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PubMed1995

Computer simulation modelling and visualization of 3D architecture of biological tissues. Simulation of the evolution of normal, metaplastic and dysplastic states of the nasal epithelium.

Recent technical improvements, such as 3D microscopy imaging, have shown the necessity of studying 3D biological tissue architecture during carcinogenesis. In the present paper a computer simulation model is developed allowing the visualization of the microscopic biological tissue architecture during the development of metaplastic and dysplastic lesions. The static part of the model allows the simulation of the normal, metaplastic and dysplastic architecture of an external epithelium. This model is associated to a knowledge base which contains only data on the nasal epithelium. The latter has been well studied by numerous authors and its lesional states are well known. An inference engine allows the initialization of the static model parameters. A statistical comparison between simulated epithelia and real epithelia is achieved by adjusting the parameter values during the simulation. The dynamic part of the model allows the simulation of a growth process on a 3D representation based on the static model. The main hypothesis is that nasal epithelium is submitted to a continuous transformation from normal to cancer through metaplasia and dysplasia. The evolution of each cell (represented by its nucleus) depends on its local environment and also on its heritage from its mother-cell. Simulation of tissue renewal of the nasal pseudostratified epithelium has been achieved. The evolution from normal to hyperplasia has been simulated. After modification of the cell cycle modelling, the simulation of the development of metaplastic foci has been obtained.

Cell Cycle↗
PubMed1998

Simulating a memory impairment: can amnesics implicitly outperform simulators?

OBJECTIVES: The purpose of this study was to examine the effectiveness of a variety of tests in differentiating simulating test performances from genuine memory-impaired and normal (control) test performances. DESIGN: A simulation design was implemented, based on an analogue design in which normal participants were given experimental instructions to feign a mental impairment and are compared to (a) other normal participants with instructions to perform honestly, and (b) a comparison group, for example, acquired brain-injured persons, with similar instructions. METHOD: Forty individuals comprised the simulating and control group and all participants were randomly assigned to the simulating and control groups. Twenty memory-impaired patients, all of whom had been diagnosed as suffering from a memory impairment following acquired brain damage, participated as the memory-impaired control group. The simulation group was directed to imitate a person with a memory impairment. The primary outcome measure involved identifying those tests, if any, where simulators were significantly different from normal and memory-impaired participants. RESULTS: On 5 of the 15 tasks administered, simulators performed significantly differently from normal and memory-impaired participants. Of these 5 tasks, the coin-in-the-hand, when administered in conjunction with the autobiographical interview, identified 95 per cent of the simulators without misclassifying any of the memory-impaired or normal participants. CONCLUSION: It is suggested that these two tests, when administered jointly, might be of use in clinical settings to assist in the detection of malingerers.

Adult↗
PubMed2005

[Comparison of classic simulation and virtual simulation in breast irradiation: prospective study on 14 patients].

PURPOSE: To compare conventional 2D simulation and virtual simulation on 14 patients with breast cancer. PATIENTS AND METHODS: Patients were simulated for treatment using standard procedure. They subsequently underwent CT scan in the treatment position. The CTV was defined as breast tissue. The PTV was obtained by adding a 3D margin of 1 cm around CTV. Organs at risk (lungs and heart) were outlined. Ballistics and dose distribution obtained with the two planning methods were compared. RESULTS: With conventional simulation, 95% of CTV received 95% of the dose prescribed. Virtual simulation significantly improved dosimetric coverage of PTV without increasing irradiation volume of lung and heart. In 2D simulation, using three slices allowed optimisation by adjusting wedge angle. The five-slice plan was a much better predictor of the maximum dose regions when compared to the three-slice plan. Using entire CT data didn't give any benefit. CONCLUSION: Variations in CTV delineation and PTV definition limit interest of virtual simulation. In classic simulation, a 5 CT slice-plan can be used to optimise dose distribution.

Breast Neoplasms↗
PubMed2005

A human factors analysis of technical and team skills among surgical trainees during procedural simulations in a simulated operating theatre.

BACKGROUND: High-risk organizations such as aviation rely on simulations for the training and assessment of technical and team performance. The aim of this study was to develop a simulated environment for surgical trainees using similar principles. METHODS: A total of 27 surgical trainees carried out a simulated procedure in a Simulated Operating Theatre with a standardized OR team. Observation of OR events was carried out by an unobtrusive data collection system: clinical data recorder. Assessment of performance consisted of blinded rating of technical skills, a checklist of technical events, an assessment of communication, and a global rating of team skills by a human factors expert and trained surgical research fellows. The participants underwent a debriefing session, and the face validity of the simulated environment was evaluated. RESULTS: While technical skills rating discriminated between surgeons according to experience (P = 0.002), there were no differences in terms of the checklist and team skills (P = 0.70). While all trainees were observed to gown/glove and handle sharps correctly, low scores were observed for some key features of communication with other team members. Low scores were obtained by the entire cohort for vigilance. Interobserver reliability was 0.90 and 0.89 for technical and team skills ratings. CONCLUSIONS: The simulated operating theatre could serve as an environment for the development of surgical competence among surgical trainees. Objective, structured, and multimodal assessment of performance during simulated procedures could serve as a basis for focused feedback during training of technical and team skills.

Attention↗
PubMed1997

Ab initio protein folding simulations with genetic algorithms: simulations on the complete sequence of small proteins.

Ab-initio folding simulations have been performed on three small proteins using a genetic algorithm- (GA-) based search method which operates on an all atom representation. Simulations were also performed on a number of small peptides expected to be independent folding units. The present genetic algorithm incorporates the results of developments made to the method first tested in CASP1. Additional operators have been introduced into the search in order to allow the simulation of longer sequences and to avoid the simulation of longer sequences and to avoid premature free energy convergence. Secondary structure information derived from a consensus of eight methods and Monte Carlo simulations on sets of homologous sequences has been used to bias the starting populations used in the GA simulations. For the fragment simulations, the results generally have approximately correct local structure, but tend to be too compact, leading to poor RMS error values. One of the three small protein structures has the topology and most of the general organization correct, although many of the details are incorrect.

Algorithms↗
PubMed1995

Simulation of micropopulations in epidemiology: tutorial. 4. Evaluations of simulation models. A series of tutorials illustrated by coronary heart disease models.

The first tutorial in this series (Ackerman E: Simulation of micropopulations in epidemiology: Tutorial 1. Simulation: an introduction, Int J Biomed Comput, 36 (1994) 229-238) introduces the general approach of simulation of micropopulation models of coronary disease using Monte Carlo techniques. The modeling process includes the selection of functional forms to represent the probability of state transfers. Alternative functional forms are described in the second tutorial (Ackerman E: Simulation of micropopulations in epidemiology: Tutorial 2. Analytic forms of event probabilities, Int J Biomed Comput, 37 (1994) 139-149). The third tutorial (Ackerman E: Simulation of micropopulations in epidemiology: Tutorial 3. Simulation model evaluation methods, Int J Biomed Comput, 37 (1994) 195-204) considers the actual risk factors used in the models and the compartmentalization of the population. However, that tutorial emphasizes the methods of evaluating different models of coronary heart disease. In the current tutorial, the evaluation methods are applied to the models previously introduced. Essential to this is the concept of degrees of freedom. Limitations of that concept are discussed with specific reference to models of coronary heart disease. The estimation of optimal values for the risk coefficients is considered further. The various tests of appropriateness are applied to specific models and the role of sensitivity analysis is further illustrated. Discussions of intervention strategies and their simulation is deferred to the following tutorial.

Adult↗
PubMed2006

Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems.

An ability to accurately simulate the dynamic behavior of concentrated macromolecular solutions would be of considerable utility in studies of a wide range of biological systems. With this goal in mind, a Brownian dynamics (BD) simulation method is reported here that allows systems to be modeled that comprise in excess of 1000 protein molecules, all of which are treated in atomic detail. Intermolecular forces are described in the method using an energy function that incorporates electrostatic and hydrophobic interactions and that is calibrated to reproduce experimental thermodynamic information with a single adjustable parameter. Using the method, BD simulations have been performed over a wide range of pH and ionic strengths for three proteins: hen egg white lysozyme (HEWL), chymotrypsinogen, and T4 lysozyme. The simulations reproduce experimental trends in second virial coefficients (B(22)) and translational diffusion coefficients, correctly capture changes in B(22) values due to single amino acid substitutions, and reveal a new explanation for the difficulties reported previously in the literature in reproducing B(22) values for protein solutions of very low ionic strength. In addition, a strong correlation is found between a residue's probability of being involved in a protein-protein contact in the simulations and its probability of being involved in an experimental crystal contact. Finally, exploratory simulations of HEWL indicate that the simulation model also gives a promising description of behavior at very high protein concentrations (approximately 250 g/L), suggesting that it may provide a suitable computational framework for modeling the complex behavior exhibited by macromolecules in cellular conditions.

Bacteriophage T4↗
PubMed1990

Using molecular dynamics simulations on crambin to evaluate the suitability of different continuum dielectric and hydrogen atom models for protein simulations.

Molecular dynamics simulations of enzymes with enough explicit waters of solvation to realistically account for solute-solvent interactions can burden the computational resources required to perform the simulation by more than two orders of magnitude. Since enzyme simulations even with an implicit solvation model can be imposing for a supercomputer, it is important to assess the suitability of different continuum dielectric models for protein simulations. A series of 100-picosecond molecular dynamics simulations were performed on the X-ray crystal structure of the protein crambin to examine how well computed structures, obtained using seven continuum dielectric and two hydrogen atom models, agreed with the X-ray structure. The best level of agreement between computed and experimental structures was obtained using a constant dielectric of 2 and the all-hydrogen model. Continuum dielectric models of 1, 1r, and 2r also led to computed structures in reasonably good agreement with the X-ray structure. In all cases, the all-hydrogen model gave better agreement than the united atom model, although, in one case, the difference was not significant. Dielectric models of 4, 80, and 4r with either hydrogen model yielded significantly poorer fits. It is especially noteworthy that the observed trends did not semiquantitatively converge until about 50 picoseconds into the simulations, suggesting that validation studies for protein calculations based on energy minimizations or short simulations should be viewed with caution.

Computer Simulation↗
PubMed2003

Research use of the AIDA www.2aida.org diabetes software simulation program: a review--part 2. Generating simulated blood glucose data for prototype validation.

The purpose of this review is to describe research applications of the AIDA diabetes software simulator. AIDA is a computer program that permits the interactive simulation of insulin and glucose profiles for teaching, demonstration, and self-learning purposes. Since March/April 1996 it has been made freely available on the Internet as a noncommercial contribution to continuing diabetes education. Up to May 2003 well over 320,000 visits have been logged at the main AIDA Website--www.2aida.org--and over 65,000 copies of the AIDA program have been downloaded free-of-charge. This review (the second of two parts) overviews research projects and ventures, undertaken for the most part by other research workers in the diabetes computing field, that have made use of the freeware AIDA program. As with Part 1 of the review (Diabetes Technol Ther 2003;5:425-438) relevant research work was identified in three main ways: (i) by personal (e-mail/written) communications from researchers, (ii) via the ISI Web of Science citation database to identify published articles which referred to AIDA-related papers, and (iii) via searches on the Internet. Also, in a number of cases research students who had sought advice about AIDA, and diabetes computing in general, provided copies of their research dissertations/theses upon the completion of their projects. Part 2 of this review highlights some more of the research projects that have made use of the AIDA diabetes simulation program to date. A wide variety of diabetes computing topics are addressed. These range from learning about parameter interactions using simulated blood glucose data, to considerations of dietary assessments, developing new diabetes models, and performance monitoring of closed-loop insulin delivery devices. Other topics include evaluation/validation research usage of such software, applying simulated blood glucose data for prototype training/validation, and other research uses of placing technical information on the Web. This review confirms an unexpected but useful benefit of distributing a medical program, like AIDA, for free via the Internet--demonstrating how it is possible to have a synergistic benefit with other researchers--facilitating their own research projects in related medical fields. A common theme that emerges from the research ventures that have been reviewed is the use of simulated blood glucose data from the AIDA software for preliminary computer lab-based testing of other decision support prototypes. Issues surrounding such use of simulated data for separate computer prototype testing are considered further.

Blood Glucose↗
PubMed1996

A totally integrated simulation technique for three-field breast treatment using a CT simulator.

A method was devised to simulate patients with breast cancer in the actual treatment position utilizing a diagnostic CT spiral scanner, 3-D Image Workstation for virtual simulation, and a laser coordinate system to transfer planning parameters to the patient's skin. It was desired to produce non-divergent tangential beams through the lung as well as a matched line for tangential and supraclavicular fields. The patients were immobilized in an Alpha CradleTM cast. Radio-opaque markers were placed on the superior, inferior, medial, and lateral margins of the field so as to afford appropriate initial field set-up approximations. The patient was scanned. The data set was then transferred to the workstation where an isocenter was chosen. The patient was marked. Virtual simulation was then performed. This method employed a half beam technique for the posterior edge of the tangential fields. Table rotation and blocking of the superior margin of the tangential fields were used to produce a vertical edge to match a supraclavicular field. Using a beam's eye view the lateral tangent was matched to the medial exit. A digitally reconstructed radiograph was created to define the tangent fields and place the supraclavicular block. Our initial experience with 50 patients verifies that this is a reproducible and accurate technique. Time required for immobilization and tangential field simulation is approximately 30 minutes. Data is available for 3-D treatment planning or 2-D treatment planning on a reconstructed transverse slice angled to match the collimator angle through the patient. Using a CT simulator for simulation of breast cancer affords accuracy of at least equal magnitude to conventional simulators as determined by beam films and ease of set-up. This technique also affords greater ease in changing treatment parameters without having to resimulate the patient.

Breast Neoplasms↗
PubMed1995

A simulation model of the epidemiology of urban dengue fever: literature analysis, model development, preliminary validation, and samples of simulation results.

We have developed a pair of stochastic simulation models that describe the daily dynamics of dengue virus transmission in the urban environment. Our goal has been to construct comprehensive models that take into account the majority of factors known to influence dengue epidemiology. The models have an orientation toward site-specific data and are designed to be used by operational programs as well as researchers. The first model, the container-inhabiting mosquito simulation model (CIMSiM), a weather-driven dynamic life-table model of container-inhabiting mosquitoes such as Aedes aegypti, provides inputs to the tranmission model, the dengue simulation model (DENSiM); a description and validation of the entomology model was published previously. The basis of the transmission model is the simulation of a human population growing in response to country- and age-specific birth and death rates. An accounting of individual serologies is maintained by type of dengue virus, reflecting infection and birth to seropositive mothers. Daily estimates of adult mosquito survival, gonotrophic development, and the weight and number of emerging females from the CIMSiM are used to create the biting mosquito population in the DENSiM. The survival and emergence values determine the size of the population while the rate of gonotrophic development and female weight estimates influence biting frequency. Temperature and titer of virus in the human influences the extrinsic incubation period; titer may also influence the probability of transfer of virus from human to mosquito. The infection model within the DENSiM accounts for the development of virus within individuals and its passage between both populations. As in the case of the CIMSiM, the specific values used for any particular phenomenon are on menus where they can be readily changed. It is possible to simulate concurrent epidemics involving different serotypes. To provide a modicum of validation and to demonstrate the parameterization process for a specific location, we compare simulation results with reports on the nature of epidemics and seroprevalence of antibody in Honduras in low-lying coastal urbanizations and Tegucigalpa following the initial introduction of dengue-1 in 1978 into Central America. We conclude with some additional examples of simulation results to give an indication of the types of questions that can be investigated with the models.

Adolescent↗
PubMed2006

Simulator-assisted setting of scan protocols for X-ray CT: development and clinical usefulness of the Scan Plan Simulator.

To assist in the selection of complicated computed tomography (CT) scan protocols and to obtain stable image SD values, prototype "Scan Plan Simulator" software with the following functions was developed and evaluated. 1) The image SD value that will be obtained in actual scanning is estimated by entering the patient's body size and scan protocol, after which a simulated image is displayed so that the estimated image SD value can be checked. The exposure dose can also be estimated in the Scan Plan Simulator. 2) The appropriate tube current is automatically set by entering the required image SD value. We evaluated the accuracy of the Scan Plan Simulator by comparing the simulation results with the image SD values and exposure dose obtained in actual scanning and assessed the usefulness of this method using Monte Carlo simulation based on body thickness data obtained in clinical examinations. The results showed that the Scan Plan Simulator not only stabilizes image SD by minimizing the effects of body size but also permits the exposure dose to be reduced by optimizing tube current.

Body Constitution↗
PubMed1976

Computer simulation of the precordial QRS complex: effects of simulated changes in ventricular wall thickness and volume.

The cardiac electric field generated by depolarization of the human ventricle is simulated with a computer model which utilizes 1,500 dipoles. The configuration of the ventricles utilized in the model assumed that the cross-sectional shape of the left ventricle was circular and the right ventricular free wall was a portion of an ellipse. The torso was assumed to be homogeneous and infinite. The activation sequence was based on the measurements of Durrer. The depolarizational wave was simulated by dipole layers. The output of the model is presented as a standard multilead precordial ECG. The ECG complexes generated by the model closely resemble the precordial QRS complexes of normal man. Simulated increases in wall thickness (1 to 2.2 X control) were associated with changes in the calculated precordial QRS complexes which were characteristic of left ventricular hypertrophy. Voltage (R in V5 or V6 and S in V1) and QRS duration increased linearly as a function of calculated left ventricular mass. Increases in ventricular activation time were related nonlinearly to changes in left ventricular mass and did not occur in the absence of a simulated increase in wall thickness. The effects of simulated changes in left ventricular volume (0.6 to 3.0 X control) on the QRS complex were mainly dependent on the resultant increase in left ventricular mass. This model may be useful in simulating the precordial QRS complexes that result from isolated or combined changes in ventricular volume or wall thickness or other disorders of the heart. Furthermore, it may be useful whenever a simulation of a QRS generator is needed.

Cardiac Volume↗
PubMed2004

Simulated patients in the community pharmacy setting. Using simulated patients to measure practice in the community pharmacy setting.

BACKGROUND: Performance measurement and quality of care in community pharmacy settings is problematic because of the lack of formal patient registration and the resultant risk of selection bias. Although simulated patients have been used for teaching and education purposes, particularly in medical settings, their use as a research tool requires exploration in other health settings. The purpose of this paper is to describe how we used simulated patients to measure professional performance of community pharmacy staff. METHOD: Sixty pharmacies participated in a randomised controlled trial (RCT) to evaluate the effectiveness and efficiency of two guideline implementation strategies in the community pharmacy setting. The primary outcome measure for the study was derived from assessment forms completed by simulated patients following covert visits to participating pharmacies. RESULTS: Of the 420 simulated patient visits scheduled, 384 (91%) were completed. Nine visits were reported by pharmacy staff using reply-paid postcards, four of which concurred with known SP visits. Each detected visit was made by a different SP. In a post-intervention survey, 26 (52%) pharmacists stated they had been apprehensive about the use of simulated patients as part of the study, however, 41 (82%) pharmacists agreed that SP visits were an acceptable research method to use in a community pharmacy setting. DISCUSSION: Simulated patients are a feasible method of assessing professional performance in community pharmacy settings and overcome the methodological problems of other measurement methods. Further research is needed to assess the reliability and validity of simulated patients.

Adult↗
PubMedDate not supplied

The role of a conventional simulator in multileaf-plan simulation: a proposal.

Modern computer networks provide satisfying levels of data recording and verification between the treatment planning system (TPS) and the accelerators, while the main weakness of the preparation chain remains the simulation. When a conventional simulator is employed, it may adversely affect the three-dimensional treatment planning system (3DPS) process because of the difficulty to document the leaf positions on the simulator location films and on the patient's skin. With a conventional simulator, hard copies of the DRRs of each field and CT scans at isocenter level are needed. In an attempt to transfer more information displayed from a BEV perspective from the 3DPS to simulator radiographs, this study aimed to reduce the quality loss by using a 2D conventional simulator in a 3DPS process. We realized an acetate photocopy of TPS data for each field, from a BEV perspective, containing: DRR, wire frames of the PTV, organs at risk and MLC aperture. The photocopies, with an appropriate magnification factor to obtain a correct projective value (ratio 1:1) at isocenter level, are carefully placed on the radiographic images on the same hard copy which allows us to better understand possible setup errors and obliges us to correct these. The method provides reliable documentation, facilitates treatment verification, and fulfils the criteria for MLC simulation. It is accurate, simple, and very inexpensive.

Humans↗
PubMed1991

A simulation model of AIDS in San Francisco: II. Simulations, therapy, and sensitivity analysis.

The HIV and AIDS incidences each year for homosexual men in San Francisco are estimated from data. A computer simulation model for HIV transmission dynamics and progression to AIDS is used to reconstruct the HIV epidemic. Using some a priori parameter estimates, simulations are found that give good fits to the incidence data. In the stimulations the populations is divided into risk groups whose sexual activities are found to be strongly connected. There is saturation in the high-risk group, but changes in sexual behavior are more important in obtaining adequate fits. The simulation modeling yields useful parameter estimates, but the remaining uncertainty in parameter values implies that the simulation forecasts are also uncertain. Changes in HIV incidence lead to changes in AIDS incidence about 6-10 years later. Simulation models with and without zidovudine treatment both fit the incidence data; thus the effects of therapy on AIDS incidence are unclear. The fits of the simulation model are most sensitive to the yearly migration rate, the number of stages in the progression to AIDS, and the average number of new sexual partners per month; thus better estimates of these parameters would be desirable.

Acquired Immunodeficiency Syndrome↗
PubMed2005

Comparison of simulator-CT versus simulator fluoroscopy versus surface marking based radiation treatment planning: a prospective study by three-dimensional evaluation.

BACKGROUND AND PURPOSE: Field placement for Radiation Treatment Planning can be done based on the surface markings or simulator fluoroscopy or simulator with CT facilities. A prospective study was carried out to compare these three techniques of radiation treatment planning to quantitatively find out the difference in normal tissue dosages and target volume coverage in the three groups after three-dimensional evaluation. PATIENTS AND METHODS: The CT scans of 30 patients in the treatment position, taken on a Shimadzu SCT-3000 TF scanner at 1cm intervals, were transferred to Theraplan-500 three-dimensional radiation treatment planning computer. The normal tissues and target volumes (GTV and CTV) were outlined on all the CT slices as per (ICRU) Report no. 50. Three types of radiation treatment planning was done sequentially: Plan I-based on the surface markings alone, Plan II-based on simulator-fluoroscopy, and Plan III-based on Simulator-CT. RESULTS: The mean dose to 95% of the clinical target volume (D95) was increased by 4.4 and 6.4% by Plans II and III as compared with Plan I. The mean dose to 3/3rd (D(3/3)) to all the critical organs was decreased by 6.6 and 8.4% by Plans II and III as compared to Plan I. The mean time, in simulator room, for field placement for Plans I-III was 6.2, 14.6 and 44 min, respectively. CONCLUSIONS: Thus for adequate coverage of target volumes and sparing normal tissues, Simulator-CT based radiation treatment planning is the best method of radiation treatment planning though it is more time consuming.

Adult↗
PubMed1999

Molecular dynamics simulations of the ErbB-2 transmembrane domain within an explicit membrane environment: comparison with vacuum simulations.

Two 500-ps molecular dynamics simulations performed on the single transmembrane domain of the ErbB-2 tyrosine kinase receptor immersed in a fully solvated dilauroylphosphatidyl-ethanolamine bilayer (DLPE) are compared to vacuum simulations. One membrane simulation shows that the initial alpha helix undergoes a local pi helix conversion in the peptide part embedded in the membrane core similar to that found in simulation vacuum. Lipid/water/peptide interaction analysis shows that in the helix core, the intramolecular peptide interactions are largely dominant compared to the interactions with water and lipids whereas the helix extremities are much more sensitive to these interactions at the membrane interfaces. Our results suggest that simulations in a lipid environment are required to understand the dynamics of transmembrane helices, but can be reasonably supplemented by in vacuo simulations to explore rapidly its conformational space and to describe the internal deformation of the hydrophobic core.

Amino Acid Sequence↗