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At least 91 records · Page 5Linked to original sources

Patterns of glycogen turnover in liver characterized by computer modeling.

We used a computer model of liver glycogen turnover to reexamine the data of Devos and Hers, who reported the time course of accumulation in and loss from glycogen of label originating in [1-14C]galactose injected at different times after the start of refeeding of 40-h fasted mice or rats. In the present study computer representation of individual glycogen molecules was utilized to account for growth and degradation of glycogen according to specific hypothetical patterns. Using this model we could predict the accumulation and localization within glycogen of labeled glucose residues and compare the predictions with the previously published data. We considered three specific hypotheses of glycogen accumulation during refeeding: 1) simultaneous, 2) sequential, and 3) accelerating growth. Hypothetical patterns of glycogen degradation were 1) ordered and 2) random degradation. The pattern of glycogen synthesis consistent with experimental data was a steadily increasing number of growing glycogen molecules, whereas during degradation glycogen molecules are exposed to degrading enzymes randomly, rather than in a specific reverse order of synthesis. These patterns predict the existence of a specific mechanism for the steadily increasing "seeding" of new glycogen molecules during synthesis.

Computer Simulation↗

Computer modelling for patient observation.

Computer modelling can be used to help release nurses from administrative functions and enable them to spend more time with patients. In this article, the authors describe pilot project in mental health nursing designed to make the planning of patient observation more efficient.

Computer Simulation↗

Stereochemical complementarity of progesterone, RU486 and cavities between base pairs in partially unwound double stranded DNA assessed by computer modelling and energy calculations.

Computer modeling was used to examine the relative fit of progesterone and RU486 in cavities constructed between base pairs in double stranded DNA. Progesterone was capable of forming two stereospecific hydrogen bonds between the carbonyl groups and protonated phosphate groups on adjacent strands. Favorable van der Waals and electrostatic energies were exhibited upon insertion of progesterone into DNA indicating an excellent fit. While RU486 could be accommodated between the base pairs and formed hydrogen bonds, there was a high van der Waals energy in the resulting complex. When the complexes were subjected to energy minimization, the conformation of the DNA was significantly altered in the RU486-DNA complex but not in the progesterone-DNA complex. No mechanistic interpretation of these results is proffered; however, such information may have evolutionary significance and could prove useful in designing new progesterone agonists and antagonists.

Base Composition↗

Computational models of collective behavior.

Computational models of human collective behavior offer promise in providing quantitative and empirically verifiable accounts of how individual decisions lead to the emergence of group-level organizations. Agent-based models (ABMs) describe interactions among individual agents and their environment, and provide a process-oriented alternative to descriptive mathematical models. Recent ABMs provide compelling accounts of group pattern formation, contagion and cooperation, and can be used to predict, manipulate and improve upon collective behavior. ABMs overcome an assumption that underlies much of cognitive science--that the individual is the crucial unit of cognition. The alternative advocated here is that individuals participate in collective organizations that they might not understand or even perceive, and that these organizations affect and are affected by individual behavior.

Cognition↗

Metabolism of the acutely ischemic dog heart. I. Construction of a computer model.

Construction of a computer model of glycolysis, the Krebs cycle, and related metabolism in acutely ischemic dog heart, involving 122 metabolites, 65 enzymes, and 406 chemical reactions, is described. A previous model of the same metabolism in normal-flow rat heart was modified to fit ischemic dog heart experimental data to within experimental error. The result resembles other models of ischemic heart preparations, implying common underlying mechanisms. The principal change made was reduction of enzyme amounts, consistent with the generally slower metabolism of large animals, suggesting that differing enzyme amounts are a major component of interspecies metabolic difference. Glycolytic intermediates oscillate, asynchronously and with large changes in level; pyridine nucleotides become highly reduced; pH falls, but mitochondria stay alkaline relative to cytoplasm even after oxidative phosphorylation stops.

Animals↗

Optimization of peritoneal dialysis prescription using computer models of peritoneal transport.

Computer models are valuable clinical tools in the effort to improve quality of life for dialysis patients. At present, two software programs have been validated clinically in adult and pediatric populations. They are the Personal Dialysis Capacity (PDC: Gambro Lundia AB, Lund, Sweden) and PD Adequest (Baxter Healthcare Corporation, Deerfield, IL, U.S.A.). Both programs seem to give accurate predictions of small-solute clearance, but the PDC seems to be superior in predicting ultrafiltration volumes. Indeed, the software programs have several important differences that affect their accuracy and, hence, their clinical value. The PDC software introduces the concepts of capillary physiology to the field of peritoneal dialysis. It gives a functional description of the peritoneal membrane of the individual patient. Recently, its "new" area parameter (A0/delta x) was shown to be superior to the peritoneal equilibration test (PET) in predicting transperitoneal exchange.

Adult↗

A comprehensive PC-based computer model for microdosimetry of BNCT.

A computer model is described that performs microdosimetric calculations of the radiation dose delivered to tumour and normal tissue in boron neutron capture therapy (BNCT) by simulating capture reactions in a predefined three-dimensional space. The role of intracellular boron distributions and cellular dimensions on the radiation dose in clinical and experimental BNCT has been studied using a PC-based computer model. In order to calculate the radiation dose to low boron uptake cells, the extent of irradiation by boron containing adjacent cells (cross fire) is also dealt with. Radiation doses from boron and nitrogen neutron capture are converted to a biological effect by means of relative individual ion track segment efficacies, based on linear energy transfer along the particle track. A good correlation was found after comparing predicted values with previously published experimental data. A number of examples is given to illustrate the program's features.

Boron Neutron Capture Therapy↗

Computer modeling of prostate cancer treatment. A paradigm for oncologic management?

This article discusses the relevance of computer modeling to the management of prostate cancer. Several computer modeling techniques are reviewed and the advantages and disadvantages of each are discussed. An example that uses a computer model to compare alternative strategies for clinically localized prostate cancer is examined in detail. The quality of the data used in computer models is critical, and these models play an important role in medical decision making.

Adenocarcinoma↗

Computational models in immunological methods: an historical review.

The utilization of computational models in immunology dates from the birth of the science. From the description of antibody-antigen binding to the structural models of receptors, models are utilized to bring fundamental understandings of the processes together with laboratory measurements to uncover implications of these data. In this review, an historical view of the role of computational models in the immunology laboratory is presented, and short mathematical descriptions are given of fundamental assays. In addition, the range of current uses of models is explored -- especially as seen through papers which have appeared in the Journal of Immunological Methods from volume 1 (1971/1972) to volume 208 (1997). Each paper which introduced a new mathematical, statistical, or computer simulation model, or introduced an enhancement to an instrument through a model in those volumes is cited and the type of computational model noted.

History, 20th Century↗

Voxel-based computational models of real human anatomy: a review.

Computational models of human anatomy are mathematical representations of human anatomy designed to be used in dosimetry calculations. They have been used in dosimetry calculations for radiography, radiotherapy, nuclear medicine, radiation protection and to investigate the effects of low frequency electromagnetic fields. Tomographic medical imaging techniques have allowed the construction of digital three-dimensional computational models based on the actual anatomy of individual humans. These are called voxel models, tomographic models or phantoms. Their usefulness lies in their faithful representation of human anatomy and the flexibility they afford by being able to be scaled in size to match the required human dimensions. Segmenting medical images in order to make voxel models is very time-consuming so semi-automatic segmentation techniques are being developed. Some 21 whole or partial body models currently exist and more are being prepared. These models are listed and discussed.

Adult↗

Novel computational model for the interaction of dopamine with the D2 receptor.

With the use of molecular modelling and computational chemistry, two models were obtained showing the binding of dopamine to part of the D2 receptor. These models consist of a molecular complex containing dopamine, the transmembrane domains (TM) 3, 4 and 5, a small part of the extracellular loop just before TM3 and a larger part of the loop connecting TM4 and TM5. The models are further characterized by the presence of two disulphide bonds: one between TM3 and TM4 and a second linking the Cys residue before TM3 with the Cys residue in the loop between TM4 and TM5. In the first model, the beta-adrenergic receptor is used as a reference with the catechol moieties of dopamine interacting with two Ser residues in TM5, and the Asp residue in TM3 interacting with the protonated nitrogen of dopamine. In the second model, dopamine is positioned between the TM without interaction assumptions. In both models the TM positions are close to the arrangement of the alpha-helix ordering as found in bacteriorhodopsin. Energy minimization was accomplished using these two starting structures. The two minimized complexes show different molecular interactions that make good chemical sense and are in agreement with reported X-ray data of different proteins. The disulphide bond between TM3 and 4 is apparently unique to the D2 and D3 receptors. The first minimized complex revealed that not Ser194, as in the beta-receptor, but Ser 193 interacted with the meta-hydroxyl of dopamine, although a proper hydrogen bond with Ser194 was initially present in the starting structure. The para-hydroxyl group interacted with Ser197.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

A computational model of oxygen transport from red blood cells to mitochondria.

A computational model of oxygen transport from red blood cells to mitochondria with subsequent reaction to water is presented. This computational model consists of a five region convection-diffusion-reaction mathematical model which is solved using a standard numerical time-split method. The unique feature of this mathematical model is the treatment of the red blood cells and the plasma as two separate flows. The numerical method is second order accurate overall. This computational model is useful for analyzing residue data from positron emission tomography or data from multiple indicator dilution curves.

Biological Transport↗

Computer model simulating medical care in hospital.

A computer model has been constructed to simulate the activities and events concerned in the care of patients in hospital. After validation of the model it has been used to examine the consequences of certain changes in the mode of working in the hospital, including the scheduling of items of service and a system of progressive care. It is concluded that computer models of this kind are likely to prove of value in the management of hospital resources.

Computers↗

Computer modeling and simulation of human movement. Applications in sport and rehabilitation.

Computer modeling and simulation of human movement plays an increasingly important role in sport and rehabilitation, with applications ranging from sport equipment design to understanding pathologic gait. The complex dynamic interactions within the musculoskeletal and neuromuscular systems make analyzing human movement with existing experimental techniques difficult but computer modeling and simulation allows for the identification of these complex interactions and causal relationships between input and output variables. This article provides an overview of computer modeling and simulation and presents an example application in the field of rehabilitation.

Algorithms↗

Algorithms for the computer modelling of mechanical interactions with soft tissue.

The computer modelling of soft tissue has applications in the simulation of surgical procedures, product design, and in CAD generally as well as in motion pictures. We begin by reviewing computer modelling techniques in a range of applications. Algorithms are described to predict where surfaces interact mechanically, aiming as far as possible to use geometric modelling methods available within high level CAD systems. After an initial 2-Dimensional evaluation, 3-dimensional surfaces were used throughout. A model was developed to predict the region of impact of two surfaces in an environment of many surface patches. We report the results of this modelling and the application of refinement algorithms to reduce the computation requirements. We then go on to discuss the applicability of this work in the modelling of the deformation behaviour of soft tissues.

Algorithms↗

A performance adequate computational model for auditory localization.

A computational model of auditory localization resulting in performance similar to humans is reported. The model incorporates both the monaural and binaural cues available to a human for sound localization. Essential elements used in the simulation of the processes of auditory cue generation and encoding by the nervous system include measured head-related transfer functions (HRTFs), minimum audible field (MAF), and the Patterson-Holdsworth cochlear model. A two-layer feed-forward back-propagation artificial neural network (ANN) was trained to transform the localization cues to a two-dimensional map that gives the direction of the sound source. The model results were compared with (i) the localization performance of the human listener who provided the HRTFs for the model and (ii) the localization performance of a group of 19 other human listeners. The localization accuracy and front-back confusion error rates exhibited by the model were similar to both the single listener and the group results. This suggests that the simulation of the cue generation and extraction processes as well as the model parameters were reasonable approximations to the overall biological processes. The amplitude resolution of the monaural spectral cues was varied and the influence on the model's performance was determined. The model with 128 cochlear channels required an amplitude resolution of approximately 20 discrete levels for encoding the spectral cue to deliver similar localization performance to the group of human listeners.

Humans↗

The enteric neural network and three dimensional computer modelling of intestinal peristalsis.

A computer model of the enteric nervous system has been developed using MATLAB in order to determine the extent to which the nature of intestinal activity can be explained by our current understanding of the projections and connectivity of enteric neurons. The model is based on repeated, identical overlapping modules, each of which contains the same number of neurones and circular muscle. The connections between modules were derived from microanatomical data. This simple model explains some characteristic features of the generation of an intestinal motor pattern.

Animals↗

Computational models of association cortex.

Recent computational models, or mathematical realizations of neurobiological theories, are providing insights into the organization and workings of the association cortex. Such models concern the construction of cortical maps, the neural basis of cognitive functions such as visual perception, reward-motivated learning and some aspects of consciousness.

Animals↗