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PubMed1985

Fine structure of wide and narrow vertebrate muscle Z-lines. A proposed model and computer simulation of Z-line architecture.

A model of the structure of vertebrate Z-lines and Z-line analogs is introduced and supported by evidence from electron microscope studies of wide Z-lines (rat and feline soleus, and feline and canine cardiac muscles), narrow Z-lines (guppy, newt and frog skeletal muscles), and Z-rods (from a patient with nemaline myopathy and from cardiac muscles of aged dog). The model is based on a pair of Z-filaments (termed a Z-unit), which are linked near their centers at a 90 degrees angle and form bridges between neighboring antipolar thin (actin) filaments. A square lattice of four Z-filament pairs (the basic structure of the Z-line, termed a Z-line unit) defines the geometrical position of the I-square unit. In this native state of the Z-line, small square and large square net forms appear in cross-section. Other cross-sectional patterns of Z-lines, including basket-weave and diagonal-square net patterns, can be explained by detachment of the Z-filament from the Z-filament binding region within each Z-filament pair due to chemical or physical stress. Dissection of Z-lines and Z-line analogs with calcium-activated neutral protease provides evidence that the width of all wide Z-line structures is determined by the amount of overlap of antipolar thin filaments from adjacent sarcomeres. Longitudinal patterns of narrow and wide Z-lines are shown and described in relation to the model. To test the proposed model, the dynamics of the Z-line unit structure were computer-simulated. An attempt was made to correlate longitudinal (z direction) and cross-sectional (x and y directions) patterns and to determine the amount of movement of thin or Z-filaments that is required to explain the diversity observed in cross-sectional patterns of Z-lines. The computer simulations demonstrated that the structural transitions among the small square, and therefore large square net, as well as basket-weave and diagonal-square net forms seen in cross-sections could be caused by movements of thin filaments less than 10 nm in any direction (x, y or z).(ABSTRACT TRUNCATED AT 400 WORDS)

Actins↗

PubMed1990

Computer simulation of zinc finger motifs from cellular nucleic acid binding protein and their interaction with consensus DNA sequences.

We report here a computer simulation of the three-dimensional structures of seven zinc finger motifs from cellular nucleic acid binding protein involved in negative feedback inhibition of cholesterol biosynthesis. The structures are optimised using steric constraints imposed by tetrahedral coordination of the zinc ion with Cys and His residues, by molecular mechanics technique. We have also optimised the structure of a finger-I with GpT sequence. The model for the interaction of seven fingered protein with single-stranded d(GTGCGGTG) from sterol regulatory element (SRE) is given on the basis of these results. We also propose a scheme for recognition of a multifingered regulatory protein with small single-stranded DNA fragments.

Amino Acid Sequence↗

PubMed2004

Adolescent and adult pertussis vaccination: computer simulations of five new strategies.

Approximately one million adult pertussis cases occur annually in the US, and infants still die from pertussis. Computer simulations were used to predict the impact of vaccination of children, adults and/or adolescents, and household members of newborns (cocoon strategy). Childhood vaccination greatly reduced cases in children, but increased the incidence in adolescents and adults. Routine adolescent and adult vaccination had a large direct effect, whereas the cocoon strategy had a predominantly indirect effect on young infants. The number needed to vaccinate (NNV) to prevent a case of typical pertussis in the entire population was lowest for the adolescent strategy. The cocoon strategy had the lowest NNV to prevent a case of typical pertussis in young infants. The current vaccination schedule, local epidemiological data, age-specific cost of pertussis cases, and accessibility of the target population will determine which strategy has the highest likelihood of success in achieving the public health goal.

Adolescent↗

PubMed1977

Computer-simulated clinical encounter. II. Case flow and program content.

The completed computer-simulated case study provides the student with a written model of all components and steps involved in providing nutritional care to a patient. The completed study provides the instructor with a written record of the student's knowledge, her/his response to the patient's inquiries, and her/his organization of the clinical encounter and patient counseling. It is through this written record that student and instructor can analyze and strengthen the student's clinical skills.

Clinical Competence↗

PubMed1999

The impact of smoking on future pancreatic cancer: a computer simulation.

BACKGROUND: We studied the impact of several smoking cessation-based scenarios on future pancreatic cancer incidence in the European Union by means of computer simulation. MATERIAL AND METHODS: Among other data, published data on pancreatic cancer incidence rate and smoking prevalence in ten member states of the European Union, and on the relative risk of smoking were entered into a simulation model. Four different scenarios were simulated: one reference scenario, one based on theoretically maximal smoking reduction and two feasible scenarios based on WHO's Health for All targets. In each scenario, pancreatic cancer incidence was computed from 1994 up to the year 2020. Results were extrapolated to the European Union as a whole. RESULTS: When the percentage of smokers remains unchanged, 627,000 and 588,000 newly diagnosed pancreatic cancer cases among males and females respectively will arise in the European Union up to 2020. Theoretically, if all smokers would give up smoking instantly, this number can be reduced by 133,000 cases among men and 43,000 cases among women. In more feasible scenarios up to 35,500 male and 32,500 female pancreatic cancer cases can be prevented. CONCLUSION: Giving up smoking substantially reduces future burden of pancreatic cancer up to almost 68,000 patients in the European Union up to the year 2020.

Computer Simulation↗

PubMed1998

[Characterization of dose profile of remifentanil with computer simulation: comparative study with fentanyl and alfentanyl].

OBJECTIVES: To estimate the optimum dosing regimen and delivery system for remifentanil, a new opioid, using computer simulations based on information from pharmacokinetic and pharmacodynamic models available for fentanyl, alfentanil and remifentanil, as well as from clinical trials of fentanyl and alfentanil. PATIENTS AND METHODS: We estimated the site concentration ranges likely to be needed to blunt response to anesthetic or surgical stimuli and to recover from spontaneous ventilation. Dosing guidelines for remifentanil, fentanyl and alfentanil were estimated for three methods of administration (bolus, bolus + variable continuous infusion or constant continuous infusion). To that end, the time course of opioid concentration was simulated for hypothetical balanced anesthesia lasting 60 min. We then studied the number of boluses, the number of infusion rate steps, time taken to reach the terapeutic threshold, and time from turning off the infusion until reaching a concentration compatible with spontaneous ventilation. RESULTS: The estimated "effect site" concentration ranges for remifentanil were 6 to 10 ng.ml-1 during intubation; 4 to 6 ng.ml-1 during cutaneous incision; 4 to 7 ng.ml-1 for maintenance; and less than 2.5 ng.ml-1 for recovery of spontaneous ventilation. Simulated bolus administration indicated that 21 boluses of remifentanil, 4 boluses of fentanyl and 7 boluses of alfentanil were needed during one hour. The therapeutic threshold was reached within the first minute with remifentanil, within 2 minutes with fentanyl and within 1 min with alfentanil. Time until recovery of spontaneous ventilation was 7 min with remifentanil, 22 min with fentanyl and 14 min with alfentanil. In the simulation of bolus plus variable infusion, the initial bolus of remifentanil was 100 micrograms, the infusion rate for induction and maintenance was 25 micrograms.min-1 and the maintenance rate was 15 micrograms.min-1. The initial bolus of fentanyl was 300 micrograms, the infusion rate for induction and maintenance was 5 micrograms.min-1. The initial bolus of alfentanil was 2,000 micrograms, the infusion rate for induction was 200 micrograms.min-1 and the maintenance rates were 75 and 25 micrograms.min-1. The therapeutic threshold was reached in 1 min with remifentanil, in 2 min with fentanyl and within 1 min with alfentanil. Spontaneous ventilation was recovered 4 min after turning off the infusion of remifentanil, 4 min afterwards with fentanyl and 6 min afterwards with alfentanil. The simulated constant infusion rate for remifentanil of 15 micrograms.min1 (8 micrograms.min-1 for fentanyl and 75 micrograms.min-1 for alfentanil) allowed the therapeutic threshold to be reached in 10 min with remifentanil, in 22 min with fentanyl and in 17 min with alfentanil. Recovery of spontaneous ventilation occurred 5 min after closure of the infusion pump with remifentanil (24 min with fentanyl and 17 min with alfentanil). CONCLUSIONS: Information from pharmacokinetic and pharmacodynamic models allows us to establish the effect site concentration ranges for remifentanil and determine the ideal administration technique for this drug. The simulation also allows us to compare the properties of remifentanil to those of other common opioids such as fentanyl and alfentanil. The results are fairly consistent with clinical evidence, demonstrating the power of pharmacokinetic and pharmacodynamic models for rationally establishing opioid dosing guidelines.

Adult↗

PubMed1999

An operating room scheduling strategy to maximize the use of operating room block time: computer simulation of patient scheduling and survey of patients' preferences for surgical waiting time.

UNLABELLED: Determining the appropriate amount of block time to allocate to surgeons and selecting the days on which to schedule elective cases can maximize operating room (OR) use. We used computer simulation to model OR scheduling. Inputs in the computer model included different methods to determine when a patient will have surgery (on-line bin-packing algorithms), case durations, lengths of time patients wait for surgery (2 wk is the median longest length of time that the outpatients [n = 367] surveyed considered acceptable), hours of block time each day, and number of blocks each week. For block time to be allocated to maximize OR utilization, two parameters must be specified: the method used to decide on what day a patient will have surgery and the average length of time patients wait to have surgery. OR utilization depends greatly on, and increases as, the average length of time patients wait for surgery increases. IMPLICATIONS: Operating room utilization can be maximized by allocating block time for the elective cases based on expected total hours of elective cases, scheduling patients into the first available date provided open block time is available within 4 wk, and otherwise scheduling patients in "overflow" time outside of the block time.

Anesthesia↗

PubMed1975

Computer simulation of immunochemical interactions.

A computer model for simulation of the interactions between a macromolecular antigen and its corresponding IgG has been developed. The model takes all possible immune complexes into account, and it calculates the most probable immune complex distribution patterns on the basis of basic thermodynamic principles from the valences and initial concentrations of antigen and antibody, respectively, together with an association constant assumed to be common to all mutual interactions. In antigen excess small antigen-rich complexes are predicted. At or near equivalence a rich variety of relatively small complexes is predicted, while in antibody excess complexes of the type AgAbn are found to be the most probable. By further assuming that the precipitate consists of antibody excess complexes, a precipitin curve can be calculated. The agreement between calculated results and experimentally obtained data is found to be good. It is of special interest that this theory implies that the outcome of immunochemical interactions depend equally well on the concentrations of antigen and of antibody.

Animals↗

PubMed1975

Computer simulation of flagellar movement. III. Models incorporating cross-bridge kinetics.

A computer simulation procedure is used to analyze the generation of propagated bending waves by flagellar models in which active sliding is generated by a cycle of cross-bridge activity. Two types of cross-bridge cycle have been examined in detail. In both cycles, cross-bridge attachment is followed immediately by a configurational change in the cross-bridge, which transfers energy to a stretched elastic element and generates a shearing force between the filaments. In the first model, which has cross-bridge behavior close to current ideas about cross-bridge behavior in muscle, cross-bridge attachment is proportional to curvature of the flagellum and detachment is an exponential decay process. The configurational change is equivalent to an angular deviation of pi/5 radians. In the second type of cross-bridge cycle, cross-bridge attachment occurs rapidly when a critical curvature is reached, and detachment occurs when a critical curvature in the opposite direction is reached. With this cycle, an unrealistically large angular deviation of the cross-bridges, equivalent to 3.0 radians, is required to obtain bending waves of normal amplitude. Both models generate bending wave patterns similar to those obtained in earlier work. However, the behavior of the second type of cross-bridge model more closely matches the actual behavior of flagella under experimental conditions: the chemical turnover rate per beat cycle remains constant as the viscosity is increased, and reduction in the number of active cross-bridges can cause a reduction in beat frequency, with little change in amplitude or wavelength.

Binding Sites↗

PubMed2001

Synthesis and structure-activity relationships of a new model of arylpiperazines. Study of the 5-HT(1a)/alpha(1)-adrenergic receptor affinity by classical hansch analysis, artificial neural networks, and computational simulation of ligand recognition.

A classical quantitative structure-activity relationship (Hansch) study and artificial neural networks (ANNs) have been applied to a training set of 32 substituted phenylpiperazines with affinity for 5-HT(1A) and alpha(1)-adrenergic receptors, to evaluate the structural requirements that are responsible for 5-HT(1A)/alpha(1) selectivity. The resulting models provide a significant correlation of electronic, steric, and hydrophobic parameters with the biological affinities. Although the derived linear Hansch correlations give good statistics and acceptable predictions, the introduction of nonlinear relationships in the analysis gives more solid models and more accurate predictions. In the ANN models on the basis of the obtained 3D plots, the 5-HT(1A) affinity has a nonlinear dependence on F, V(o), V(m), and pi(o), although the nonlinear relationship is not far from a planar one. The alpha(1)-adrenergic receptor affinity has a clear nonlinear dependence on F, V(o), V(m), pi(o), and pi(m). A comparison of both analyses gives an additional understanding for 5-HT(1A)/alpha(1) selectivity: (a) high F values increase the binding affinity for 5-HT(1A) receptors and decrease the affinity for alpha(1) sites; (b) the hydrophobicity at the meta-position has only influence for the alpha(1)-adrenergic receptor; (c) the meta-position seems to be implicated in the 5-HT(1A)/alpha(1) selectivity. While the 5-HT(1A) receptor is able to accommodate bulky substituents in the region of its active site, the steric requirements of the alpha(1)-adrenergic receptor at this position are more restricted. This information was used for the design of the new ligand EF-7412 (33) (5-HT(1A): K(i exptl) = 27 nM, alpha(1): K(i exptl) > 1000 nM; 5-HT(1A): K(i pred) (ANN) = 36 nM, alpha(1): K(i pred ANN) = 2745 nM) which was characterized as an antagonist in vivo in pre- and postsynaptic 5-HT(1A)R sites. Computational simulations of the complex between EF-7412 (33) and a 3D model of the transmembrane domain of the 5-HT(1A) receptor allowed us to define the molecular details of the ligand-receptor interaction that includes: (i) the ionic interaction between the protonated amine of the ligand and Asp 3.32; (ii) the hydrogen bonds between the m-NHSO(2)Et group of the ligand and Asn 7.39; and the hydrogen bonds between the hydantoin moiety of the ligand and (iii) Thr 3.37, (iv) Ser 5.42, and (v) Thr 5.43. These QSAR and ANN results in combination with computational simulations of ligand recognition will be useful for the design of potent selective 5-HT(1A) ligands.

Animals↗

PubMedDate not supplied

An interactive computer simulation program for the design of statistical control procedures in clinical chemistry.

A computer simulation program has been developed to aid in the design of statistical quality control procedures in clinical chemistry. This 'QC simulator' permits the user to study the effects of parameters in the analytical procedure (method standard deviation, components of variance, rounding of data) and parameters in the control procedure (choice of statistics, control limits, decision criteria, number of control observations). The performance of the control procedures being studied are characterized by their probability for ejection, estimated at several different levels of random and systematic error, and presented by plots of statistical power vs the size of the analytical errors. The relative performance of different control procedures can be compared based on these performance characteristics. Another important application of the program is in the design of control procedures to assure that a specified level of analytical quality is achieved in routine laboratory analyses. The utility of this interactive simulation tool is illustrated in two typical sample runs.

Chemistry, Clinical↗

PubMed1992

[The effects of fear on individual and group escape in a computer simulated maze].

UNLABELLED: The purpose is to compare the effects of fear on escape behavior of individual and group conditions, in a computer-simulated maze. CRT display did not provide a bird's eye view of the maze, to the subjects, but only cues, what they would see, if they were actually inside of the maze. In the group escape condition, bodies and behaviors of other people were also shown in the maze. Subjects often got too close each other and collided with each other. THE RESULTS: Fear increased the time and locomotion required to reach the exit, because of the occurrence of a "traffic jam" in the group escape condition, however, fear reduced time in the individual escape condition. In addition, fear influenced types of escape behavior, depending on the form of maze.

Adult↗

PubMed2005

Computer simulation of nematic reentrance in a simple molecular model.

We report a computer simulation study of a system of parallel hard ellipsoids with attractive interactions represented by a spherically symmetric square well of range lamba. For suitable values of the results are consistent with the sequence of phases nematic (N), smectic-A (SmA), reentrant nematic (N(re)), and crystal (Cr) under pressure. Both the N-SmA and the SmA-N(re) transitions are found to be first order or continuous depending on temperature. Moreover, we show that a generalized van der Waals-type theory provides a qualitative description of the observed phase behavior.

Journal Article↗

PubMed2004

Computer simulation of Gd(III) speciation in human interstitial fluid.

The speciation and distribution of Gd(III) in human interstitial fluid was studied by computer simulation. The results show that at the background concentration, all the Gd(III) species are soluble and no precipitates appear. However as the total concentration of Gd(III) rises above 2.610 x 10(-9) mol/l, the insoluble species become predominant. GdPO4 is formed first as a precipitate and then Gd2(CO3)3. Among soluble species, free Gd(III), [Gd(HSA)] , [Gd(Ox)] and the ternary complexes of Gd(III) with citrate as the primary ligand are main species when the total concentration of Gd(III) is below 2.074 x 10(-2) mol/l. With the total concentration of Gd(III) further rising, [Gd3(OH)4] begins to appear and gradually becomes a predominant species.

Computer Simulation↗

PubMed2006

Oral absorption of poorly water-soluble drugs: computer simulation of fraction absorbed in humans from a miniscale dissolution test.

PURPOSE: The purpose of this study was to develop a new system for computer simulation to predict fraction absorbed (F(a)) of Biopharmaceutical Classification System (BCS) class II (low solubility-high permeability) drugs after oral administration to humans, from a miniscale dissolution test. METHODS: Human oral absorption of 12 lipophilic drugs was simulated theoretically by using the dissolution and permeation parameters of the drugs. A miniscale dissolution test and a solubility study were carried out in a conventional buffer and a biorelevant medium (pH 6.5). A dissolution parameter, which can simulate in vivo dissolution, was obtained from the in vitro dissolution curve. Human intestinal permeability was estimated assuming that the permeation was limited by diffusion through the unstirred water layer. The F(a) in humans was predicted and then compared with clinical data. RESULTS: The dissolution and solubility of most model drugs were faster and higher in a biorelevant medium than in a conventional buffer. The simulated absorption was limited by the drug dissolution rate and/or solubility. Predicted F(a) was significantly correlated with clinical data (correlation coefficient r2 = 0.82, p < 0.001) when the dissolution profiles in biorelevant medium were used for the simulation. CONCLUSIONS: This new system quantitatively simulated human absorption and would be beneficial for the prediction of human F(a) values for BCS class II drugs.

Absorption↗

PubMed1992

Computer simulation of erythrocyte transit in the cerebrocortical capillary network.

The relationship between erythrocyte flow path length and transit time was studied using a probabilistic computer simulation of erythrocyte transit in morphometrically reconstructed cerebrocortical microvascular network of the rat. The results suggest (1) a near-cubic relationship between erythrocyte flow and vessel diameter, (2) preferential pathways of erythrocyte flow, (3) an exponential relationship between erythrocyte transit time and flow path length.

Animals↗

PubMed2000

Accuracy analysis for RSA: a computer simulation study on 3D marker reconstruction.

In this paper, error analysis of three-dimensional marker coordinates reconstructed from noisy two-dimensional measurement in RSA was performed. Mathematical models to predict error propagation of focus position and object points were derived and computer simulations were performed to validate these models. Two clinical calibration cages were compared by testing the error propagation at each RSA step. The results revealed that errors of reconstructed object points were related to the focus position error, two-dimensional measurement error, position of focus and positions of object points, while errors of reconstructed focus position were determined by the two-dimensional measurement error, number of control points and location of the focus. The maximum difference between the mathematical model and the simulation for the assessment of errors of focus position was 14 microm and the maximum difference of object point positions was 1.1 microm. These differences were small and judged irrelevant, hence the simulations indicated that our models were accurate.

Computer Simulation↗

PubMed1994

[The spinal cord evoked potential by computer simulation: elucidation of killed-end potentials and augmentation caused by the conduction block phenomenon].

Single nerve fiber action potential (single-NAP) was computer simulated using solid angle approximation theory. The simulated spinal cord evoked potential (Simulated-SCEP) was then produced by summing the simulated single-NAPs according to the data of the fiber diameter spectrum of the human spino-cerebellar tract. To model the conduction block phenomenon in the spinal cord, it was assumed that each fiber impulse which reached the conduction block point could not go through the point and gradually became smaller. When the largest 10% of the constituent fibers had become blocked, there was augmentation of the negative peak at just before the conduction block point and at every point after the block. As the percentage of the blocked fibers increased, the amplitude of the simulated-SCEP decreased at every point except at just before the block. When 50% or more of the largest fibers were blocked, then augmentation of the negative peak still remained at just before the conduction block. However at the points just after the conduction block there was a monophasic positive waveform which is known as the killed-end potential. Phase cancellation normally dictates the wave forms of compound action potential. However, the killed-end potential and the augmentation of the amplitude associated with the conduction block can be explained by the loss of the phase cancellation.

Action Potentials↗