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PubMed2001

[Statistical quality control of clinical laboratory analyses using Chi squared criterion (use of computer modeling)].

Models of analytical series simulating good results and series with systematic errors were created on the basis of data bank of results of clinical biochemical analyses by computer simulation method. The quality of analyses was evaluated using chi 2 test. This parameter reacts to slight systematic errors and depends little on changes in the examined patient population; on the other hand, its sensitivity is the higher the longer is the analytical series. Statistical method for quality control by the chi 2 test is highly sensitive, absolutely objective, and requires no extra expenses for control studies.

Chi-Square Distribution↗
PubMed1994

Computer modelling of the interaction between human choriogonadotropin and its receptor.

Primary structural homology between the hormone binding site of the LH/CG receptor and the enzyme binding site of chymotrypsin inhibitor has been identified. This has led to the application of a knowledge-based approach of molecular modelling to describe the interaction of choriogonadotropin (CG) with the LH/CG receptor. A tertiary structural model for the mode of recognition between the hormone and the receptor has been proposed. As in other such processes at the molecular level, the recognition between CG and its receptor is mediated through non-covalent interactions. The specificity of recognition is achieved by complementarity in van der Waals surfaces, hydrogen bonding and non-polar associations. The model shows nine hydrogen bonds between the hormone and the receptor involving polar side chains as well as backbone amine and carbonyl groups. A hydrophobic cluster involving side chain groups at the interface is also important in stabilization of the intermolecular interactions.

Amino Acid Sequence↗
PubMed1998

A computer model of intracranial dynamics integrated to a full-scale patient simulator.

The ability to visualize intracranial dynamics during simulated clinical scenarios is a valuable tool for teaching brain physiology and the consequences of different medical interventions on the brain. Studies have isolated physiologic variables and shown their effects on brain dynamics. However, no studies have shown the combined effects of these variables on intracranial dynamics. This brain model offers one approach that brings all these relationships together and shows how they affect the dynamics of the brain. The brain model obtains its physiologic inputs from a full-scale patient simulator which responds to clinical interventions. This integration allows individuals working on the patient simulator to see the effects of their actions on brain dynamics. The brain model gives a real-time display of intracranial events (cerebral metabolic rate, cerebral blood flow, cerebral blood volume, cerebral perfusion pressure, and intracranial pressure) and responds to changes in the pulmonary and cardiovascular condition of the patient simulator.

Blood Volume↗
PubMed1993

Computer modelling in predicting carcinogenicity.

The cytochrome P450-dependent mixed-function oxidases are the most important enzyme system in the oxidation of chemicals to their reactive intermediates which then interact with cellular components to provoke toxicity and carcinogenicity. These enzymes comprise a multifamily of proteins, two families of which, namely CYP1A and CYP2E, activate planar and small molecular weight compounds, respectively. A computer graphic procedure (COMPACT) has been developed which, based on the molecular shape and electronic structure of the chemical, determines whether the chemical will interact with these two particular cytochrome P450 families and thus be metabolized to toxic and carcinogenic intermediates. As the basal levels of these enzyme families are low, the ability of the chemical to induce them selectively, on repeated administration, is an important determinant of its carcinogenic potential. Inductive capability may be determined in short-term experiments (ENACT) utilizing a small number of animals. Thus the combination of COMPACT and ENACT provides a rapid and inexpensive means for the preliminary screening of chemicals, before the long term and expensive rodent lifetime bioassays are undertaken.

Animals↗
PubMed2005

Hypoxaemia during open-airway apnoea: a computational modelling analysis.

Hypoxaemia during open-airway apnoea, e.g. during brainstem death testing, may cause organ damage. The effect of ambient oxygen fraction on the extent of hypoxaemia has not been established. We validated the Nottingham Physiology Simulator in this context by reproducing the methodologies and results of four published clinical studies. We then used the simulator to examine the effects of different ambient oxygen fractions (0.21-1.0) and shunt fractions (1-30% of cardiac output) during apnoea. Increasing ambient oxygen fraction from 0.9 to 1.0 more than doubled the time to haemoglobin desaturation at all shunt fractions, and extended apnoea longer than when the ambient oxygen fraction was increased from 0.21 to 0.9. When ambient oxygen fraction and shunt fraction were large, arterial oxygen tension transiently increased during apnoea. A very high ambient oxygen fraction and a patent airway are likely to delay dangerous hypoxaemia during apnoea.

Apnea↗
PubMedDate not supplied

Computational model to evaluate port wine stain depth profiling using pulsed photothermal radiometry.

We report on development of an optical-thermal model to evaluate the use of pulsed photothermal radiometry (PPTR) for depth profiling of port wine stain (PWS) skin. In the model, digitized histology sections of a PWS biopsy were used as the input skin geometry. Laser induced temperature profiles were reconstructed from simulated PPTR signals by applying an iterative, non-negatively constrained conjugate gradient algorithm. Accuracy of the following PWS skin characteristics extracted from the reconstructed profiles was determined: (1) average epidermal thickness (z(epi)), (2) maximum epidermal temperature rise (DeltaT(epi,max)), (3) depth of PWS upper boundary (z(PWS)), and (4) depth of maximum PWS temperature rise (z(PWS,max)). Comparison of the actual and reconstructed profiles from PPTR data revealed a good match for all four PWS skin characteristics. Results of this study indicate that PPTR is a viable approach for depth profiling of PWS skin.

Algorithms↗
PubMedDate not supplied

A computational model for cell differentiation.

In this paper, we present a word set generating mechanism, called cell-differentiation system, inspired by the tissue process formation in multicellular organisms, which might model some properties of evolving communities of living cells at the syntactical level. The tools utilized to model these biological phenomena belong to the formal language theory. In this context chromosomal mutations are defined as operations on strings and the differentiation according to the control of gene expression is represented by some random-context conditions in formal languages. In the presented formal framework we prove that in a simplified form of this formalism, with only one cell-type which is regular, one single cell and no mitosis involved, the problem of establishing whether or not the set of vectors of integers indicating the number of cells in each population, is finite, linear or semilinear, is recursively undecidable. However, one can algorithmically decide whether or not a cell-differentiation system of finite cell-type can produce a specific generation of cells.

Algorithms↗
PubMed1983

A computer model of jaw and hyoid movement in the cat.

A digital model was used to study the varying movements of the feline jaw and hyoid in the sagittal plane. The effect of mandibular movement on the path of movement of the hyoid relative to the palate was investigated for model paths of movement of the hyoid, i.e. paths of movement that were always elliptical relative to the mandible. Major effects upon the path of movement of the hyoid relative to the palate were produced by two factors: (1) the presence of a fast open/fast close complex within the profile of jaw movement; (2) the time relationship of the backwards movement of the hyoid relative to that of the fast open/fast close complex. The average antero-posterior position of the hyoid in the mandibular plane and the angle of the major axis of the ellipse to that plane were less important factors. Within limits (relative to the mandible), the overall amplitude of the hyoid movement, its vertical position and the direction in which the ellipse was travelled were all unimportant factors in determining the general nature of hyoid movement relative to the palate.

Animals↗
PubMed1992

Development of a computer model to predict strains in the individual fibers of a ligament across the ligamentous occipito-atlanto-axial (C0-C1-C2) complex.

A fresh ligamentous occipito-atlanto-axial (C0-C1-C2) complex was appropriately prepared and serially sectioned into thin slices along the transverse planes. The bony outlines from these slices were digitized and assembled in the proper manner to obtain a three-dimensional model of the complex using the AutoCAD system. Various ligaments were identified on the model and strains in individual fibers of a ligament were predicted based on the principles of rigid body mechanics. The ligament behaviors in axial rotation, flexion, and extension modes were analyzed. The capsular ligament fibers were predicted to undergo strains in all modes. Furthermore, these ligaments experienced the largest strain among the ligaments analyzed. Fibers within a ligament were found to respond differently; some were more active than the others and some did not experience any strain at all. A differential behavior in the right and left side alar ligament fibers was also found in axial rotation. The transverse ligament was predicted to wrap around the dens during axial rotation. The strain within a fiber was found to be a function of the initial length (ligament laxity) and its distance from the center of rotation.

Atlanto-Axial Joint↗
PubMed2004

Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code.

Numerous investigations in the last years focused on chromosome arrangements in interphase nuclei. Recent experiments concerning the radial positioning of chromosomes in the nuclear volume of human and primate lymphocyte cells suggest a relationship between the gene density of a chromosome territory (CT) and its distance to the nuclear center. To relate chromosome positioning and gene density in a quantitative way, computer simulations of whole human cell nuclear genomes of normal karyotype were performed on the basis of the spherical 1 Mbp chromatin domain model and the latest data about sequence length and gene density of chromosomes. Three different basic assumptions about the initial distribution of chromosomes were used: a statistical, a deterministic, and a probabilistic initial distribution. After a simulated decondensation in early G1, a comparison of the radial distributions of simulated and experimentally obtained data for CTs Nos. 12, 18, 19, and 20 was made. It was shown that the experimentally observed distributions can be fitted better assuming an initial probabilistic distribution. This supports the concept of a probabilistic global gene positioning code depending on CT sequence length and gene density.

Biophysics↗
PubMedDate not supplied

[Methods of computer modeling and conformational mobility of DNA duplexes].

The review is focused on issues of transferability of the context-sensitive conformational characteristics of DNA estimated from crystallographic structural data on the DNA in aqueous solution. The state of the art in molecular dynamics of charged biopolymers in aqueous solution is covered. Elaboration of expedient force fields and algorithms of calculating long-range electrostatic interactions and solving combined equations of atomic motion have made it possible to generate stable nanosecond trajectories of thermal atomic motion of the biopolymer in aqueous solution in the presence of counterions and salt ions over reasonable time. Tools for analyzing the atomic statistical trajectories of DNA duplexes in aqueous solution to infer context-sensitive conformational dynamic characteristics are discussed together with advances in simulating the mechanisms of global axial bend in DNA duplexes. These techniques allow one to consecutively analyze relationships between the contextual composition of the duplex and the basic modes of essential motions, their amplitude and extent of fluctuation. Development of satisfactory methods for estimating the free energy of biopolymer conformations in solution permits qualitative assessment of the conformational thermodynamic stability of biopolymers and their complexes.

Computer Simulation↗
PubMed1985

Evolve II: a computer model of an evolving ecosystem.

The Evolve II program is a model of an ecosystem in which organisms are allowed to evolve. Organisms are subject to a changeable environment and competition from other organisms for a limited food supply. The gene structure may change through mutation. A feature of Evolve II is that the magnitude of phenotypic change resulting from mutation is itself a property of the gene. The system was studied under a number of environmental variation schemes. We report three significant findings. Two species (lineages with distinctly different survival strategies) evolved and coexisted in the same environmental conditions. Organisms developed a resistance to phenotypic change in response to mutation in slowly varying environments. However, traits which favor survival of the individual at the expense of reproduction could in some cases undergo phenotypic change in response to mutation despite the fact that this did not favor the survival of the offspring. This demonstrates that gene structures can evolve which are advantageous from the standpoint of the lineage, but not advantageous from the standpoint of individual offspring.

Aging↗
PubMed1987

Estimation of the determinants of transcutaneous oxygen tension using a dynamic computer model.

A dynamic model for oxygen transport within the outer layers of the skin and a tcPO2 sensor has been developed. By comparing model simulations with clinical measurements from adults, it is possible to analyze some of the physiologic and physical determinants of the tcPO2 measurement. The results indicate that the permeability of the epidermis is a significant parameter when using a microcathode sensor. Using this model, the values obtained for normalized stratum papillare blood flow and metabolic oxygen consumption of the dermis are higher than those seen for other models.

Adult↗
PubMed2004

A computational model of human granulopoiesis to simulate the hematotoxic effects of multicycle polychemotherapy.

Moderate intensification of conventional multicycle chemotherapy has recently been shown to improve treatment results in malignant lymphomas and might prove to be beneficial also in other malignancies. However, the feasibility of such regimens is mainly limited by their granulopoietic toxicity. To identify and quantify the basic cell kinetic mechanisms of damage and stimulation caused by cytotoxic drugs and recombinant human granulocyte colony-stimulating factor (rhG-CSF), respectively, we developed a mathematical model of human granulopoiesis that allows simulation of leukocyte concentration profiles under 10 different multicycle polychemotherapy regimens with varying drug composition, dosage, and scheduling, including rhG-CSF assistance. Clinical data on leukocyte profiles were obtained from large numbers of patients treated within several multicenter trials. Simulation studies show that the leukocyte profiles of all regimens can be appropriately fitted using one single set of assumptions and parameters for the cell kinetic effects of cytotoxic drugs and rhG-CSF. Furthermore, the model can be used to explain the interindividual heterogeneity of hematotoxicity by a differential chemosensitivity, which might be useful in drug scheduling for specific risk groups. It is demonstrated that the model can be used to design and to select new drug schedules for subsequent clinical trial testing.

Computer Simulation↗