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PubMed1991

A computer simulation of the natural history of HIV infection: insights and implications.

Computer simulation of the natural history of HIV infection shows that the progression from a silent infection to serious disease need not depend upon any particular biological event but only requires the passage of time. It likewise illustrates why modest efficacy from an antiretroviral agent can go a long way toward treating HIV infection, but a cure will be difficult to develop.

CD4-Positive T-Lymphocytes↗
PubMed1999

A computer simulation designed for problem-based learning.

OBJECTIVES: As problem-based learning is increasingly used in medical education, there is a growing need to capture the diversity of the events occurring during problem-based learning sessions in order to understand the way in which students learn. The computer simulation described attempts to analyse a posteriori how students reason and learn during such sessions. DESIGN: A computer simulation was designed to perform a detailed analysis of the following features: pattern of information searched, formulation of working hypothesis and identification of learning issues. The program, which has been running successfully for 2 years, was developed using local resources and accepts any clinical problem, provided it is written in a suitable text file format. The program has been applied in the discipline of pathophysiology. SETTING: Faculty of Medical Sciences of Lisbon, Portugal. SUBJECTS: Medical students. RESULTS: An example is presented of how prints were analysed in order to evaluate the 'progression profile' of the students, and a comparison is made with other similar instruments. CONCLUSIONS: The program improved understanding of the relationships between the inquiry strategy and hypothesis formulation and also of how self-learning (triggered by learning issues) influenced further analysis of the cases.

Computer Simulation↗
PubMed2005

Computer simulations of polymer chain structure and dynamics on a hypersphere in four-space.

There is a rapidly growing interest in performing computer simulations in a closed space, avoiding periodic boundary conditions. To extend the range of potential systems to include also macromolecules, we describe an algorithm for computer simulations of polymer chain molecules on S3, a hypersphere in four dimensions. In particular, we show how to generate initial conformations with a bond angle distribution given by the persistence length of the chain and how to calculate the bending forces for a molecule moving on S3. Furthermore, we discuss how to describe the shape of a macromolecule on S3, by deriving the radius of gyration tensor in this non-Euclidean space. The results from both Monte Carlo and Brownian dynamics simulations in the infinite dilution limit show that the results on S3 and in R3 coincide, both with respect to the size and shape as well as for the diffusion coefficient. All data on S3 can also be described by master curves by suitable scaling by the corresponding values in R3. We thus show how to extend the use of spherical boundary conditions, which are most effective for calculating electrostatic forces, to polymer chain molecules, making it possible to perform simulations on S3 also for polyelectrolyte systems.

Journal Article↗
PubMed2002

Laser-tattoo removal--a study of the mechanism and the optimal treatment strategy via computer simulations.

BACKGROUND AND OBJECTIVE: The physical mechanisms for laser-tattoo interactions and the tattoo particle breakup process are not well understood. This study investigates whether the mechanism of the breakup process can be identified via computer simulations and proposes a treatment strategy that can potentially minimize the collateral damage to the surrounding tissues. Note that the "removal" of tattoo particles is defined here as breakup of particles into smaller ones with sizes approaching or smaller than the visible wavelength of light so that they become less visible. STUDY DESIGN/MATERIALS AND METHODS: The radiation-hydrodynamics code LATIS is used for the modeling. We first identify the magnitude of the tensile stress generated inside graphite tattoo particles as functions of laser pulse length and particle size. We then calculate the relationship between the surface laser fluence (defined as the time integrated energy flux) and the tensile strength of the tattoo particle at a given depth. RESULTS: If the laser pulse length is sufficiently short, strong acoustic waves with tensile strengths exceeding the fracture thresholds for graphite are generated. The strength of the wave decreases with particle size and increases as the laser pulse length decreases. Simulation results are in general agreement with clinical studies. Although temperatures of the tattoo particles never reach the melting point, a cavitation bubble around the particle can be formed. The steam generated can get into the cracked particles and induce steam-carbon reactions. Laser energy density decreases rapidly with the skin depth. Therefore, the minimum surface laser fluence, for a given pulse length, required for breaking up tattoo particles at a given skin depth, increases with particle depth. CONCLUSIONS: Computer simulations confirm that the breakup of tattoo particles is photoacoustic. For the same amount of laser energy, a shorter pulse is more efficient. The optimal pulse length is approximately 10-100 picosecond to minimize the laser fluence and the collateral damage. It is more difficult to break up the smallest tattoo particles that have diameters smaller than 10 nm; however, smaller particles are less important because they are less visible. Tissue surrounding the tattoo particles can be damaged by cavitation bubbles. These bubbles could be the cause of the empty vacuoles in the ash-white lesions throughout the dermis seen after treatment. Steam-carbon reactions can be induced. Particles then become grossly transparent because of this reaction. Different laser intensity should be used for pigments at different depths in order to minimize the collateral damage to the dermis.

Computer Simulation↗
PubMed2006

Computer-simulated assessment of methods of transporting severely injured individuals in disaster--case study of an airport accident.

A system utilizing computer simulations was developed in order to compare (1) situations wherein critically wounded individuals are, at first, ranked and classified into subgroups based on criticalness of the wounds, and then be evaluated and re-ordered within the subgroups before transported to hospitals, with (2) those situations in which the conventional method of transport was employed. The objective of the study is to infer whether there is a further possibility for enhancing the possibility of the wounded individual's survival rate at the time of arrival at the hospital. The variables that are required to be entered include the number of patient subgroups, the number of patients in each of the subgroups, the total number of patients to be transported, the time required to assess the severity of each patient, the speed of the ambulance, the interval between the ambulances' arrivals and departures, and the distance between the site at which the transportation begins and the destination or the hospital. Utilizing the same system, a virtual simulation of a large-scale disaster at airport was used as sample data. As a result, it was confirmed that the survival rate would improve under certain conditions, if the values for some of the variables, such as geographic conditions, were altered and then calculated.

Accidents↗
PubMed1991

Computer simulations as a measure of nursing students' decision-making skills.

Use of computer simulations was studied as a strategy to evaluate clinical decision-making skills of 64 senior baccalaureate nursing students who were randomly assigned to experimental and control groups. All students completed Kolb's Learning Style Inventory, a pre- and posttest that was a computer assisted instruction (CAI) clinical simulation specific to the student's clinical placement, and a 36 item attitudinal and evaluative questionnaire developed for the study. The experimental group complete three additional simulations over a 7 week period. Change scores from pre- and posttests were analyzed to determine: 1) if students completing a CAI series demonstrated higher achievement on information-gathering and decision-making skills than students who did not complete the series; 2) if there was a correlation between achievement and clinical grades; and 3) if there was a relationship between achievement and a particular learning style. Although all students demonstrated that significant learning had occurred during the semester, there was no difference between the students completing the full CAI series and those who did not. Students who made significant improvements in decision-making scores also earned higher clinical grades. Success on the CAI series was found to be independent of learning style. Most students expressed positive attitudes about CAI.

Computer Simulation↗
PubMed2006

A computer simulation study comparing lesion detection accuracy with digital mammography, breast tomosynthesis, and cone-beam CT breast imaging.

Although conventional mammography is currently the best modality to detect early breast cancer, it is limited in that the recorded image represents the superposition of a three-dimensional (3D) object onto a 2D plane. Recently, two promising approaches for 3D volumetric breast imaging have been proposed, breast tomosynthesis (BT) and CT breast imaging (CTBI). To investigate possible improvements in lesion detection accuracy with either breast tomosynthesis or CT breast imaging as compared to digital mammography (DM), a computer simulation study was conducted using simulated lesions embedded into a structured 3D breast model. The computer simulation realistically modeled x-ray transport through a breast model, as well as the signal and noise propagation through a CsI based flat-panel imager. Polyenergetic x-ray spectra of Mo/Mo 28 kVp for digital mammography, Mo/Rh 28 kVp for BT, and W/Ce 50 kVp for CTBI were modeled. For the CTBI simulation, the intensity of the x-ray spectra for each projection view was determined so as to provide a total average glandular dose of 4 mGy, which is approximately equivalent to that given in conventional two-view screening mammography. The same total dose was modeled for both the DM and BT simulations. Irregular lesions were simulated by using a stochastic growth algorithm providing lesions with an effective diameter of 5 mm. Breast tissue was simulated by generating an ensemble of backgrounds with a power law spectrum, with the composition of 50% fibroglandular and 50% adipose tissue. To evaluate lesion detection accuracy, a receiver operating characteristic (ROC) study was performed with five observers reading an ensemble of images for each case. The average area under the ROC curves (Az) was 0.76 for DM, 0.93 for BT, and 0.94 for CTBI. Results indicated that for the same dose, a 5 mm lesion embedded in a structured breast phantom was detected by the two volumetric breast imaging systems, BT and CTBI, with statistically significant higher confidence than with planar digital mammography, while the difference in lesion detection between BT and CTBI was not statistically significant.

Algorithms↗
PubMed1987

Computer simulation of the variable agarose fiber dimensions on the basis of mobility data derived from gel electrophoresis and using the Ogston theory.

Agarose gel electrophoresis of viruses and proteins was evaluated for estimating fiber dynamics of agarose by computer simulation based on the extended Ogston theory. By introducing functions, in place of previously used constant parameters, into the equations derived from the Ogston theory it was demonstrated that the effective fiber properties are variable as a function of both gel concentration and the size of the particle passing through the gel. This variability accounts for the curvature of plots of log(mobility) vs gel concentration in agarose gel electrophoresis as well as for the apparent dichotomy between fiber properties obtained from the electrophoresis of either viruses or proteins. Specifically, computer simulation based on the electrophoretic mobility values of five viruses and seven proteins by use of an eight (gel-specific) parameter model yielded functions relating gel concentration and/or particle size with electrophoretic mobility of particles, the retardation coefficient, K'R, and effective fiber radius, length, and volume. The simulations give further insights into, as well as mathematical basis for, a number of previously made assumptions (such as variation of agarose fiber structure with gel concentration, variation of fiber volume with particle size, continuity of the K'R vs radius plot from 0 to 45 nm), thus demonstrating the continued usefulness of the Ogston model. The mathematical model provides the elements for an improved method for the determination of particle size, charge, and potentially shape by agarose gel electrophoresis, and can be regarded as the basis for future elaboration of a computer program for the routine determination of these parameters.

Computer Simulation↗
PubMed2005

Carbamazepine extended-release capsules vs. oxcarbazepine: computer simulations of the effect of missed doses on drug plasma concentrations.

OBJECTIVE: Plasma concentrations of antiepileptic drugs (AEDs) can vary and are not always an indication of clinical utility. However, adverse event occurrence can be correlated to fluctuations in plasma drug levels that occur with varying dosing regimens of the many AEDs. In this study, we present the results of computer simulations of plasma concentrations of the AEDs carbamazepine (CBZ) extended-release capsules (CBZ-ERC) (Carbatrol) and oxcarbazepine (OXC). RESEARCH DESIGN AND METHODS: A one-compartment open model with first-order absorption and elimination was generated from the results of a previous study measuring plasma concentrations following one 400 mg fasting dose of CBZ-ERC. This model was used to simulate plasma concentrations of CBZ following multiple 400 mg doses of CBZ-ERC at 12-hour intervals, and then when a missed dose is taken 3, 6, or 9 hours late; when two doses are taken at one time; and when a single dose is taken at the time of the next dosing. In comparison, similar modeling was done for monohydroxy derivative (MHD) of OXC at doses of 600 or 1200 mg. RESULTS: Plasma drug concentrations after 24 hours without medication were 4.1 mg/L for CBZ-ERC, 8 mg/L for 600 mg OXC, and 16 mg/L for 1200 mg OXC. If a patient was to take only a single dose 24 hours late, it would take 24 hours to reach steady-state trough values for CBZ-ERC, 36 hours for 600 mg OXC, and 2 days for 1200 mg OXC. The trough plasma concentration following a missed dose and the peak plasma concentration following a double dose (administered 12 hours after the missing of a dose) differed by a factor of two in the CBZ-ERC simulation, compared with a factor of three in both OXC simulations. CONCLUSIONS: The ultimate goal of antiepileptic therapy is a seizure-free state without side effects. The current computer simulation study indicates that AEDs such as CBZ-ERC and OXC, which produce relatively stable plasma concentrations, should be useful in attaining this goal. Nonetheless, simulated plasma concentrations resulting from CBZ-ERC treatment tended to oscillate less dramatically compared with simulated plasma concentrations resulting from treatment with 600 or 1200 mg OXC.

Anticonvulsants↗
PubMed1989

Regulation of the cytoplasmic pH by a proton-translocating ATPase in Streptococcus faecalis (faecium). A computer simulation.

Earlier work from this laboratory led to the proposal that the cytoplasmic pH of streptococcal cells is regulated solely by changes in the amount and activity of a proton-translocating ATPase, F1F0 complex [Kobayashi, H., Suzuki, T. & Unemoto, T. (1986) J. Biol. Chem. 261, 627-630]. We have now examined the proposal with the aid of computer simulation. We find that an increase in the amount of the H+-ATPase is necessary for pH regulation and is sufficient to maintain a constant steady-state cytoplasmic pH. An increase in H+-ATPase activity is insufficient by itself to maintain a constant cytoplasmic pH, but suppresses the initial fluctuation of the pH. When both variations were allowed, the simulated cytoplasmic pH remained constant despite large perturbations, suggesting that this regulatory system has ample capacity to compensate for pH changes. The present work shows that a computer simulation is a useful way to examine a model for biological regulatory system; application of the simulation to other regulatory systems is discussed.

Computer Simulation↗
PubMed2004

[Effect of motion correction associated with echo train length and number of blades in propeller MRI-computer simulation].

The PROPELLER (periodically rotated overlapping parallel lines with enhanced reconstruction) MRI method is available with a technique for motion correction. We studied changes in correction according to differences in echo train length (ETL) and number of blades, and measured correction accuracy according to linear translation and rotation, using computer simulation. A T(2)-weighted axial image of the head taken by FSE was utilized as the basic MR image. We reconstructed other images with differences in quantity of motion, ETL, and number of blades, also using computer simulation. After motion correction was performed, we measured correction accuracy with cross-correlation to the basic image. The method of motion correction was performed by the conversion of k-space data for each blade step using 2D Fourier-transform. After motion correction of the obtained image had been carried out, the image was converted to k-space data using reverse Fourier-transform. For data of 30 pixels with horizontal translation, cross-correlation coefficients for the stationary image were 0.6 for FSE without motion correction, 0.74 for the PROPELLER (ETL 8, blades 32) image without motion correction, and 0.99 for the PROPELLER (ETL 8, blades 32) image with motion correction. For data of 24 degrees with rotation, cross-correlation coefficients were 0.38 for FSE without motion correction, 0.53 for the PROPELLER (ETL 8, blades 32) image without motion correction, and 0.93 for the PROPELLER (ETL 8, blades 32) image with motion correction. The cross-correlation coefficient of liner translation is higher than its rotation. Correction accuracy was better with larger numbers of ETL than without motion correction. The spatial resolution of the image was decreased in the corrected image more by rotation than linear translation. This study indicated that the PR method was able to inspect the imaging technique with little influence on movement.

Computer Simulation↗
PubMedDate not supplied

Evaluating the capability of information technology to prevent adverse drug events: a computer simulation approach.

BACKGROUND: The annual cost of morbidity and mortality due to medication errors in the U.S. has been estimated at $76.6 billion. Information technology implemented systematically has the potential to significantly reduce medication errors that result in adverse drug events (ADEs). OBJECTIVE: To develop a computer simulation model that can be used to evaluate the effectiveness of information technology applications designed to detect and prevent medication errors that result in adverse drug effects. METHODS: A computer simulation model was constructed representing the medication delivery system in a hospital. STELLA, a continuous simulation software package, was used to construct the model. Parameters of the model were estimated from a study of prescription errors on two hospital medical/surgical units and used in the baseline simulation. Five prevention strategies were simulated based on information obtained from the literature. RESULTS: The model simulates the four stages of the medication delivery system: prescribing, transcribing, dispensing, and administering drugs. We simulated interventions that have been demonstrated in prior studies to decrease error rates. The results suggest that an integrated medication delivery system can save up to 1,226 days of excess hospitalization and $1.4 million in associated costs annually in a large hospital. The results of the analyses regarding the effects of the interventions on the additional hospital costs associated with ADEs are somewhat sensitive to the distribution of errors in the hospital, more sensitive to the costs of an ADE, and most sensitive to the proportion of medication errors resulting in ADEs. CONCLUSIONS: The results suggest that clinical information systems are potentially a cost-effective means of preventing ADEs in hospitals and demonstrate the importance of viewing medication errors from a systems perspective. Prevention efforts that focus on a single stage of the process had limited impact on the overall error rate. This study suggests that system-wide changes to the medication delivery system are required to drastically reduce mediation errors that may result in ADEs in a hospital setting.

Clinical Pharmacy Information Systems↗
PubMedDate not supplied

Computer simulations of patellofemoral joint surgery. Patient-specific models for tuberosity transfer.

BACKGROUND: Variable clinical outcomes of tibial tuberosity transfer surgery have been reported. HYPOTHESES: The biomechanical outcome of surgery is patient-specific; no single procedure produces superior results for all patients. Use of patient-specific computer models can optimize choice of procedure. STUDY DESIGN: Computer simulation study using clinical data. METHODS: We used patient-specific multibody models of the patellofemoral joints of 20 patients with a diagnosis of patellar subluxation and osteoarthritis. Four tibial tuberosity transfer procedures (two anterior and two anteromedial) were simulated for each patient and compared with their preoperative model. RESULTS: When results for all patients were averaged, all simulated operations produced a statistically significant decrease in surface-wide mean contact stress, although no significant difference was found among them. CONCLUSIONS: The simulated surgical outcomes were patient-specific: no single procedure was consistently superior at decreasing peak or mean stress and each procedure produced a potentially detrimental outcome, an increase in either mean stress or peak stress, in at least one patient. CLINICAL RELEVANCE: Computer simulation may serve as a valuable tool for tailoring procedures to specific patients.

Biomechanical Phenomena↗
PubMed1993

Adaptive bone remodeling around bonded noncemented total hip arthroplasty: a comparison between animal experiments and computer simulation.

Severe loss of bone related to stress-shielding is one problem threatening the long-term integrity of noncemented total hip arthroplasty. It is widely accepted that this phenomenon is caused by adaptive bone remodeling according to Wolff's law. Recently, quantitative bone-remodeling theories have been proposed, suitable for use in computer-simulation models in combination with finite-element codes, which can be applied to simulate the long-term effect of the remodeling process. In the present paper, the results of such a computer simulation are compared with those in an animal experiment. A three-dimensional finite-element model was constructed from an animal experimental configuration concerning the implantation of a fully coated femoral hip prosthesis in dogs. The simulation results of the adaptive bone-remodeling process (geometric adaptations at the periosteal surface and density adaptations within the cancellous bone) were compared with cross-sectional measurements of the canine femurs after 2 years of follow-up. The detailed comparison showed that long-term changes in the morphology of bone around femoral components of total hip replacements can be fully explained with the present quantitative adaptive bone-remodeling theory.

Adaptation, Physiological↗
PubMedDate not supplied

Computer simulation of plasma exchange therapy in autoimmune disease.

Computer simulation of plasma exchange in autoimmune disease shows that a single treatment may reduce the amount of antibody bound to antigen by as much as 60-80%. The reduction is greatest when autoantibody is of low affinity and there is an excess of antibody compared to antigen.

Anemia, Hemolytic, Autoimmune↗
PubMed1996

A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature.

An assessment of 10 tetrameric restriction enzymes (TREs) was conducted by using a computer-simulated restriction fragment length polymorphism (RFLP) analysis for over 100 proximally and distally related bacterial small-subunit (SSU) rRNA gene sequences. Screening SSU rDNA clone libraries with TREs has become an effective strategy because of logistic simplicity, commercial availability, and economy. However, the rationale for selecting the type and number of TREs has not been systematically evaluated. Our objective was to identify the optimal combination of TREs for RFLP screening of cloned SSU rRNA genes from undefined bacterial clone libraries. After computer-simulated TRE digestion, the resultant fragments were categorized on the basis of the frequency of different restriction fragment size classes. Three groups of distribution patterns for the TREs were determined and further examined via graphical exploratory data analysis. The RFLP size-frequency distribution data for each group of enzymes were then used to infer phylogenetic relationships via the neighbor-joining method. The resulting bootstrap values and the correct placement of node bifurcations were used as additional criteria to evaluate the efficacy of the selected TREs. These RFLP data were compared with known phylogenetic relationships based on SSU rRNA sequence analysis as defined by the Ribosomal Database Project. A heuristic approach testing random combinations of TREs showed that three or more TRE combinations detected > 99% of the operational taxonomic units (OTUs) within the model data set. OTUs that remained undetected after three TRE treatments had a median sequence similarity of 96.1%. Of the 10 restriction enzymes examined, HhaI, RsaI, and BstUI (group 3) were the most efficacious at detecting and differentiating bacterial SSU rRNA genes on the basis of their ability to correctly classify OTUs. Group 3 TREs are therefore recommended for screening in studies using bacterial SSU rRNA genes as descriptors of in situ microbial diversity.

Computer Simulation↗
PubMed2005

Calculation of the properties of digital mammograms using a computer simulation.

A Monte Carlo computer model of mammography has been developed to study and optimise the performance of digital mammographic systems. The program uses high-resolution voxel phantoms to model the breast, which simulate the adipose and fibroglandular tissues, Cooper's ligaments, ducts and skin in three dimensions. The model calculates the dose to each tissue, and also the quantities such as energy imparted to image pixels, noise per image pixel and scatter-to-primary (S/P) ratios. It allows studies of the dependence of image properties on breast structure and on position within the image. The program has been calibrated by calculating and measuring the pixel values and noise for a digital mammographic system. The thicknesses of two components of this system were unknown, and were adjusted to obtain a good agreement between measurement and calculation. The utility of the program is demonstrated with the calculations of the variation of the S/P ratio with and without a grid, and of the image contrast across the image of a 50-mm-thick breast phantom.

Adipose Tissue↗