doubling time of 27 min was found to have a DNA replication period (C) of 43 min and an average postreplication period (D) of 22 to 23 min. Similar cell cycle parameters were found for a 60-min B/r A culture. Initiations of DNA replication at multiple origins in one and the same cell were shown to be essentially synchronous. A slowly growing B/r A culture (doubling time, 5.5 h) had an average prereplication period (B) of 2.3 h; C = 2.4 h and D = 0.8 h. It was concluded the the C period has a constant duration of 43 min (at 37 degrees C) at fast growth rates (doubling times, less than 1 h) but increases at slow growth rates. Thus, our results obtained with unperturbed exponential cultures in steady state support the model of Cooper and Helmstetter which was based on data obtained with synchronized cells.

Cell Division↗
PubMed1989

Changes in the histograms of nerves resulting from growth and various modalities of damage. A computer simulation.

A computer program simulates the changes in a nerve's histogram during normal growth and from various neuropathies. The program shows how a nerve's histogram will change from various percentages of fiber damage or from preferential damage to either thick or thin fibers, or from various degrees of fiber restitution, or from single-event or repetitive damage. In single-event damage, the main alteration is a preponderance of thin (regenerating) fibers. Patterns of selective fiber vulnerability are difficult to deduce from the shape of the histogram. Repetitive damage remodels the histogram to a broad unimodal fiber distribution at reduced mean caliber. Comparison of simulated changes with data from an experimental isoniazid neuropathy yielded a close match between observed changes and simulation.

Animals↗
PubMed2004

[Normal and adverse genetic processes in subdivided populations of the island type: computer simulation].

A computer model simulating genetic dynamics of a subdivided population at the level of a one-locus diallele system is proposed. In contrast to the earlier publications, this model is based on Wright's island model. The computer experiments were focused on genetic changes occurring during relatively short time intervals comparable to the duration of economic activities of humans (tens of generations). The process of attaining stationary state and reorganization of the genetic structure of the system under anthropogenic influence were simulated. The results are interpreted graphically as a spatial-temporal distribution of subpopulations by classes of gene frequencies as well as in quantitative terms of Nei's G-statistics.

Alleles↗
PubMed2002

Structures of neat and hydrated 1-octanol from computer simulations.

Molecular dynamics computer simulations of 1-octanol and its mixtures with water have been performed. The liquid is composed of regions enriched in either hydrocarbons or hydroxyl groups. In neat octanol, the hydroxyl groups form clusters of long, thin chains. Upon the addition of water, the clusters become longer and more spherical, forming a structure that can be described as consisting of "overlapping elongated inverse micelles". The structures of the mixtures obtained at different hydration levels are consistent with those of experimental diffraction studies of water/octanol mixtures and previous computer simulations of neat and water-saturated octanol. The saturation point of the model has been calculated using the cavity-bias particle insertion method. The solubility of water in octanol is slightly too low compared to experimental results, and suggestions for possible improvements to the force field are made.

1-Octanol↗
PubMed1992

[Computer simulation of blood level profiles. Drug liberation from two sustained-release preparations and computer simulation of single- and multiple-dose pharmacokinetics].

A series of computer programs (BASIC) is introduced for the evaluation of in vitro dissolution data as well as for the calculation of pharmacokinetic parameters and for blood level curve fitting to the respective in vitro data. Furthermore, programs are offered for the simulation of blood level profiles under variable conditions. In order to demonstrate the practical use of these programs, the expected blood level profiles following the administration of two commercial sustained-release dosage forms containing the drug pentoxifylline have been compared.

Computer Simulation↗
PubMed1992

On the interpretation of biochemical data by molecular dynamics computer simulation.

The application of computer simulation to molecular systems of biochemical interest is reviewed. It is shown that computer simulation is a tool complementary to experimental methods, which can be used to access atomic details inaccessible to experimental probes. Examples are given in which computer simulation augments the experimental information by providing an atomic picture of high resolution with respect to space, energy or time. The usefulness of a computer simulation largely depends on its quality. The most important factors that limit the accuracy of simulated results are discussed. The accuracy of different simulation studies can differ by orders of magnitude. The accuracy will depend on the type of biomolecular system and process studied. It will also depend on the choice of force field, the simulation set-up and the protocol that is used. A list of quality-determining factors is given, which may be useful when interpreting simulation studies appearing in the literature.

Biochemical Phenomena↗
PubMed2005

A computer-simulated liver phantom (virtual liver phantom) for multidetector computed tomography evaluation.

OBJECTIVE: The purpose of study was to develop a computer-simulated liver phantom for hepatic CT studies. A computer-simulated liver phantom was mathematically constructed on a computer workstation. MATERIALS AND METHODS: The computer-simulated phantom was calibrated using real CT images acquired by an actual four-detector CT. We added an inhomogeneous texture to the simulated liver by referring to CT images of chronically damaged human livers. The mean CT number of the simulated liver was 60 HU and we added numerous 5-to 10-mm structures with 60+/-10 HU/mm. To mimic liver tumors we added nodules measuring 8, 10, and 12 mm in diameter with CT numbers of 60+/-10, 60+/-15, and 60+/-20 HU. Five radiologists visually evaluated similarity of the texture of the computer-simulated liver phantom and a real human liver to confirm the appropriateness of the virtual liver images using a five-point scale. RESULTS: The total score was 44 in two radiologists, and 42, 41, and 39 in one radiologist each. They evaluated that the textures of virtual liver were comparable to those of human liver. CONCLUSIONS: Our computer-simulated liver phantom is a promising tool for the evaluation of the image quality and diagnostic performance of hepatic CT imaging.

Computer Simulation↗
PubMed1990

The simulation of aerial movement--IV. A computer simulation model.

A computer simulation model of human airborne movement is described. The body is modelled as 11 rigid linked segments with 17 degrees of freedom which are chosen with a view to modelling twisting somersaults. The accuracy of the model is evaluated by comparing the simulation values of the angles describing somersault, tilt and twist with the corresponding values obtained from film data of nine twisting somersaults. The maximum deviations between simulation and film are found to be 0.04 revolutions for somersault, seven degrees for tilt and 0.12 revolutions for twist. It is shown that anthropometric measurement errors, from which segmental inertia parameters are calculated, have a small effect on a simulation, whereas film digitization errors can account for a substantial part of the deviation between simulation and film values.

Anthropometry↗
PubMedDate not supplied

Determination of the optimal imaging parameters of the RODEO pulse sequence by computer simulation.

A computer program has been developed for evaluating the NMR signal response of various imaging parameters and its efficiency in fat suppression of the RODEO (ROtating Delivery of Excitation Off-resonance) pulse sequence. Both spoiled and refocused RODEO pulse sequences have been considered. By numerically solving the Bloch equation modified for a three-dimensional volume of spins, for realistic RF excitations and Lorentzian distribution of the frequency spectrum for both fat and water, the program permits the imaging contrast and fat suppression of the RODEO pulse sequences to be assessed quantitatively. We have found that excellent fat suppression can be achieved by choosing appropriate imaging parameters. Imaging contrast for different tissues can be enhanced by using longer repetition time (TR) in the spoiled scheme. The complex pattern of NMR signal response and imaging contrast has been observed in the refocused scheme.

Adipose Tissue↗
PubMed2002

Site-specific OH attack to the sugar moiety of DNA: a comparison of experimental data and computational simulation.

Little computational or experimental information is available on site-specific hydroxyl attack probabilities to DNA. In this study, an atomistic stochastic model of OH radical reactions with DNA was developed to compute relative OH attack probabilities at individual deoxyribose hydrogen atoms. A model of the self-complementary decamer duplex d(CCAACGTTGG) was created including Na(+) counter ions and the water molecules of the first hydration layer. Additionally, a method for accounting for steric hindrance from nonreacting atoms was implemented. The model was then used to calculate OH attack probabilities at the various C-H sites of the sugar moiety. Results from this computational model show that OH radicals exhibit preferential attack at different deoxyribose hydrogens, as suggested by their corresponding percentage solvent-accessible surface areas. The percentage OH attack probabilities for the deoxyribose hydrogens [1H(5')+2H(5'), H(4'), H(3'), 1H(2')+2H(2'), H(1')] were calculated as approximately 54.6%, 20.6%, 15.0%, 8.5% and 1.3%, respectively, averaged across the sequence. These results are in good agreement with the latest experimental site-specific DNA strand break data of Balasubramanian et al. [Proc. Natl. Acad. Sci. USA 95, 9738-9742 (1998)]. The data from this stochastic model suggest that steric hindrance from nonreacting atoms significantly influences site-specific hydroxyl radical attack probabilities in DNA. A number of previous DNA damage models have been based on the assumption that C(4') is the preferred site, or perhaps the only site, for OH-mediated DNA damage. However, the results of the present study are in good agreement the experimental results of Balasubramanian et al. in which OH radicals exhibit preferential initial attack at sugar hydrogen atoms in the order 1H(5')+2H(5') > H(4') > H(3') > 1H(2')+2H(2') > H(1').

Algorithms↗