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PubMed1975

[Computer simulation of cell renewal systems].

This paper deals with a block diagram which describes the structure of the control of erythropoiesis by negative feedback loops. The model is transformed into an adequate simulation program using a special block-oriented programming language called ASIM (Analoge SIMulation). For both normal and diseased states of the blood forming process the dynamic responses of the erythrocytes and reticulocytes are simulated by a digital computer analysis. The computer simulation includes different forms of anemia caused by parameter variations as well as by structural alterations. Rising oscillations are obtained too in multiloop control systems containing complex paths with minor loops, which for example take into account the erythrocytic chalones. The described model shows that rising oscillations, that are unstable control loops, can be produced by changing the control-loop structure as well as by parameter changes. In case of malignant disorders such failures becoming effective in oscillations are discussed as parts of disturbed homoeostasis. The results of these studies obtained by simulation should especially stimulate scientists working in the fields of biology and medicine to new test series to verify the proposed hypothesis.

Anemia↗
PubMed1998

Computer simulations of enzyme catalysis: finding out what has been optimized by evolution.

The origin of the catalytic power of enzymes is discussed, paying attention to evolutionary constraints. It is pointed out that enzyme catalysis reflects energy contributions that cannot be determined uniquely by current experimental approaches without augmenting the analysis by computer simulation studies. The use of energy considerations and computer simulations allows one to exclude many of the popular proposals for the way enzymes work. It appears that the standard approaches used by organic chemists to catalyze reactions in solutions are not used by enzymes. This point is illustrated by considering the desolvation hypothesis and showing that it cannot account for a large increase in kcat relative to the corresponding kcage for the reference reaction in a solvent cage. The problems associated with other frequently invoked mechanisms also are outlined. Furthermore, it is pointed out that mutation studies are inconsistent with ground state destabilization mechanisms. After considering factors that were not optimized by evolution, we review computer simulation studies that reproduced the overall catalytic effect of different enzymes. These studies pointed toward electrostatic effects as the most important catalytic contributions. The nature of this electrostatic stabilization mechanism is far from being obvious because the electrostatic interaction between the reacting system and the surrounding area is similar in enzymes and in solution. However, the difference is that enzymes have a preorganized dipolar environment that does not have to pay the reorganization energy for stabilizing the relevant transition states. Apparently, the catalytic power of enzymes is stored in their folding energy in the form of the preorganized polar environment.

Animals↗
PubMed2001

Virtual reality computer simulation.

BACKGROUND: Objective assessment of psychomotor skills should be an essential component of a modern surgical training program. There are computer systems that can be used for this purpose, but their wide application is not yet generally accepted. The aim of this study was to validate the role of virtual reality computer simulation as a method for evaluating surgical laparoscopic skills. METHODS: The study included 14 surgical residents. On day 1, they performed two runs of all six tasks on the Minimally Invasive Surgical Trainer, Virtual Reality (MIST VR). On day 2, they performed a laparoscopic cholecystectomy on living pigs; afterward, they were tested again on the MIST VR. A group of experienced surgeons evaluated the trainees' performance on the animal operation, giving scores for total performance error and economy of motion. During the tasks on the MIST VR, errors and noneconomy of movements for the left and right hand were also recorded. RESULTS: There were significant correlations between error scores in vivo and three of the six in vitro tasks (p < 0.05). In vivo economy scores correlated significantly with non-economy right-hand scores for five of the six tasks and with non-economy left-hand scores for one of the six tasks (p < 0.05). CONCLUSION: In this study, laparoscopic performance in the animal model correlated significantly with performance on the computer simulator. Thus, the computer model seems to be a promising objective method for the assessment of laparoscopic psychomotor skills.

Animals↗
PubMed2007

3D heart model for computer simulations in cardiac surgery.

For a satisfactory computer simulation, a model, which imitates a natural situation, is needed. The Human heart is an irregular 3D object and thus difficult to reproduce. Basic data was taken from Visible Human Dataset (VHD), National Library of Medicine. The heart area was cut out of the original cross-sections and different tissues segmented. All the slices also had to be aligned to assure precise overlapping of the structures. A 3D computer heart model with the resolution of 1mm was designed. The heart model was dedicated to simulations of heat transfer during heart surgery however, it is applicable also to other medical simulations.

Cardiac Surgical Procedures↗
PubMed1979

Spatial firing patterns of auditory neuron network modelling by computer simulation.

This communication examines, in digital computer simulated network, input signals and response patterns established at excitatory neurons' level i.e. the membrane potential of neuron soma. It is restricted to spatial patterns of the auditory neuron networks and time factor for nervous conduction and transmission is neglected compared with long maintained membrane potentials of neuron somas. The model analyzes the change in the spatial patterns of the membrane potential in the two dimensional networks of the auditory system. In order to evaluate the contribution of the various parameters, it is started that the simplest model has only one parameter, lateral inhibition. The other parameters are then added, one at a time, to successive models. The lateral inhibition is a necessary condition in the auditory nervous system if any sharpening of the response areas in the single neurons is to occur. A necessary condition for the validity of the model is that is should be applicable to the other senses such as vision and chemical patterns, taste. The threshold feature of auditory neurons aids in producing a sharpening in the neuron of the auditory relay nuclei. It does this clipping the spatial response patterns in one dimensional arrays of excitatory neurons. Recurrent inhibition seems a necessary condition in the sensory nervous system that any kinds of input signals are to be preserved over a wide range of stimulus intensity. In other words, this network has a wide dynamic range against any kinds of input signals. A simple self-recurrent negative feedback does not contribute to the sharpening, but more complex socalled averaged type does. A neuron network is capable of responding stably to stimuli with a wide range of intensity and with any kind of spatial patterns if there is a simple negative feedback mechanism. When there is no negative feedback, input signals soon disappear or saturate in the neuron network. Therefore, recurrent inhibition is the most important mechanism. Spontaneous activity appears to aid in the sharpening by providing a kind of contrast, that is by reducting the amount of activity in neurons adjacent to the excitatory area. Moreover, the effect of spontaneous activity in the model seems to make repples around the excitatory area and suggests that an introduction of activity at any stage of the networks, from whatever source for example reticulum formation and thalamus, might appreciably alter the response patterns at subsequent neuron network. This suggests that the mechanism of the consciousness that might be controlled by the thalamus and or reticular formation. These two dimensional neuron networks may be expanded to three dimensional neuron networks. The former might simulate the auditory nervous system while the latter might simulate the visual system.

Animals↗
PubMed1996

[Analysis by computer simulation of cell kinetics of the liver].

A computer simulation model of cell kinetics is established to represent the variations of rat hepatocyte populations in several circumstances: normal growth, circadian rythms, response to partial hepatectomy under different conditions. This model differs from usual mathematical models-sets of equations--by the use of digital simulation techniques. Each cell in the population is represented by a set of variables in the computer memory. When experiments are simulated, the values of these variables are modified step by step according to the hypotheses we want to test. Counts and statistics derived at each step from the simulation are then compared to experimental values, in order to assess the validity of our hypotheses. This procedure enables us to establish a minimal set of conditions and outside causal effects necessary to mimic the behaviour of the liver under experimental situations similar to those we simulate. Such modelisation suggests further work on the mechanisms governing cell kinetics in the normal liver and during cancerisation.

Animals↗
PubMed2005

Evaluation of a novel method of noise reduction using computer-simulated mammograms.

A novel method of noise reduction has been tested for mammography using computer-simulated images for which the truth is known exactly. This method is based on comparing two images. The images are compared at different scales, using a cross-correlation function as a measure of similarity to define the image modifications in the wavelet domain. The computer-simulated images were calculated for noise-free primary radiation using a quasi-realistic voxel phantom. Two images corresponding to slightly different geometry were produced. Gaussian noise was added with certain properties to simulate quantum noise. The added noise could be reduced by >70% using the proposed method without any noticeable corruption of the structures. It is possible to save 50% dose in mammography by producing two images (each 25% of the dose for a standard mammogram). Additionally, a reduction of the anatomical noise and, therefore, better detection rates of breast cancer in mammography are possible.

Artifacts↗
PubMed1999

Assessment of coronary stenoses by Doppler wires: a validation study using in vitro modeling and computer simulations.

The present study evaluates the use of intracoronary velocity measurements by Doppler guidewires for assessing coronary obstructions. In vitro experiments were performed in a flow model using acrylic phantoms of coronary stenoses with different configurations (stenosis area: 56%, 75% and 89%; stenosis length: 1 and 5 mm; stenosis border: tapering or abrupt). Nonpulsatile laminar flow conditions of a test fluid were established at flow rates ranging from 0.5 to 2.0 mL/s to simulate baseline flow and flow after vasodilation. Peak Doppler velocity was measured proximal to, within and distal to the model stenoses. Computer simulations were employed to calculate radial flow profiles with and without a Doppler wire aligned with the vessel center. In 84 in vitro flow experiments, peak Doppler velocity correlated well with the average flow velocity as calculated from the actual flow rate and the vessel's cross-sectional area proximal to (r = 0.98, SEE = 1.4, p < 0.001) and within (r = 0.97, SEE = 16.4, p < 0.001) the stenosis. However, the ratio of calculated average velocity to Doppler-measured peak velocity was significantly different from 0.5, the expected value for a parabolic flow profile (0.76+/-0.08, 0.81+/-0.14; p < 0.001). Acceptable accuracy was found for the Doppler estimation of stenosis severity using the continuity equation (error: 0.9+/-1.2% and -4.6+/-3.5% for stenosis with a length of 5 mm and 1 mm, respectively). Doppler velocity reserve significantly underestimated the true flow reserve for the 56% and 75% stenoses (p < 0.01). Computer simulations demonstrated significant alterations of flow profiles by the wire, which explained the observed underestimation of the true flow reserve by the Doppler velocity reserve. Thus, Doppler guidewire measurements of intracoronary flow velocities are useful to assess the severity of coronary stenoses. However, the in vitro results and computer simulations indicate that guidewires alter the flow profile, so that Doppler velocity reserve may underestimate the true flow reserve.

Analysis of Variance↗
PubMed1997

Analysis of the role of the Spitzenkörper in fungal morphogenesis by computer simulation of apical branching in Aspergillus niger.

High-resolution video microscopy, image analysis, and computer simulation were used to study the role of the Spitzenkörper (Spk) in apical branching of ramosa-1, a temperature-sensitive mutant of Aspergillus niger. A shift to the restrictive temperature led to a cytoplasmic contraction that destabilized the Spk, causing its disappearance. After a short transition period, new Spk appeared where the two incipient apical branches emerged. Changes in cell shape, growth rate, and Spk position were recorded and transferred to the FUNGUS SIMULATOR program to test the hypothesis that the Spk functions as a vesicle supply center (VSC). The simulation faithfully duplicated the elongation of the main hypha and the two apical branches. Elongating hyphae exhibited the growth pattern described by the hyphoid equation. During the transition phase, when no Spk was visible, the growth pattern was nonhyphoid, with consecutive periods of isometric and asymmetric expansion; the apex became enlarged and blunt before the apical branches emerged. Video microscopy images suggested that the branch Spk were formed anew by gradual condensation of vesicle clouds. Simulation exercises where the VSC was split into two new VSCs failed to produce realistic shapes, thus supporting the notion that the branch Spk did not originate by division of the original Spk. The best computer simulation of apical branching morphogenesis included simulations of the ontogeny of branch Spk via condensation of vesicle clouds. This study supports the hypothesis that the Spk plays a major role in hyphal morphogenesis by operating as a VSC-i.e., by regulating the traffic of wall-building vesicles in the manner predicted by the hyphoid model.

Aspergillus niger↗
PubMedDate not supplied

A computer simulation model for cost-effectiveness analysis of cardiovascular disease prevention.

In this paper a computer simulation model for cost-effectiveness analysis of cardiovascular disease prevention is presented. Cost-effectiveness analysis makes it possible to compare the cost-effectiveness of different interventions in order to maximize the health effects for a given amount of resources. The computer simulation model was written in Turbo-Pascal to be used on an IBM-PC-compatible. The model was based on the 8-year logistic multivariate risk equations for CHD and stroke from the Framingham Heart Study, but the regression coefficients can easily be changed if local data exist. The main advantages with the model are that it is easy to use, transparent, and flexible. The model was mainly developed for scientific purposes, but should be useful also for educational purposes and clinical decision analysis. The modelling approach used should also be useful in many other medical areas.

Adult↗
PubMed2004

An experimental method for measuring the mean length of cerebellar parallel fibers: validation and derivation of a correction factor by computational simulation and probability analysis.

The length of cerebellar parallel fibers is important for information integration by the Purkinje cells. Based on the Copernican principle for analyzing the length of stochastic events, we have recently devised a stochastic method to estimate the mean length of parallel fibers within a given cerebellar region. The purpose of the present report is to provide validation of this methodology via computational simulations. We create virtual parallel fibers with known lengths and program each step of our stochastic method for computational simulation. We then compare the observed mean length obtained from our computational simulation with the known mean length of the virtual parallel fibers. In particular, we investigate the effect of cutting parallel fibers into segments during histological sectioning. Our computational results reveal an over-estimation factor ranging from 1.0 (no correction is necessary) to 2.0 as the parallel fiber segmentation becomes increasingly severe. Based on probability theory considerations, we have confirmed the existence of this over-estimation. We have further determined the cause of this over-estimation to be an artificial consequence of one of the sampling steps in our stochastic method. These results provide validation of our methodology, as well as a correction factor, which can be derived directly from the experimentally measured parameters and used to obtain the true mean length of parallel fibers. Potential applications of the stochastic method include a comparative analysis of the length of parallel fibers as an approach to gain clues about cerebellar circuit principles and function. In addition, the stochastic method may also find promising applications in other functionally important axonal systems in the brain.

Cerebellar Cortex↗
PubMed1990

Computer simulation in template-directed oligonucleotide synthesis.

A computer simulation (KINSIM) modeling up to 33 competing reactions was used in order to investigate the product distribution in a template-directed oligonucleotide synthesis as a function of time and concentration of the reactants. The study is focused on the poly(C)-directed elongation reaction of an oligoguanylate (a 7-mer is chosen) with guanosine 5'-monophosphate-2-methyl-imidazolide (2-MeImpG), the activated monomer. It is known that the elongation of oligoguanylates to form oligomeric products such as 8-mer, 9-mer, 10-mer, etc., is in competition with (1) the dimerization and further oligomerization reaction of 2-MeImpG that leads to the formation of dimers and short oligomers, and (2) the hydrolysis of 2-MeImpG that forms inactive guanosine 5'-monophosphate, 5'-GMP. Experimentally determined rate constants for the above three processes at 37 degrees C and pH 7.95 were used in the simulation; the initial concentrations of 2-MeImpG, [M]o, and of the oligoguanylate primer, [7-mer]o, were varied, and KINSIM calculated the distribution of products as a function of time until equilibration was reached, i.e., when all the activated monomer has been consumed. In order to sort out how strongly the elongation reaction may be affected by the competing hydrolysis and dimerization, we also simulated the idealized situation in which these competing reactions do not occur.(ABSTRACT TRUNCATED AT 250 WORDS)

Biopolymers↗
PubMed1982

Teaching the uptake and distribution of halothane. A computer simulation program.

A computer aided learning program for teaching the kinetics of uptake and distribution of the inhalational anaesthetic halothane is described. The program is based on a seven-compartment model which simulates the action of halothane on ventilation and on the cardiovascular system. The program is available to the student in four forms: one with no changes in circulation or respiration, one with the cardiovascular effects of halothane included, one with respiratory effects only, and one with both of these effects combined. The student can study the importance of the influence of halothane on respiration and blood circulation by comparing results from simulations on different models. The simulation is presented as graphs which are continuously displayed on an alphanumeric visual display terminal. Interaction with the program is possible at all times to change the simulation speed, the variables being graphed, the inspired halothane fraction, and the fresh gas flow.

Anesthesia, Inhalation↗
PubMed1985

Computer simulation of a cerebellar cortex compartment. II. An information learning and its recall in the Marr's memory unit.

Computer simulation experiments are described regarding information storage and retrieval at a network consisting of one Purkinje cell and 20,000 granule cells. The information content depends on a scheme type and the properties of Purkinje cells. It is shown that a practically attainable information record efficiency is of the order 0.6 bit per binary memorising synapse. Associative information recall is demonstrated for the Marr's memory unit and expressions are derived for an information-content estimation based on parameter values obtained by simulation. The consequences of this computer simulation for physiological experiments are extensively discussed.

Animals↗
PubMedDate not supplied

Community as client: environmental issues in the real world. A SimCity computer simulation.

The ability to think critically has become a crucial part of professional practice and education. SimCity, a popular computer simulation game, provides an opportunity to practice community assessment and interventions using a systems approach. SimCity is an interactive computer simulation game in which the player takes an active part in community planning. SimCity is supported on either a Windows 95/98 or a Macintosh platform and is available on CD-ROM at retail stores or at www.simcity.com. Students complete a tutorial and then apply a selected scenario in SimCity. Scenarios consist of hypothetical communities that have varying types and degrees of environmental problems, e.g., traffic, crime, nuclear meltdown, flooding, fire, and earthquakes. In problem solving with the simulated scenarios, students (a) identify systems and subsystems within the community that are critical factors impacting the environmental health of the community, (b) create changes in the systems and subsystems in an effort to solve the environmental health problem, and (c) evaluate the effectiveness of interventions based on the game score, demographic and fiscal data, and amount of community support. Because the consequences of planned intervention are part of the simulation, nursing students are able to develop critical-thinking skills. The simulation provides essential content in community planning in an interesting and interactive format.

Community Health Nursing↗
PubMed2002

Key issues in the computational simulation of GPCR function: representation of loop domains.

Some key concerns raised by molecular modeling and computational simulation of functional mechanisms for membrane proteins are discussed and illustrated for members of the family of G protein coupled receptors (GPCRs). Of particular importance are issues related to the modeling and computational treatment of loop regions. These are demonstrated here with results from different levels of computational simulations applied to the structures of rhodopsin and a model of the 5-HT2A serotonin receptor, 5-HT2AR. First, comparative Molecular Dynamics (MD) simulations are reported for rhodopsin in vacuum and embedded in an explicit representation of the membrane and water environment. It is shown that in spite of a partial accounting of solvent screening effects by neutralization of charged side chains, vacuum MD simulations can lead to severe distortions of the loop structures. The primary source of the distortion appears to be formation of artifactual H-bonds, as has been repeatedly observed in vacuum simulations. To address such shortcomings, a recently proposed approach that has been developed for calculating the structure of segments that connect elements of secondary structure with known coordinates, is applied to 5-HT2AR to obtain an initial representation of the loops connecting the transmembrane (TM) helices. The approach consists of a simulated annealing combined with biased scaled collective variables Monte Carlo technique, and is applied to loops connecting the TM segments on both the extra-cellular and the cytoplasmic sides of the receptor. Although this initial calculation treats the loops as independent structural entities, the final structure exhibits a number of interloop interactions that may have functional significance. Finally, it is shown here that in the case where a given loop from two different GPCRs (here rhodopsin and 5-HT2AR) has approximately the same length and some degree of sequence identity, the fold adopted by the loops can be similar. Thus, in such special cases homology modeling might be used to obtain initial structures of these loops. Notably, however, all other loops in these two receptors appear to be very different in sequence and structure, so that their conformations can be found reliably only by ab initio, energy based methods and not by homology modeling.

Algorithms↗
PubMed2005

The influence of pellet shape, size and distribution on capsule filling--a preliminary evaluation of three-dimensional computer simulation using a Monte-Carlo technique.

A computer simulation based on a Monte-Carlo technique has been developed and used to investigate the influence of pellet size, dispersity, shape and aggregation on the filling of hard shell capsules. The simulations are in general agreement with experimental observations previously reported. The results also confirm recent findings that filling is a function of pellet shape and that above an aspect ratio value of 1.2 filling reproducibility is reduced. The methodology is simple and rapid in execution allowing many computer-based experiments to be performed with minimum effort.

Capsules↗