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Results for “Monte Carlo Method”

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PubMed2004

Statistical methods for linking health, exposure, and hazards.

The Environmental Public Health Tracking Network (EPHTN) proposes to link environmental hazards and exposures to health outcomes. Statistical methods used in case-control and cohort studies to link health outcomes to individual exposure estimates are well developed. However, reliable exposure estimates for many contaminants are not available at the individual level. In these cases, exposure/hazard data are often aggregated over a geographic area, and ecologic models are used to relate health outcome and exposure/hazard. Ecologic models are not without limitations in interpretation. EPHTN data are characteristic of much information currently being collected--they are multivariate, with many predictors and response variables, often aggregated over geographic regions (small and large) and correlated in space and/or time. The methods to model trends in space and time, handle correlation structures in the data, estimate effects, test hypotheses, and predict future outcomes are relatively new and without extensive application in environmental public health. In this article we outline a tiered approach to data analysis for EPHTN and review the use of standard methods for relating exposure/hazards, disease mapping and clustering techniques, Bayesian approaches, Markov chain Monte Carlo methods for estimation of posterior parameters, and geostatistical methods. The advantages and limitations of these methods are discussed.

Case-Control Studies↗

PubMed1990

Probabilities of orders in linkage calculations.

The present state of linkage estimation procedures is surveyed. When information on linkage between several loci on one chromosome is given in the form of lod scores or likelihoods, a method is developed for finding the probabilities of the different possible orders of the loci, and the distribution of the map distances between them. This depends largely on a Monte Carlo method of integrating the probabilities.

Female↗

PubMed2006

Uncertainty of calculation results in vehicle collision analysis.

In the analysis of road accidents two types of calculation result uncertainty can be distinguished: modelling uncertainty and uncertainty in calculation results [R.M. Brach, M. Brach, Vehicle Accident Analysis & Reconstruction Methods, SAE International Publisher, Warrendale, 2005]. The problem becomes very important first of all when minor modifications of input parameters or application of different models of the phenomenon lead to a fundamentally different answer to the question posed by the court. The aim of the paper was to prove the necessity of including the problem of uncertainty in calculations related to vehicle collision mechanics and to justify the application of different error analysis methods recommendable in vehicle collision reconstruction. The data file from crash test No. 7 [H. Burg, M. Lindenmann, Unfallversuche, Verlag Information Ambs, Kippenheim, 1982] was used, the selection restricted to the range typical of average police records of collision place. Collision speeds were calculated using two methods: reconstruction and simulation. The analysis of uncertainty was carried out. Maximum and mean square uncertainty were calculated by means of total differential of relevant forms. Since the reconstruction resulted in very broad error intervals of uniform distribution, additional calculations were performed by the Monte Carlo method using algorithm described in [W. Wach, J. Unarski, Determination of vehicle velocities and collision location by means of Monte Carlo simulation method, Special Publication Accident Reconstruction SP-1999, SAE Paper No. 2006-01-0907, 2006].

Journal Article↗

PubMedDate not supplied

The impact of unmeasured clinical variables on the accuracy of hospital report cards: a Monte Carlo study.

PURPOSE: Hospital report cards are commonly produced using administrative data. The objective of this study was to determine the impact of unmeasured clinical data on the accuracy of hospitals' report cards. METHODS: Monte Carlo simulations were based on both administrative and detailed clinical data for patients hospitalized with an acute myocardial infarction in Ontario, Canada. Data were simulated such that the true performance of each hospital was known. Both clinical and administrative risk scores were randomly generated for each patient. The ability of hospital report cards to correctly identify hospitals that truly had higher than acceptable mortality was compared when both clinical and administrative data were used and when only administrative data were used. By using Monte Carlo simulations, we were able to incrementally increase the divergence between the 2 risk scores. RESULTS: In a wide range of settings, sensitivity and specificity of hospital report cards was only negligibly greater when both administrative and clinical data were used compared to when only administrative data were used. CONCLUSIONS: Unmeasured clinical data have at most a minor impact on the accuracy of cardiac hospital report cards.

Hospital Administration↗

PubMed2006

Optimization of the Monte Carlo code for modeling of photon migration in tissue.

The Monte Carlo method is frequently used to simulate light transport in turbid media because of its simplicity and flexibility, allowing to analyze complicated geometrical structures. Monte Carlo simulations are, however, time consuming because of the necessity to track the paths of individual photons. The time consuming computation is mainly associated with the calculation of the logarithmic and trigonometric functions as well as the generation of pseudo-random numbers. In this paper, the Monte Carlo algorithm was developed and optimized, by approximation of the logarithmic and trigonometric functions. The approximations were based on polynomial and rational functions, and the errors of these approximations are less than 1% of the values of the original functions. The proposed algorithm was verified by simulations of the time-resolved reflectance at several source-detector separations. The results of the calculation using the approximated algorithm were compared with those of the Monte Carlo simulations obtained with an exact computation of the logarithm and trigonometric functions as well as with the solution of the diffusion equation. The errors of the moments of the simulated distributions of times of flight of photons (total number of photons, mean time of flight and variance) are less than 2% for a range of optical properties, typical of living tissues. The proposed approximated algorithm allows to speed up the Monte Carlo simulations by a factor of 4. The developed code can be used on parallel machines, allowing for further acceleration.

Light↗

PubMed1987

Normalized auto- and cross-covariance functions for neuronal spike train analysis.

The normalized auto- and cross-covariance functions of discrete-time stochastic point process, used for quantitatively analyzing neuronal spike trains, were derived from the corresponding functions of general stochastic process using Kronecker delta functions. The auto-correlation and cross-correlation properties can be described as numerical differences on a monotonic scale ranging from -1 -1 to +1. A segmental integration method and a significance test for the normalized cross-covariance function estimate are suggested. Examples from real spike trains are illustrated, and Monte Carlo methods are used for controls and for testing the algorithms and computer programs.

Action Potentials↗

PubMed1997

An algorithm for haplotype analysis.

This paper proposes an algorithm for haplotype analysis based on a Monte Carlo method. Haplotype configurations are generated according to the distribution of joint haplotypes of individuals in a pedigree given their phenotype data, via a Markov chain Monte Carlo algorithm. The haplotype configuration which maximizes this conditional probability distribution can thus be estimated. In addition, the set of haplotype configurations with relatively high probabilities can also be estimated as possible alternatives to the most probable one. This flexibility enables geneticists to choose the haplotype configurations which are most reasonable to them, allowing them to include their knowledge of the data under analysis.

Algorithms↗

PubMed2006

Continuous and tractable models for the variation of evolutionary rates.

We propose a continuous model for variation in the evolutionary rate across sites and over the phylogenetic tree. We derive exact transition probabilities of substitutions under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in financial applications. The model directly extends the standard gamma distributed rates across site model, with one additional parameter governing changes in rate down the tree. The parameters of the model can be estimated directly from two well-known statistics: the index of dispersion and the gamma shape parameter of the rates across sites model. The CIR model can be readily incorporated into probabilistic models for sequence evolution. We provide here an exact formula for the likelihood of a three-taxon tree. The likelihoods of larger trees can be evaluated using Monte-Carlo methods.

Base Sequence↗

PubMed2001

Spectral deconvolution and operational use of stripping ratios in airborne radiometrics.

Spectral deconvolution using stripping ratios for a set of pre-defined energy windows is the simplest means of reducing the most important part of gamma-ray spectral information. In this way, the effective interferences between the measured peaks are removed, leading, through a calibration, to clear estimates of radionuclide inventory. While laboratory measurements of stripping ratios are relatively easy to acquire, with detectors placed above small-scale calibration pads of known radionuclide concentrations, the extrapolation to measurements at altitudes where airborne survey detectors are used bring difficulties such as air-path attenuation and greater uncertainties in knowing ground level inventories. Stripping ratios are altitude dependent, and laboratory measurements using various absorbers to simulate the air-path have been used with some success. Full-scale measurements from an aircraft require a suitable location where radionuclide concentrations vary little over the field of view of the detector (which may be hundreds of metres). Monte Carlo simulations offer the potential of full-scale reproduction of gamma-ray transport and detection mechanisms. Investigations have been made to evaluate stripping ratios using experimental and Monte Carlo methods.

Air Pollution, Radioactive↗

PubMed1975

Dose distributions and mean doses in cylindrical cavities of bone marrow on X-ray irradiation.

Dose distributions as well as mean doses to cylindrical cavities of bone marrow on X-ray irradiation have been calculated using (a) Monte Carlo method and (b) a simplified straight line approximation method. The results are compared with earlier published ones. Point doses differ appreciably from the earlier results by as much as 40 percent at some points, whereas mean doses agree to within 10 percent for all the three methods.

Bone Marrow↗

PubMed1987

Statistical evaluation of nonisothermal prediction of drug stability.

Nonisothermal prediction of drug stability based on direct nonlinear estimation of the shelf-life was compared with the isothermal approach. The reliability of the statistics for the estimates of the shelf-life (the time period required for a drug to degrade to 90% remaining at 25 degrees C) and activation energy obtained by the two methods was evaluated by the Monte Carlo method of computer simulations. The accuracy and precision of the estimates obtained by the nonisothermal method depended largely on the experimental conditions, such as experimental periods, sampling time, and temperature rise programs. The uncertainty of the estimates was determined mainly by the extents of drug degradation and temperature change achieved during the experiment. The nonisothermal method needed suitable experimental designs and precise assay methods of drug contents to provide reliable parameter estimates.

Computers↗

PubMed2003

Results supporting calculated wall correction factors for cavity chambers.

Thick walled cavity ionization chambers are used by primary standard laboratories as primary air kerma standards in 137Cs and 60Co gamma-rays. Application of the cavity theory requires correction for the effects of photon attenuation and scattering in the chamber walls. For more than a decade there have been intensive discussions about the validity of wall correction factors determined by more traditional extrapolation methods versus those calculated by Monte Carlo methods. For existing primary standards the alternative methods lead to results that differ by up to 50% of the correction itself. This report presents both experimental and theoretical results which strongly support the validity of calculated wall correction factors. Moreover, it is demonstrated that, in selected cases, the application of a linear extrapolation method leads to errors in the determination of the air kerma reaching up to 13%.

Algorithms↗

PubMed2003

[Analysis of p53 mutational spectra of esophageal squamous cell carcinomas from Linzhou, comparison with esophageal and other cancers from other areas].

OBJECTIVE: To study the etiological clues involved (in esophageal cancer in Linzhou, Henan, a high-incidence area for esophageal cancer) by analyzing p53 mutational spectrum from esophageal precancerous and cancerous lesions. METHODS: Using bolt bioinformatic and Monte Carlo methods to analyze p53 mutation spectra from "The IARC Database of Somatic p53 Mutations in Human Tumors and Cell Lines", "p53 Database at Institute Curic" and to establish a local database based on these data using the FileMark Pro 3.0 software to allow fast and off-line analysis on a PC from the authors' laboratory. RESULTS: We found that esophageal squamous cell carcinomas from Linzhou had a lower prevalence of base substitutions associated with strand bias than those from other areas (32.8% vs 39.8%). However, a higher prevalence of G:C-->A:T transitions at CpG site (29.6% vs16.4%) was found. Esophageal squamous cell carcinomas from Linzhou displayed a distinctive profile of mutation hotspots, including codons 273 (covers 11.3% of all missense mutations), 175 (9.7%), 158 (9.7%), 159 (6.5%) and 282 (6.5%), all of which were at the CpG site. Statistical analysis showed that the p53 mutation profiles between esophageal squamous cell carcinomas from Linzhou and those from other areas were different (P = 0.02). The p53 mutation profiles of esophageal squamous cell carcinomas from Linzhou and from other areas were also different from cancer of the head and neck. CONCLUSION: Data showed that the p53 mutational spectrum of esophageal squamous cell carcinomas from Linzhou baring the characteristics of those caused both by endogenous and exogenous mutagenic agents, suggesting the potential involvement of chronic inflammation, unique dietary habits and carcinogen exposure in the pathogenesis of esophageal squamous cell carcinoma in Linzhou.

Carcinogens, Environmental↗

PubMed2006

[Methods estimating gallbladder volume].

An increasing incidence of liver and biliary tract diseases brings about an increasing necessity of their precise diagnosis. The procedure of estimation of gallbladder volume seems to be useful in ultrasonic examination of gallbladder motility and is widely applied in human medicine all over the world. The methods estimating gallbladder volume can be divided into two groups. The first group comprises the application of rather simple formulas approximating the actual gallbladder shape to the given geometric solid. These methods are precise when the actual gallbladder shape is at least roughly similar to the approximated solid. The second group is more uniform methods since their precision is principally not dependent on the gallbladder shape. The aim of this article was the description and comparison of more or less known methods ascribed to the both groups. Among the methods of the first group, one of the firstly applied and less precise methods usually lowering the results is the method approximating the gallbladder shape to a cone. More common and precise is the ellipsoid method, but this method sometimes also approximates the gallbladder shape not very accurately. The other methods approximating the gallbladder shape to a barrel, cylinder, sphere, trapezoid or frustum of cone and the modifications of some of these methods like the method of cone and ellipsoid, are comparable with the ellipsoid method. The planimetric group of the methods can be included into the second group and in these methods the calculation of the area of the organ longitudinal image is followed by estimation of the organ's volume. Other validated methods are: the random points method based on the known group of mathematical methods (Monte Carlo) representing practically one ofplanimetric methods, the commonly used sum-of-cylinder method and the Simpson method. The reported data indicate that Simpson method is currently the most accurate method estimating the gallbladder volume while the planimetric and sum-of-cylinder methods are believed to be also accurate. The applied method estimating gallbladder volume should be selected in the manner that guarantees its possibly maximal accuracy.

Gallbladder↗

PubMed2002

An EGS4 based Monte Carlo code for the calculation of organ equivalent dose to a modified Yale voxel phantom.

Organ or tissue equivalent dose, the most important quantity in radiation protection, cannot be measured directly. Therefore it became common practice to calculate the quantity of interest with Monte Carlo methods applied to so-called human phantoms, which are virtual representations of the human body. The Monte Carlo computer code determines conversion coefficients, which are ratios between organ or tissue equivalent dose and measurable quantities. Conversion coefficients have been published by the ICRP (Report No. 74) for various types of radiation, energies and fields, which have been calculated, among others, with the mathematical phantoms ADAM and EVA. Since then progress of image processing, and of clock speed and memory capacity of computers made it possible to create so-called voxel phantoms, which are a far more realistic representation of the human body. Voxel (Volume pixel) phantoms are built from segmented CT and/or MRI images of real persons. A complete set of such images can be joined to a 3-dimensional representation of the human body, which can be linked to a Monte Carlo code allowing for particle transport calculations. A modified version of the VOX_TISS8 human voxel phantom (Yale University) has been connected to the EGS4 Monte Carlo code. The paper explains the modifications, which have been made, the method of coupling the voxel phantom with the code, and presents results as conversion coefficients between organ equivalent dose and kerma in air for external photon radiation. A comparison of the results with published data shows good agreement.

Adult↗

PubMed1993

Genetic algorithms for protein folding simulations.

Genetic algorithms methods utilize the same optimization procedures as natural genetic evolution, in which a population is gradually improved by selection. We have developed a genetic algorithm search procedure suitable for use in protein folding simulations. A population of conformations of the polypeptide chain is maintained, and conformations are changed by mutation, in the form of conventional Monte Carlo steps, and crossovers in which parts of the polypeptide chain are interchanged between conformations. For folding on a simple two-dimensional lattice it is found that the genetic algorithm is dramatically superior to conventional Monte Carlo methods.

Algorithms↗

PubMed1998

Rapid modeling of diffuse reflectance of light in turbid slabs.

An efficient and accurate hybrid model of the Monte Carlo technique and the diffusion theory was developed to simulate the diffuse reflectance of light in a turbid slab due to an infinitely narrow light beam. The narrow beam was normally incident on the top surface of the slab. The hybrid model was accurate in modeling the diffuse reflectance near the light source, where the diffusion theory was most inaccurate. The hybrid model was much faster than a pure Monte Carlo method by a factor as great as several hundred, depending on the optical properties, the thickness of the slab, and the settings of the hybrid and the Monte Carlo computations. The computation speed of the hybrid model was insensitive to the optical properties of the medium, in contrast to the pure Monte Carlo technique. The diffusion theory was accurate in modeling both the diffuse reflectance far from the source and the diffuse transmittance. The hybrid model and the diffusion theory should be used in conjunction for efficient and accurate computation of diffuse reflectance and diffuse transmittance.

Diffusion↗

PubMed1998

Monte Carlo simulation of electron cones used in electron beam therapy.

A Siemens Mevatron KV2 accelerator installed at the Royal Adelaide Hospital employs cylindrical solid-walled electron cones for some electron collimation. The cones being used at present result in treatment fields that do not always conform with the International Electrotechnical Commission (IEC) Standards (particularly at high energies). The aim of this project was to simulate the existing cones using Monte Carlo methods in order to evaluate potential cone modifications required to overcome the field irregularities. Simulations were performed using the EGS4 (Electron Gamma Shower version 4, distribution II) Monte Carlo code installed on a DEC Alpha workstation at the University of South Australia. To rigorously simulate the existing electron cones it was necessary to also simulate various components within the treatment head of the linear accelerator. Results of simulations for existing cones were found to be consistent with experimental data. (obtained from Royal Adelaide Hospital beam quality assurance measurements). Two proposed changes to the cones were then simulated and the effects of these alterations were assessed. This study has shown how treatment head simulation techniques can be used to assess the changes in dose distribution that result from alterations to the treatment head and accessories. Within practical engineering constraints modifications to an existing electron collimation system were proposed and theoretically evaluated.

Biophysical Phenomena↗