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PubMed2003

Minimizing dilutional coagulopathy in exsanguinating hemorrhage: a computer simulation.

BACKGROUND: Current massive transfusion guidelines are derived from washout equations that may not apply to bleeding trauma patients. Our aim was to analyze these guidelines using a computer simulation. METHODS: A combined hemodilution and hemodynamic model of an exsanguinating patient was developed to calculate the changes in prothrombin time (PT), fibrinogen, and platelets with bleeding. The model was calibrated to data from 44 patients. Time intervals to subhemostatic values of each coagulation test were calculated for a range of replacement options. RESULTS: Prolongation of PT is the sentinel event of dilutional coagulopathy and occurs early in the operation. The key to preventing coagulopathy is plasma infusion before PT becomes subhemostatic. The optimal replacement ratios were 2:3 for plasma and 8:10 for platelets. Concurrent transfusion of plasma with blood is another effective strategy for minimizing coagulopathy. CONCLUSION: Existing protocols underestimate the dilution of clotting factors in severely bleeding patients. The model presents an innovative approach to optimizing component replacement in exsanguinating hemorrhage.

Blood Component Transfusion↗
PubMed1992

Computer simulation for the prediction of separation as a function of pH for reversed-phase high-performance liquid chromatography. I. Accuracy of a theory-based model.

Computer simulation software (DryLab I/mp) is described for predicting high-performance liquid chromatographic separation as a function of changes in mobile phase pH. Three experimental runs with pH (only) varied are used to derive values of pKa plus capacity factors (k') for the ionized and non-ionized form of each ionizable solute. Various tests of the experimental data then allow classification of each solute as acidic, basic, neutral (including strong or weak acids or bases) and amphoteric. Experimental data are reported for the separation of several substituted anilines as a function of pH and solvent composition (%B). Experimental requirements for the accurate prediction of separation (ca. +/- 2-4% in alpha) as a function of pH are discussed. The reliability of the software is demonstrated for three different samples: mixtures of (a) substituted benzoic acids, (b) substituted anilines and (c) catecholamine-related compounds.

Aniline Compounds↗
PubMed1994

Hydration of cytidine, 2'-deoxycytidine and their phosphate salts in the aqueous solutions. A molecular dynamics computer simulation study.

To compare the hydration pattern of the cytidine (Cyd) and 2'-deoxycytidine (dCyd) in the aqueous solutions at the level of microscopic interactions. Molecular Dynamics (MD) computer simulations have been undertaken. The results indicate that the hydration of the heterocyclic base moiety in cytidine and 2'-deoxycytidine has a hydrophobic character. None of the three potential Watson-Crick base pair centres hydrogen bonds with the water molecules and the formation of something akin to a clathrate cage structure of water around base moieties of nucleosides in the aqueous solution is suggested. In contrast, the hydration of Cyd and dCyd sugar moieties shows a hydrophilic character and the three-dimensional networks of H-bonds involving all hydrophilic centres are formed differently around the ribose and 2'-deoxyribose. The sugar hydroxyl groups participate in the hydrogen bonding with water both as H-donor and as H-acceptor. Their donor-acceptor abilities have been evaluated and compared. The coordination numbers, the geometrical data of the first hydration shell, and the number of hydrogen bonds have been calculated. The changes in the pattern of hydration with the increased concentration of nucleosides and upon nucleoside protonation are discussed. The analysis of the pairwise interaction energies are also presented.

Computer Simulation↗
PubMed1994

The process of cellular uptake of iron from transferrin. A computer simulation program.

In an attempt to improve our understanding of the complex interplay between cell compartments and chemical species during cellular uptake of iron from transferrin, we designed a computer simulation program based on current models of receptor-mediated endocytosis and pinocytosis. The program calculates and visualizes, as a function of time, the changes in transferrin, apotransferrin, and iron concentrations occurring in all relevant cellular compartments during cellular iron acquisition from transferrin. Simulation of literature data showed that the program generates results that are in accordance with experimental data. Furthermore, from measurements of the uptake of [carboxyl-14C]dextran we could utilize the program to suggest rate constants characteristic for the pinocytic process in rat reticulocytes. Moreover, simulations indicate that the apparent difference in the iron uptake process observed between reticulocytes and hepatocytes may be explained by the contribution made by pinocytosis to the iron uptake process. Finally, the present program should have potential as an educational tool during introduction to the field of receptor-mediated endocytosis in general and to cellular iron metabolism in particular.

Animals↗
PubMed2001

Comparison of the likelihood ratio and identity-by-state scoring methods for analyzing sib-pair test cases: a study using computer simulation.

To assess the power and significance of the likelihood ratio (LR) and the identity-by-state scoring (IBS) methods for a pair of siblings, we performed computer simulations by use of 10 DNA markers (HLA-DQalpha, D1S80, and 8 short tandem repeat loci) that were frequently analyzed in paternity tests in Japan. The combined power of discrimination of these 10 markers in the Japanese population is 0.999 999 999 98. Pedigrees each consisting of 10,000 pair of full-siblings, half-siblings and unrelated individuals were generated and typed on all markers as random samples. Both the summation of log10 LR and IBS of each group had approximate standard normal distribution with significant differences between the means. Statistical studies showed that the LR method has 91% power to detect unrelated individuals and 38% power to detect half-siblings as not full-siblings with a 5% false-positive rate, whereas the IBS method does 87% and 42% powers, respectively. In 62% of full-siblings, in contrast with only 0.2% of unrelated individuals, the values of LR exceeded 100 which was equivalent to 0.99 of probability of full-sibship at 50% prior probability. The advantage of the LR method over IBS method was convincing especially for the detection of unrelated individuals as not half-siblings, however, the latter would be also informative for sib-pair tests if sufficient number of polymorphic markers are available.

Algorithms↗
PubMed2004

Computer simulation in conjunction with medical thermography as an adjunct tool for early detection of breast cancer.

BACKGROUND: Mathematical modelling and analysis is now accepted in the engineering design on par with experimental approaches. Computer simulations enable one to perform several 'what-if' analyses cost effectively. High speed computers and low cost of memory has helped in simulating large-scale models in a relatively shorter time frame. The possibility of extending numerical modelling in the area of breast cancer detection in conjunction with medical thermography is considered in this work. METHODS: Thermography enables one to see the temperature pattern and look for abnormality. In a thermogram there is no radiation risk as it only captures the infrared radiation from the skin and is totally painless. But, a thermogram is only a test of physiology, whereas a mammogram is a test of anatomy. It is hoped that a thermogram along with numerical modelling will serve as an adjunct tool. Presently mammogram is the 'gold-standard' in breast cancer detection. But the interpretation of a mammogram is largely dependent on the radiologist. Therefore, a thermogram that looks into the physiological changes in combination with numerical simulation performing 'what-if' analysis could act as an adjunct tool to mammography. RESULTS: The proposed framework suggested that it could reduce the occurrence of false-negative/positive cases. CONCLUSION: A numerical bioheat model of a female breast is developed and simulated. The results are compared with experimental results. The possibility of this method as an early detection tool is discussed.

Body Temperature↗
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↗
PubMedDate not supplied

Computer simulation of the circulatory system during support with a rotary blood pump.

In order to investigate the performance characteristics of nonpulsatile centrifugal pumps and their interaction with the pulsating heart, a computer simulation model was developed. A model of the pump, including the cannulae and the interference of the cannula and the left atrial wall, was added to a simulator of the circulation. It was implemented on a PC-AT using the analog simulating software AGO1000. An interval of 1 msec real-time per calculation step was evaluated to provide stable results. The calculation speed was approximately 100 msec per step. First simulation studies showed that both the positioning and resistance of the cannulae exert a major influence on system performance and equalized the different pressure-flow characteristics of vaneless and impeller pumps (difference of dp/dQ decreases from more than 6 times without cannulae to 130% with cannulae). In addition, the effects of suction in the atrial cannula, and changes of ventricular performance during changes in pumping power, could be properly simulated. The comparison with animal tests proved that the model is a suitable tool for testing control algorithms for centrifugal pumps.

Algorithms↗
PubMed1988

Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation.

A theoretical description of aqueous hydration in the minor groove of a B-form DNA is presented on the basis of a liquid-state Monte Carlo computer simulation on a system consisting of the oligonucleotide duplex d(CGCGAATTCGCG).d(GCGCTTAAGCGC) in a canonical B-form together with 1777 water molecules contained in a hexagonal prism cell and treated under periodic boundary conditions. The results are analyzed in terms of solvent density distributions. The calculated minor-groove solvent density shows considerable localization, indicative of discrete solvation sites and providing theoretical evidence for a well-defined ordered water structure. In the AATT sequence, this corresponds to the "spine of hydration" described by H. R. Drew and R. E. Dickerson [(1981) J. Mol. Biol. 151, 535-556] based on the x-ray crystal structure of the dodecamer hydrate. We find, however, that the calculated ordered water structure also extends into the CGCG flanking sequences, supported by the N2 hydrogen bond donors of the guanine residues and indicating that the spine of hydration could thus extend throughout the minor groove of a B-form DNA. This provides a possible explanation of the positive binding entropies observed by L. A. Marky and K. J. Breslauer [(1984) Proc. Natl. Acad. Sci. USA 84, 4359-4363] for both A.T and C.G sequences on the complexation of netropsin to the minor groove of DNAs. Implications of these results with regard to the thermodynamic stability of DNA in water and the sequence specificity of the minor groove hydration are discussed.

Computer Simulation↗
PubMed1983

Electrophoresis: mathematical modeling and computer simulation.

A mathematical model of electrophoretic separation processes has been developed and adapted for computer simulations. The model is used to predict the characteristic behavior of a variety of electrophoretic techniques from a knowledge of chemical equilibria and physical transport phenomena. The model provides a unifying basis for a rational classification of all electrophoretic processes.

Computers↗
PubMed2004

Three-dimensional diffusion of non-sorbing species in porous sandstone: computer simulation based on X-ray microtomography using synchrotron radiation.

The diffusion pathways of porous sandstone were examined by a three-dimensional (3-D) imaging technique based on X-ray computed tomography (CT) using the SPring-8 (Super Photon ring-8 GeV, Hyogo, Japan) synchrotron radiation facility. The analysis was undertaken to develop better understanding of the diffusion pathways in natural rock as a key factor in clarifying the detailed mechanism of the diffusion of radionuclides and water molecules through the pore spaces of natural barriers in underground nuclear waste disposal facilities. A cylindrical sample (diameter 4 mm, length 6 mm) of sandstone (porosity 0.14) was imaged to obtain a 3-D image set of 450(3) voxels=2.62(3) mm(3). Through cluster-labeling analysis of the 3-D image set, it was revealed that 89% of the pore space forms a single large pore-cluster responsible for macroscopic diffusive transport, while only 11% of the pore space is made up of isolated pores that are not involved in long-range diffusive transport. Computer simulations of the 3-D diffusion of non-sorbing random walkers in the largest pore cluster were performed to calculate the surface-to-volume ratio of the pore, tortuosity (diffusion coefficient in free space divided by that in porous rock). The results showed that (i) the simulated surface-to-volume ratio is about 60% of the results obtained by conventional pulsed-field-gradient proton nuclear magnetic resonance (NMR) laboratory experiments and (ii) the simulated tortuosity is five to seven times larger than the results of laboratory diffusion experiments using non-sorbing I(-) and Br(-). These discrepancies are probably attributed to the intrinsic sample heterogeneity and limited spatial resolution of the CT system. The permeability was also estimated based on the NMR diffusometry theory using the results of the random walk simulations via the Kozeny-Carman equation. The estimated permeability involved an error of about 20% compared with the permeability measured by the conventional method, suggesting that the diffusometry-based NMR well logging with gradient coils is applicable to the in-situ permeability measurement of strata. The present study demonstrated that X-ray CT using synchrotron radiation is a powerful tool for obtaining 3-D pore structure images without the beam-hardening artifacts inevitable in conventional CT using X-ray tubes.

Absorption↗
PubMed2004

Gastric flow and mixing studied using computer simulation.

The fed human stomach displays regular peristaltic contraction waves that originate in the proximal antrum and propagate to the pylorus. High-resolution concurrent manometry and magnetic resonance imaging (MRI) studies of the stomach suggest a primary function of antral contraction wave (ACW) activity unrelated to gastric emptying. Detailed evaluation is difficult, however, in vivo. Here we analyse the role of ACW activity on intragastric fluid motions, pressure, and mixing with computer simulation. A two-dimensional computer model of the stomach was developed with the 'lattice-Boltzmann' numerical method from the laws of physics, and stomach geometry modelled from MRI. Time changes in gastric volume were specified to match global physiological rates of nutrient liquid emptying. The simulations predicted two basic fluid motions: retrograde 'jets' through ACWs, and circulatory flow between ACWs, both of which contribute to mixing. A well-defined 'zone of mixing', confined to the antrum, was created by the ACWs, with mixing motions enhanced by multiple and narrower ACWs. The simulations also predicted contraction-induced peristaltic pressure waves in the distal antrum consistent with manometric measurements, but with a much lower pressure amplitude than manometric data, indicating that manometric pressure amplitudes reflect direct contact of the catheter with the gastric wall. We conclude that the ACWs are central to gastric mixing, and may also play an indirect role in gastric emptying through local alterations in common cavity pressure.

Computer Simulation↗
PubMed1991

Computer simulations of chondrocytic clone behaviour in rabbit growth plates.

The growth behaviour of chondrocytic clones in the cell columns of the proximal tibial growth plates of young rabbits was modelled in computer simulations. Simulations were performed, modelling either clones in large groups of columns or clones in one single column. The former were based on morphological data and measurements of cell columns from an earlier study while the latter utilised previous findings of cellular kinetics in rabbit growth plates. Simulation results that resembled most closely the actual observations on rabbit growth plates were those in which a distribution of values was assumed both for clone length (ranging from 1000 to 2000 microns) and for the lengths of the discontinuities between clones. When the assumption was made in the models that the disappearing (metaphyseal) end of an 'old' clone moved more rapidly than the developing (epiphyseal) end of a 'new' clone, replacing the former, the length of the discontinuity between these two clones increased with time. This assumption, which could be modelled in the simulations of clones in a single column based on cell growth behaviour, was found to provide an explanation for an earlier finding that there are more short columns at the epiphyseal side than at the metaphyseal side of a growth plate.

Animals↗
PubMed1995

Computer simulation of the electrotonic modulation of pacemaker activity in the sinoatrial node by atrial muscle.

Electrotonic interaction between the sinoatrial (SA) node and surrounding atrial muscle was investigated in a computer simulation using a modified Oxsoft HEART model (Oxsoft, Oxford, UK). When an SA node cell model was coupled to a passive atrial membrane model (RC circuit) with various coupling conductances (Gc), there was a Gc-dependent prolongation of spontaneous cycle length (SCL). At a sufficiently high value of Gc, the spontaneous activity was finally stopped. A nonlinear relationship between Gc and SCL was obtained, similar to that observed in experiments on rabbit SA node cells. When the muscarinic potassium current (iK,ACh) was activated in the SA node cell model, the coupling-induced inhibition of pacemaker activity was potentiated. Although coupling current and iK,ACh were additive, their effects on SCL were more than additive because of the nonlinear dependence of SCL on net current. A decrease in the input resistance of the atrial membrane model to stimulate the activation of iK,ACh in atrial muscle was also shown to potentiate the coupling-induced inhibition of SA node spontaneous activity.

Action Potentials↗
PubMed1991

Computer simulation model of swine production systems: II. Modeling body composition and weight of female pigs, fetal development, milk production, and growth of suckling pigs.

Theoretical concepts and relationships used to develop a deterministic computer simulation model of female pigs during their reproductive life are described. The model predicts, in a continuous form, body composition and weight of female pigs, fetal development, sow milk yield, and growth of suckling pigs according to genotype, diet, and management conditions. The model simulates growth of adult female pigs. Dietary nutrients are used first for maintenance and second for fetal growth or milk production. Any surplus is retained in the body. Energy and protein body reserves are mobilized when a nutrient deficit occurs during gestation or lactation. However, the rates of body protein and fat accretion as well as the fat/protein ratio are limited by boundaries, the values of which depend on the nutritional and physiological status of the pig. The model's ability to simulate sow body weight changes and composition, fetal growth, milk production, and suckling pig's growth is illustrated.

Animals↗
PubMed2006

High-resolution computer simulation of the dynamics of isoelectric focusing using carrier ampholytes: focusing with concurrent electrophoretic mobilization is an isotachophoretic process.

Focusing of four hemoglobins with concurrent electrophoretic mobilization was studied by computer simulation. A dynamic electrophoresis simulator was first used to provide a detailed description of focusing in a 100-carrier component, pH 6-8 gradient using phosphoric acid as anolyte and NaOH as catholyte. These results are compared to an identical simulation except that the catholyte contained both NaOH and NaCl. A stationary, steady-state distribution of carrier components and hemoglobins is produced in the first configuration. In the second, the chloride ion migrates into and through the separation space. It is shown that even under these conditions of chloride ion flux a pH gradient forms. All amphoteric species acquire a slight positive charge upon focusing and the whole pattern is mobilized towards the cathode. The cathodic gradient end is stable whereas the anodic end is gradually degrading due to the continuous accumulation of chloride. The data illustrate that the mobilization is a cationic isotachophoretic process with the sodium ion being the leading cation. The peak height of the hemoglobin zones decreases somewhat upon mobilization, but the zones retain a relatively sharp profile, thus facilitating detection. The electropherograms that would be produced by whole column imaging and by a single detector placed at different locations along the focusing column are presented and show that focusing can be commenced with NaCl present in the catholyte at the beginning of the experiment. However, this may require detector placement on the cathodic side of the catholyte/sample mixture interface.

Ampholyte Mixtures↗
PubMed2002

A computer simulation of the prevention of the transmission of Toxoplasma gondii on swine farms using a feline T. gondii vaccine.

Transmission of Toxoplasma gondii on swine farms was investigated using a deterministic dynamic computer simulation model. A primary focus was to evaluate a feline T. gondii vaccine. Animal populations (swine and cats) were compartmentalized based on the stage of T. gondii infection. Simulations were run under conditions of closed and equilibrium population size. Model parameters were varied in a factorial experimental design to test the following hypotheses: T. gondii infection in finishing pigs decreases with (1) vaccination of susceptible cats, (2) an increase in the proportion of cats captured for vaccination, (3) a decrease in the initial number of cats, (4) a decrease in the initial T. gondii prevalence in cats and (5) a decrease in oocyst-survival time. Seeding conditions included a total of 10, 20, 30, 40 or 50 cats, initial T. gondii prevalences in cats of 30, 60 or 90%, vaccination of 0, 50 or 75% of the cats and two vaccination schedules (the field schedule from a prior trial and a weaning-vaccination schedule). Simulations were run at oocyst-survival times of 52, 39 and 26 weeks. T. gondii prevalence in finishing pigs was recorded every week for 10 years. The probability of elimination of T. gondii from finishing pigs increased with a decrease in the number of cats and a decrease in oocyst-survival time. The last-year average prevalence was used as the outcome in a multiple linear regression analysis. Decreased T. gondii prevalence in finishing pigs was the result of a decrease in the initial number of cats on the farm (squared semipartial correlation coefficient (sr(2))=47%), decreased oocyst survival (sr(2)=35%), using the weaning-vaccination schedule (sr(2)=7%) and vaccination versus non-vaccination (sr(2)=5%). Unexpectedly, the initial T. gondii prevalence in cats had no effect on T. gondii prevalence in finishing pigs. The simulation supports the field trial indicating vaccine effectiveness. However, vaccination had less impact on decreasing T. gondii infection in finishing pigs than a decrease in the number of farm cats.

Animals↗