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At least 307 records · Page 17Linked to original sources
PubMed2002

Computer-simulated radiation dose reduction for abdominal multidetector CT of pediatric patients.

OBJECTIVE: Limiting CT radiation dose is especially critical when imaging children. The purpose of our study was to modify and test an accurate and safe tool for evaluating systematic dose reduction for abdominal multidetector CT (MDCT) in pediatric patients. MATERIALS AND METHODS: After validating the computer-simulation technique with a water phantom, we subjected the original digital scanning data for 26 contrast-enhanced abdominal MDCT scans (120 mA) obtained in infants and children (age range, 1 month-9 years; mean age, 3.1 years) to simulated tube current reduction (100, 80, 60, and 40 mA) by adding noise. this procedure created four additional examinations per child that were identical to the originals except for image noise. The 130 examinations were scored randomly, independently, and without prior knowledge of the children's diagnoses by three radiologists for depiction of high-visibility structures, such as adrenal glands and fat in the intrahepatic falciform ligament, and low-visibility structures, such as the extrahepatic hepatic artery, small intrahepatic vessels, and common bile duct. Aligned rank and Wilcoxon's signed rank tests were used for statistical analyses. RESULTS: Simulated tube current reduction significantly affected the detection of low-visibility structures (p < 0.001). Reduced detection in low-visibility structures was evident at a level less than or equal to 80 mA. No loss of detection in high-visibility structures was found at any tube current level (p > 0.5). CONCLUSION: The results of this computer simulation suggest that accurate abdominal MDCT can be performed in pediatric patients using substantially reduced radiation, depending on the indication for imaging. (In our case, the reduction was between 33% and 67%, depending on whether a high-visibility or low-visibility structure was being assessed.) This simulation technology can be applied to MDCT of other organ systems for systematic evaluation of radiation dose reduction.

Child↗
PubMed2004

Data-driven computer simulation of human cancer cell.

Using the Diagrammatic Cell Language trade mark, Gene Network Sciences (GNS) has created a network model of interconnected signal transduction pathways and gene expression networks that control human cell proliferation and apoptosis. It includes receptor activation and mitogenic signaling, initiation of cell cycle, and passage of checkpoints and apoptosis. Time-course experiments measuring mRNA abundance and protein activity are conducted on Caco-2 and HCT 116 colon cell lines. These data were used to constrain unknown regulatory interactions and kinetic parameters via sensitivity analysis and parameter optimization methods contained in the DigitalCell computer simulation platform. FACS, RNA knockdown, cell growth, and apoptosis data are also used to constrain the model and to identify unknown pathways, and cross talk between known pathways will also be discussed. Using the cell simulation, GNS tested the efficacy of various drug targets and performed validation experiments to test computer simulation predictions. The simulation is a powerful tool that can in principle incorporate patient-specific data on the DNA, RNA, and protein levels for assessing efficacy of therapeutics in specific patient populations and can greatly impact success of a given therapeutic strategy.

Apoptosis↗
PubMed1993

How the transition frequencies of microtubule dynamic instability (nucleation, catastrophe, and rescue) regulate microtubule dynamics in interphase and mitosis: analysis using a Monte Carlo computer simulation.

Microtubules (MTs) in newt mitotic spindles grow faster than MTs in the interphase cytoplasmic microtubule complex (CMTC), yet spindle MTs do not have the long lengths or lifetimes of the CMTC microtubules. Because MTs undergo dynamic instability, it is likely that changes in the durations of growth or shortening are responsible for this anomaly. We have used a Monte Carlo computer simulation to examine how changes in the number of MTs and changes in the catastrophe and rescue frequencies of dynamic instability may be responsible for the cell cycle dependent changes in MT characteristics. We used the computer simulations to model interphase-like or mitotic-like MT populations on the basis of the dynamic instability parameters available from newt lung epithelial cells in vivo. We started with parameters that produced MT populations similar to the interphase newt lung cell CMTC. In the simulation, increasing the number of MTs and either increasing the frequency of catastrophe or decreasing the frequency of rescue reproduced the changes in MT dynamics measured in vivo between interphase and mitosis.

Animals↗
PubMed1990

Computer simulation in the design of local exhaust hoods for shielded metal arc welding.

Computer simulations were used to examine competing exhaust hood configurations for shielded metal arc welding. The welder's breathing zone concentration appears to be an inverse linear function of the computer-predicted hood capture efficiency. Hood aspect ratio, hood flow, and the welder's position relative to the hood all have a significant effect on the breathing zone concentration. The height of the hood above the welding surface showed no significant effect in reducing breathing zone concentration. Further examination of breathing zone concentration as a function of capture efficiency is needed before reliable design methods can be developed using this parameter.

Air Movements↗
PubMed2003

Mechanistic study on analyte focusing by dynamic pH junction in capillary electrophoresis using computer simulation.

Dynamic pH junction is an on-line preconcentration method in capillary electrophoresis (CE) based on electrokinetic focusing of weakly ionic analytes with in large sample volumes in a multisection electrolyte system. In this report, experiments and computer simulations were performed to gain a better insight of the analyte focusing mechanism when a dynamic pH junction was used. A computer program, SIMUL, was used to simulate the band-narrowing process of a group for phenol derivatives under optimized buffer conditions, which were compared with experimental results. Computer simulations revealed the formation of a sharp moving pH boundary within the sample zone causing efficient focusing of long plugs of weakly acidic analytes based on their pKa. These studies offered useful information for understanding the band-narrowing process by control of the depth and lifetime of the moving pH boundary as a function of analyte pKa, sample pH, and injection length. The change in pH of the sample within the capillary was also estimated by measuring the absorbances of an analyte at two different wave-lengths. Optimization of analyte focusing resulted in enhanced detection responses of about 60-450-fold in terms of peak heights for some phenol derivatives' relation to conventional injections. Dynamic pH junction represents a novel approach to control band dispersion (peak width) and selectivity (mobility) of specific analytes for high-resolution CE separations.

Journal Article↗
PubMed1996

Computer simulation of transposable element evolution: random template and strict master models.

It has been proposed that the most extensively studied mammalian retrotransposons replicate by some form of a master template model. This conclusion has been drawn largely from DNA sequence analysis and is based on phylogenetic tree topology, the presence and ordering of shared variants, the degree of divergence between elements within a subfamily, and the shape of the distribution of pairwise differences between elements. To investigate how robust these parameters are as predictors of the model of transposition, computer simulations of the two most extreme transposition models, the Random Template Model and the Strict Master Model, were carried out. A prototype of a computer simulator for studying retrotransposition is presented. The simulator is a versatile digital workbench that maintains DNA sequence data and allows manipulation of a range of factors including reverse transcriptase and in situ mutation rates, transposition template, and transposition rate. All parameters previously used as predictors of the model of transposition were markedly different for the two extreme models when evaluated using large sample sizes of sequences from experiments simulating up to 15 million years of evolution.

Animals↗
PubMed1998

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.

Computer Simulation↗
PubMed1994

Typing of the HLA-DRB3 gene by temperature gradient gel electrophoresis. Prediction of the resolution of four allelic fragments by computational simulation of DNA melting.

Four alleles are currently recognised at the HLA-DRB3 locus (DRB3*0101, DRB3*0201, DRB3*0202 and DRB3*0301). We studied whether 271 bp fragments of the polymorphic second exon, which were prepared using the polymerase chain reaction, could be typed using temperature gradient gel electrophoresis. Thermal stability curves for the allelic DNA molecules were calculated by computer simulation and the results were validated experimentally. The DRB3*0201 and DRB3*0202 derived homoduplexes were predicted to have identical thermal stability. Thus, only three denaturation and relative mobility curves were obtained for the four homoduplex fragments DRB3*0101, DRB3*0201, DRB3*0202 and DRB3*0301. Computational analysis predicted that DRB3*0201 and DRB3*0202 could be distinguished by electrophoresis of artificially generated heteroduplexes. When verified experimentally, the results of the theoretical analyses were confirmed. We conclude, that computational simulation of the melting behaviour of DNA molecules permits the resolution of allelic sequences to be predicted by temperature gradient gel electrophoresis. We also demonstrate that temperature gradient gel electrophoresis is a powerful tool for the assessment of HLA genotypes. It may have wide application in transplantation immunology and in the study of disease associations of allelic variation at the HLA loci.

Alleles↗
PubMed1981

Computer simulation of the urea cycle: trials for an appropriate model.

Several models of the urea cycle with normal and deficient enzymes were simulated on a desk-top computer in order to test if a model fitting data of patients suffering from deficiencies of urea cycle enzymes could be obtained. Discrepancies were notable if only the four enzymes of the urea cycle were used. The effect of adding either n-acetylglutamate synthetase and CPS or the mitochondrial transport system of ornithine and its catabolism to the model were tested singly or combined. The use of the combined model with the rate constants adjusted to recent data of the human enzymes together with a transport system for N-acetylglutamate out of the mitochondrium improved the results. Computer simulations are thus a useful tool for testing concepts of the functioning of the urea cycle.

Acetyltransferases↗
PubMed1990

Computer simulation for optimization of high-performance liquid chromatography of some phenolic pollutants.

Computer simulation was used to optimize high-performance liquid chromatography of phenol and its chloro and nitro derivatives. On the basis of two linear gradient runs of different steepness (RP-18-water + methanol + 1% acetic acid), several simulated gradient runs allowed the optimum gradient programme and flow-rate to be chosen so that the time of analysis could be considerably shortened. Good agreement between simulated and experimental chromatograms was obtained in spite of changes in experimental conditions.

Air Pollutants↗
PubMed2005

The application of computer simulation in the genesis and development of intracranial aneurysms.

The genesis and development of intracranial aneurysm have long been of interest but remain not understood. In the present study we simulate the progression of intracranial aneurysms by constructing a computational model of a curved artery. It is hypothesized that high local wall shear stress above a threshold value will lead to degeneration of the arterial wall mechanical properties. And this degenerative effect may continue even after the wall shear stress has become lower than the threshold, which is referred to as the "time remaining effect" in this study. We performed several groups of studies using both assumptions and aneurysm development is observed as result of the interplay between high wall shear stress, wall degeneration and wall deformation. In the growth of aneurysms with "time-remaining effect", the increase of aneurysmal height accelerates in later steps. It is concluded that computer simulation can yield insight into the understanding of the pathophysiology of aneurysmal initiation and growth, and help in clarifying the role of certain hemodynamic parameters.

Biomechanical Phenomena↗
PubMedDate not supplied

Using a computer simulation program to assess the decision-making process in child health care.

The purpose of this paper was to describe the development and testing of a computer simulation program designed to assess the decision-making process in the public health nurses' work in child health care. The work was based primarily on theories of problem-solving and decision making; on knowledge of child development, health care, and education; and on the soft systems methodology. An authoring program and two simulations were designed and produced at the University of Turku by a team of two nurse researchers, a computer specialist, and three public health nurses. The simulations presented two typical situations encountered by the public health nurses' work in child health care. A total of 61 public health nurses from 11 health centers in the southwestern part of Finland completed the simulations. The public health nurses responded positively to the simulations and the program worked very well. The results revealed some inconsistencies in the decision-making process of the public health nurses with respect to the needs of the child and the family. The public health nurses' decisions were more closely related to the developmental stage of the child than to the unique needs of each family. The simulation is acting to test the public health nurses' ability to make decisions "here and now" but not about caring it forward. These shortcomings can be corrected by asking them to explain their decisions and thoughts after each stage and by tape recording their answers. The findings gave many answers to the question of how the computer simulation program can be developed.

Computer Simulation↗
PubMed1995

Three-dimensional structure of CA1 pyramidal cells in rat hippocampus--optical recording of LSM and computer simulation of fractal structure.

The optical recording of three-dimensional (3-D) reconstruction of CA1 pyramidal cells was derived from the studies on the CA1 region of the hippocampus in adult male Wistar rats. The recording was produced by the Confocal Laser Scan Microscope (LSM-10). The attemption was to outline the morphological neural network of CA1 pyramidal cells organization, following the trail of axo-dendritic connections in 3-D spatial distributions among neurons. The fractal structure of neurons with their dendritic and axonal trees using fractal algorithm was noticed, and 2-18 simulated cells were obtained using PC-486 computer. The simulational cells are similar in morphology to the natural CA1 hippocampal pyramidal cells. Therefore, the exploitation of an advanced neurohistological research technique combining optical recording of the LSM-10 and computer simulation of fractal structure can provide the quantitative fractal structural basis for chaosic dynamics of brain.

Animals↗
PubMed2003

Proactive monitoring and adaptive management of social carrying capacity in Arches National Park: an application of computer simulation modeling.

Public visits to parks and protected areas continue to increase and may threaten the integrity of natural and cultural resources and the quality of the visitor experience. Scientists and managers have adopted the concept of carrying capacity to address the impacts of visitor use. In the context of outdoor recreation, the social component of carrying capacity refers to the level of visitor use that can be accommodated in parks and protected areas without diminishing the quality of the visitor experience to an unacceptable degree. This study expands and illustrates the use of computer simulation modeling as a tool for proactive monitoring and adaptive management of social carrying capacity at Arches National Park. A travel simulation model of daily visitor use throughout the Park's road and trail network and at selected attraction sites was developed, and simulations were conducted to estimate a daily social carrying capacity for Delicate Arch, an attraction site in Arches National Park, and for the Park as a whole. Further, a series of simulations were conducted to estimate the effect of a mandatory shuttle bus system on daily social carrying capacity of Delicate Arch to illustrate how computer simulation modeling can be used as a tool to facilitate adaptive management of social carrying capacity.

Computer Simulation↗
PubMed2005

Direct calculation of the crystal-melt interfacial free energy via molecular dynamics computer simulation.

We review our recent work on the direct calculation of the interfacial free energy, gamma, of the crystal-melt interface via molecular dynamics computer simulation for a number of model systems. The value of gamma as a function of crystal orientation is determined using a thermodynamic integration technique employing moving cleaving walls [Phys. Rev. Lett. 2000, 85, 4751]. The calculation is sufficiently precise to resolve the small anisotropy in gamma, which is crucial in determining the kinetics and morphology of dendritic growth. We report values of gamma for the hard-sphere and Lennard-Jones systems, as well as recent results on the series of inverse-power potentials. For the inverse sixth-, seventh-, and eighth-power systems, we determine gamma for both fcc and bcc crystal structures. For these systems, the bcc-melt gamma is lower than that for fcc crystals by about 25%, consistent with recent experiments and computer simulations on fcc-forming systems that show preferential formation of bcc nuclei in the initial stages of crystallization. In addition, we show that our results give a molecular interpretation of Turnbull's rule, which is the empirical relationship between gamma and the enthalpy of fusion.

Journal Article↗
PubMed2002

The effect of anterior cruciate ligament injury on knee joint function under a simulated muscle load: a three-dimensional computational simulation.

Understanding the biomechanical effect of various factors on knee behavior after anterior cruciate ligament (ACL) injury or reconstruction is instrumental for the development of an optimal surgical treatment of ACL injury that can better restore normal knee function. This paper presents the application of a three-dimensional (3D) computational knee model for parametric studies of knee kinematics in response to simulated muscle loads. The knee model was constructed using the magnetic resonance images and biomechanical experimental data of the same cadaveric human knee specimen. The kinematics of the knee predicted by the computational model was compared with that measured from different specimens in a wide range of loading conditions and flexion angles. In general, the model predictions were within the range of experimental data. The model was then used to predict knee motion, ligament forces, and contact pressure in response to a simulated quadriceps force when the knee was ACL deficient. Partial ACL injury was simulated by reducing the stiffness of the ACL in the model. The results demonstrated that even with a reduction of 75% of the ACL stiffness, the ACL still carried a significant amount of the load (more than 58%) carried by an intact ACL. The kinematics (both tibial translation and rotation) varied less than 20% compared to that of the knee with intact ACL. The 3D computational model can be a powerful tool to simulate different variables that would influence knee function after ACL reconstruction, such as the initial tension of the ACL graft, the insertion sites of the graft, multibundle grafts, graft materials, and various physiological loading conditions.

Anterior Cruciate Ligament↗
PubMed1998

Learning with technology: use of case-based physical and computer simulations in professional education.

This paper describes a multimedia technology project in midwifery education and how it is being developed to improve student learning experiences and outcomes. The role of the university providing quality education relevant to today's world and professional practice is emphasised. A collaborative (Royal Melbourne Institute of Technology and Australian Catholic University) interdisciplinary project 'Pregnancy Simulator: Developing and Enhancing Student Learning of Pregnancy Assessment Skills' was developed with university and direct Commonwealth support. This project consists of a physical simulation of a pregnant woman at term and case-based multimedia computer simulations designed to develop and enhance student learning of abdominal assessment skills. A key feature of the development has been to design a learning experience explicitly on an authoritative theory-based view of teaching, in this case Diana Laurillard's 'Conversational Framework'.

Computer Simulation↗
PubMed1995

Cell cycle progression: computer simulation of uncoupled subcycles of DNA replication and cell growth.

A computer simulation is presented for cell proliferation in a structured cell cycle model. The simulation takes into account the idea that DNA replication and cell growth are two loosely coupled subcycles. The simulation experiments performed offer an explanation for the close correlation often found in interdivision times of sister cell pairs and demonstrate that the exponential slope of the so-called beta-curve is linked to an exponential increase in cell mass. However, in synchronization experiments, a linear increase in mean mass of a cell population develops over time. A channel is opened for a genetic and growth rate influence extending from grandparent to granddaughter. Positive and negative time correlations close to zero still occurred for mother-daughter cell cycles. The computer program leaves two sites in the cell cycle available for gene, molecular and size checkpoints, one in G1 and one in G2. The simulation experiments bridge the gap between models considering (i) size control, (ii) transition probability, and (iii) inherited properties as interpretations of cell cycle progression and are applicable to embryonic cells with the potential to differentiate, somatic cells, and to the kinetics of activation of serum-starved cells. A G0 state is also defined.

Animals↗