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PubMedDate not supplied

Computer-simulation technique for low dose computed tomographic screening.

OBJECTIVES: The purpose of this study is to assess the relative influence of noise and artifact in detecting lung nodules on low dose computed tomographic (CT) screening. METHODS: We develop the computer-simulation technique that allows tube current simulation and virtual nodule insertion in any CT images. The tube current simulation uses a reduction model that adds random Gaussian noise distribution to existing projection data. The virtual nodules are generated using a dedicated CT simulation tool with same scanner geometry. RESULTS: The coefficient of the correlations between the contrast-to-noise ratio of the actual scan and simulated tube current images was 0.98. There was no difference in CT number between virtual nodules and actual nodules [t test results = 0.60, t50(0.01) = 2.70 at 10 mA] and the coefficient of the correlations of the image noise was 0.99. CONCLUSIONS: Our technique is useful for systematic evaluation of radiation dose reduction and structure visibility in low-dose CT screening.

Computer Simulation↗
PubMed1992

Computer simulation of bidimensional growth of the gametophyte of Anemia phyllitidis (L.) Sw.

Analysis of the different cytomorphogenetic phases of the gametophyte of Anemia phyllitidis (L.) Sw. has shown that prothallial development of this fern follows a regular process. This led us to model the morphogenesis of the prothallus. In this context, using the formal language theory whose biological application was introduced by Lindenmayer and Lück and Lück, we have simulated on computer the bidimensional growth of the gametophyte. I present a new algorithm allowing computer simulation and strict drawing of the tissue shapes. This formulation can be applied to isotropic as well as anisotropic growth types. We use it now as a basis to study the transition between mono-, bi-, and tridimensional growth phases that are characteristic of the development of the gametophyte in Anemia phyllitidis (L.) Sw.

Algorithms↗
PubMed1990

Prediction of RNA secondary structure, including pseudoknotting, by computer simulation.

A computer program is presented which determines the secondary structure of linear RNA molecules by simulating a hypothetical process of folding. This process implies the concept of 'nucleation centres', regions in RNA which locally trigger the folding. During the simulation, the RNA is allowed to fold into pseudoknotted structures, unlike all other programs predicting RNA secondary structure. The simulation uses published, experimentally determined free energy values for nearest neighbour base pair stackings and loop regions, except for new extrapolated values for loops larger than seven nucleotides. The free energy value for a loop arising from pseudoknot formation is set to a single, estimated value of 4.2 kcal/mole. Especially in the case of long RNA sequences, our program appears superior to other secondary structure predicting programs described so far, as tests on tRNAs, the LSU intron of Tetrahymena thermophila and a number of plant viral RNAs show. In addition, pseudoknotted structures are often predicted successfully. The program is written in mainframe APL and is adapted to run on IBM compatible PCs, Atari ST and Macintosh personal computers. On an 8 MHz 8088 standard PC without coprocessor, using STSC APL, it folds a sequence of 700 nucleotides in one and a half hour.

Algorithms↗
PubMed1993

Preoperative assessment and prediction of postoperative results in an artificial arterial network using computer simulation.

A computer model has been developed that can be used to describe the human arterial system mathematically. It simulates the complex relationship of morphology and hydraulics in the vessel network. After entering patient data into a standard vessel model, the mean flow velocity, the flow direction, and the blood pressure at each specified point of the flow network can be calculated. The vessel picture can be altered and modified with the help of a graphic editor. Localized or diffuse stenoses, bypasses with simple or multiple anastomoses, end-to-end anastomoses, end-to-side anastomoses, etc., can be studied in terms of the hydraulic effects on the local situation or on the entire vessel system. Experimental results of ultrasonic mean flow data in vessel systems of leg and cerebral arteries of patients are compared with calculated values. The predicted and measured flow velocities show a mean difference of about 10% indicating that such a computer model may be successfully used in the optimal planning of bypass operations.

Arteries↗
PubMed1993

Partition of plasmid R1: a computer simulation.

A computer-simulated population of individual Escherichia coli cells harboring plasmid R1 parA+/parB- has been used to analyze three possible modes of plasmid segregation: equi-partition, in which plasmids are partitioned equally to daughter cells at cell division; single-site inheritance, in which the products of the most recent replication event are partitioned equally and the remaining plasmids are distributed randomly; and pair-site partition, in which a single, randomly chosen plasmid is actively partitioned to each daughter cell at division and the rest are distributed randomly. Comparison between predicted and experimental plasmid loss-frequency enabled us to rule out the first of these models as a likely mode of action in R1 but was inconclusive regarding the other two. The parA region would therefore seem to partition actively only one pair of plasmids to each daughter cell, the precise selection rule involved remaining unresolved. This question is not easily decided with current technology, as we show, but our simulation results also predict that the isolation of rep(Ts) mutants will provide an experimental system in which a clear distinction is possible between two plasmids that are the products of the most recent replication event and two that are chosen strictly at random.

Computer Simulation↗
PubMed1986

Alveolar flooding: a computer simulation.

A validated computer simulation of pulmonary microvascular exchange (J.L. Bert and K.L. Pinder, Microvasc. Res., 27 (1984) 51-70) has been extended to include exchange with the air space (alveoli). Equations which hypothetically describe characteristics associated with this additional compartment and the exchange of both fluid and plasma proteins between the lung tissue and the alveolar space are presented. These are incorporated into the simulation which has been used to predict the behavior of the pulmonary microvascular exchange system including alveolar flooding. The predicted trends associated with alveolar flooding are reasonable. However, due to the lack of specific experimental or clinical findings, the simulation remains essentially unvalidated. The effect on alveolar flooding and interstitial edema of the parameters associated with the additional relationships is presented and discussed. Primarily, results for perturbations in circulatory pressure are presented. Additionally, changes in permeability characteristics are shown and discussed.

Blood Proteins↗
PubMed1991

The one-site model of human erythrocyte glucose transport: testing its predictions using network thermodynamic computer simulations.

Network thermodynamic computer simulations were carried out using parameters experimentally derived by Lowe and Walmsley ((1987) Biochim. Biophys. Acta 903, 547-550) for two tests of the one-site model of human erythrocyte glucose transport. In the temperature-jump experiment, the simulations predicted the amplitude and relaxation time of accelerated uptake, but underestimated the net uptake due to an unexpectedly low measured basal rate. In the maltose-acceleration experiment, the dissociation constant of maltose was assessed at 0 degrees C by measuring the inhibitory effects of maltose on both cytochalasin B binding and on 3-O-methylglucose uptake, and using this value (52 mM) to calculate the dissociation constant (2.9 mM). The simulated experiment then did show a transient acceleration in uptake comparable in magnitude to that observed experimentally, except that the relaxation time was more than 10-fold longer in the simulations. Measurements of the temperature dependence of the inhibition of cytochalasin B binding by maltose and 3-O-methylglucose indicated that apparent sugar affinity is sensitive to carrier orientation at low temperatures, whereas at more physiologic temperatures the intrinsic dissociation constant predominated.

3-O-Methylglucose↗
PubMed1995

Localisation of myocardial ischaemia from the magnetocardiogram using current density reconstruction method: computer simulation study.

A computer simulation study is performed to investigate the method of current density reconstruction to localise myocardial ischaemia. A computer model of the entire human heart is used to simulate the excitation and repolarisation process in eight topographically different cases of myocardial ischaemia. The associated magnetocardiogram is calculated at 37 positions of the KRENIKON biomagnetic measurement equipment. The method of current density reconstruction is applied at the S-point (the last discernible deviation from the ST-segment at the end of the QRS-complex) of the MCG to find characteristics of the myocardial ischaemia simulated by the model. The results show that it is possible to determine the location of the ischaemia. The current density distribution may be interpreted physiologically in terms of the so-called 'injury-current'. This indicates that magnetocardiography might be a suitable method for noninvasive ischaemia diagnosis, and further investigations of the current density reconstruction method for the injury current should be performed on patients with ischaemic heart disease.

Computer Simulation↗
PubMed1986

Surveillance of birth defects: the Multicommunity Sets Technique tested by computer simulation.

Using a computer simulation for a series of births subject to various congenital malformations, the surveillance performance of the Multicommunity Sets Technique (MST) was compared to that of the Cumulative Sum Technique (CUSUM). Increases in malformation frequencies were simulated in (i) 6 out of 6 centres and (ii) only 3 out of 6 centres. MST was neither more sensitive nor more specific than CUSUM, and signalled increases with greater delay. One type of CUSUM procedure showed to accumulate more false alarms than MST in long periods of surveillance at the baseline malformation rate. The advantage of CUSUM was also shown for a single malformation with a very low baseline incidence, which according to Chen et al. (1983) should have been particularly suitable for MST surveillance.

Computer Simulation↗
PubMed1990

Load and go versus stay and play: analysis of prehospital i.v. fluid therapy by computer simulation.

A computer-simulation model of prehospital hemorrhage and fluid resuscitation was used to determine under what circumstances it is advantageous to begin fluid resuscitation in the field instead of immediately transporting to the hospital. Four hypothetical bleeding rates (15, 25, 50, and 100 mL/min) were examined for short and long prehospital times. No significant difference in survival was noted for bleeding rates of 15 mL/min for either short or long time; a small but statistically significant increase in survival was noted for bleeding rates of 25 mL/min and long transport times. For both short and long times, all higher bleeding rates showed greater survival with prehospital fluid resuscitation and higher blood pressure at the onset of definitive care.

Computer Simulation↗
PubMed1990

Social mechanisms in the population genetics of Tay-Sachs and other lethal autosomal recessive diseases: a computer simulation model.

A computer simulation model was developed to study the effects of various feudal social customs on the incidence of lethal autosomal recessive genes. Populations of 500 individuals were created in which each person was characterized by sibship, genotype, and sex. The numbered sibships were sorted into numerical order. Each individual then sought a mate from 6 or 12 sibships on either side of his or her own sibship. The resulting couples were sorted in order of the husband's sibship number, after which the couples produced children in accordance with the prevailing birth rate. This ordering of sibships made the probability of a gene remaining in one locality higher than the probability of it drifting to distant localities. A lethal autosomal recessive gene was introduced into populations at a starting carrier rate of 10%. This fell after 20 generations to 2.54 +/- 0.17% (SEM) which was significantly less than the 5.00% carrier rate predicted by a deterministic model in which random mating occurred in an infinite population. The excessive loss of the lethal gene was caused by the high incidence of consanguineous marriages and by the occurrence of random inequalities in the distribution of the gene. The avoidance of sib marriages raised the final carrier frequency (3.28 +/- 0.19%) as did reproductive compensation (4.33 +/- 0.26%). The combination of the incest taboo and reproductive compensation raised the final carrier rate to 5.05 +/- 0.28%. It is concluded that the social factors which may have operated over a period of many centuries in the past have had a significant effect on the population genetics of lethal autosomal recessive genes.

Computer Simulation↗
PubMedDate not supplied

A functional hypothesis for LGN-V1-TRN connectivities suggested by computer simulation.

We employ computer simulation to investigate the function of neural circuitries between thalamic sensory relay nuclei, primary sensory cortices, and the thalamic reticular nucleus (TRN). Computational similarities exist between these circuits and the architecture of a simple artificial neural network. We impose processing parameters on this network architecture in keeping with anatomical and physiological details of the mammalian geniculo-cortical visual pathway, and then run the simulation on a task involving multiple simultaneous inputs from the simulated visual field. After two to three loops through the simulation, activity in cortical and thalamic units whose receptive fields include the stronger stimulus remains constant, while activity in other cortical and thalamic units activated by weaker stimuli declines toward resting values. These results suggest that the modeled neural circuitry functions to "prime" selective attentional mechanisms further up the visual streams toward specific portions of the total visual stimulus. Besides extending existing models and evidence about the function of these neural circuits, our results also provide physiologists with predicted activity profiles of thalamic and cortical elements of the modeled neural system for a task not yet studied experimentally.

Animals↗
PubMed1984

Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies.

Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distribution functions based on the Proximity Criterion, and partitioned into hydrophobic, hydrophilic and ionic contributions. Color stereo views of selected hydration complexes are also presented. A preliminary discussion of the transferability of functional group coordination numbers is given. The results enable to comment on two current problems related to the hydration of nucleic acids: a) the theory of Dickerson and coworkers on the role of water in the relative stability of the A and B form of DNA and b) the idea of water bridges and filaments emerging from the computer simulation results on the hydration of DNA fragments by Clementi.

Carbohydrates↗
PubMed1984

Pulmonary microvascular exchange: an analog computer simulation.

An analog computer simulation of human pulmonary microvascular exchange was programmed and tested. This model of blood-to-lymph transport is based on a compartmental analysis of the lungs and has the capacity to describe fluid volumes, plasma protein content, flows and pressures for both normal and perturbed conditions. Normal conditions were predicted and shown to be in agreement with the literature. The trends in the response of the lungs to changes in microvascular pressure is shown also to agree with the literature both for steady state and transient predictions. The results of a sensitivity analysis, which demonstrates the response of the lungs to a variety of perturbations, is also reported. The simulation predicts reasonable results for normal, transient, and perturbed conditions in human lungs.

Blood Proteins↗
PubMed1998

Folding under inequilibrium conditions as a possible reason for partial irreversibility of heat-denatured proteins: computer simulation study.

Using computer simulations we have studied possible effects of heating and cooling at different scan rates on unfolding and refolding of macromolecules. We have shown that even the simplest two-state reversible transition can behave irreversibly when an unfavorable combination of cooling rate, relaxation time and activation energy of refolding occurs. On the basis of this finding we suppose that apparent irreversibility of some proteins denatured by heat may result from slow relaxation on cooling rather than thermodynamic instability and/or irreversible alterations of the polypeptide chain. Using this kinetic reversible two-state model, we estimated the effects of the scan rate and kinetic parameters of the macromolecule on its unfolding-refolding process. A few recommendations are suggested on how to reach maximal possible recovery after denaturation if refolding appears to be under kinetic control.

Journal Article↗
PubMed2004

Studies of translational diffusion in the smectic A phase of a Gay-Berne mesogen using molecular dynamics computer simulation.

Molecular dynamics computer simulations are used to determine the self-diffusion coefficients for a Gay-Berne model mesogen GB (4.4,20,1,1) in the isotropic, nematic and smectic A phases along two isobars. The values of the parallel and perpendicular diffusion coefficients, D(parallel) and D(perpendicular), are calculated and compared in the different phases. For the phase sequence isotropic-smectic A, D(perpendicular)*> or =D(parallel)* over the whole smectic A range with the ratio D(parallel)*/D(perpendicular)* decreasing with decreasing temperature. At a higher pressure, a nematic phase is observed between these two phases and we find that D(parallel)*>D(perpendicular)* throughout the nematic region and the inequality D(parallel)*>D(perpendicular)* remains on entering the smectic A phase. However, the ratio D(parallel)*/D(perpendicular)* decreases with decreasing temperature within the smectic A range and eventually this ratio inverts such that D(perpendicular)*>D(parallel)* at low temperatures. The temperature dependence of the parallel diffusion coefficient in the smectic A phase for this model mesogen is compared to that predicted by a theoretical model for diffusion subject to a cosine potential.

Journal Article↗
PubMedDate not supplied

Computer simulation of image intensifier-based computed tomography detector: vascular application.

This present study reports the results of a computer simulation whose aim was to predict the low-contrast imaging performance of which a conventional x-ray image intensifier with charge coupled device (CCD) camera would be capable if incorporated into a computed tomography (CT) volume imager. A vascular imaging task was modeled in our simulation. The effects of detector noise, x-ray exposure levels, analog-to-digital conversion (ADC) precision and residual levels of detected x-ray scatter were considered. The results of this simulation indicate that the low-contrast imaging performance of an image intensifier-based CT system was most limited by the CCD detector readout noise. Given this limitation the detection of greater than about 100,000 detected photons/pixel/projection gave marginal improvement in low-contrast resolution. At these exposures 12 bit ADC precision resulted in little additional image noise. The effects of detecting scattered x rays are twofold; decreasing the signal-to-noise ratio associated with our modeled artery and introducing a cupping artifact. Based on the results from the simulation, it appears that an image intensifier-based CT system is a feasible concept from a noise viewpoint, if the anticipated imaging task is intravenous angiography.

Angiography↗
PubMed2001

Colloidal aggregation with sedimentation: computer simulations.

A computer model for colloidal aggregation is presented that considers both the Brownian motion and the gravitational drift experienced by the colloidal particles and clusters. It is shown that the aggregation crosses over from diffusion-limited aggregation to another type with a higher cluster fractal dimension, a speeding up followed by a slowing down of the aggregation rate, an algebraically decaying cluster size distribution, and a higher concentration required for gelation. Although these findings are in accordance with the experimental results, some interpretations are different.

Journal Article↗