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At least 379 records · Page 21Linked to original sources
PubMed1992

A computer model to predict empty body weight in cattle from diet and animal characteristics.

A computer model was developed to predict empty BW in cattle as a function of diet (forage NDF, physical form of forage [hay vs silage and pasture], proportion of dietary concentrates) and animal (full BW) characteristics. The model was empty BW = full BW * (1 - GFILL), where GFILL is gut fill expressed as a fraction of full BW. An equation obtained from published data (GFILL = .05354 + .329 * NDF) was used to provide a base prediction of GFILL from the fraction of NDF in the forage. Predicted GFILL was then corrected for full BW, physical form of forage, and fraction of concentrates using multiplicative factors obtained from published data. The model was evaluated with data from 11 published experiments. Several breeds of cattle, a wide range of forage types, and diets with 0 to 93% concentrates were represented in these data. Observed values for empty BW were compared to model-predicted values and to values predicted by systems published by the Agricultural Research Council (ARC) and National Research Council (NRC). Sums of squared deviations of predicted values from observed (n = 64) were 3,074, 37,327, and 25,920 for the model, ARC, and NRC systems, respectively. After fitting predicted empty BW values to observed values, proportion of concentrates and forage NDF accounted for a significant (P less than .01) amount of the residual variation with the ARC and NRC systems, but not for the model. This finding suggests that the model will predict empty BW more accurately than the ARC and NRC systems with diets similar to those used in the evaluation.

Animal Feed↗
PubMed2001

A computer model of an image intensifier system working under automatic brightness control.

A computer model of a fluoroscopy unit operating under automatic brightness control has been developed. The model has been validated by simulating one particular unit but is very general in nature and can easily be applied to other fluoroscopy systems. The model was developed by breaking the operation of a fluoroscopy unit down into its constituent parts then implementing each part in a module of code. It is controlled using the input air kerma to the intensifier face. Discrepancies from the situation when the model is controlled by the energy deposited in the input phosphor have been investigated and shown to be negligible over the operating range. To calculate entrance surface dose rates (ESDRs) to water and polymethylmethacrylate (PMMA) phantoms, Monte Carlo techniques were used to generate backscatter factors for these materials using the beam geometry and range of possible tube potentials and field sizes of a typical mobile image intensifier unit. The model was validated by calculating ESDRs to different thicknesses of water and PMMA phantoms. The predictions generated by the model were in good agreement with experimental measurements. Potential uses of the model include evaluation of dose reduction techniques, investigation of the balance between patient dose and image quality, and assessment of scatter dose.

Algorithms↗
PubMedDate not supplied

[Computer modeling of mechanisms of the information processing in the olfactory bulb. II. Mechanisms of identification and short-term storage in the olfactory bulb: results of the computer experimentation].

The results of experimentation with the computer model of the olfactory bulb are presented. The architecture and scenario of the work of the model were described previously. The dynamic character of the identification process and the mechanism of memorizing short-term of smell stimuli are described. During the identification, a self-adjustment of the olfactory bulb to incoming signals occurs. The self-modification of mitral and tufted cell synapses enhances responses of the cells; upon subsequent presentation of the stimulus, the olfactory bulb responds with a higher activity. The modeling confirmed the validity of the assumption that the functions of mitral and tufted cells are to identify the components of a complex smell and the image of the smell as the whole.

Animals↗
PubMed1998

A computational model of how the basal ganglia produce sequences.

We propose a systems-level computational model of the basal ganglia based closely on known anatomy and physiology. First, we assume that the thalamic targets, which relay ascending information to cortical action and planning areas, are tonically inhibited by the basal ganglia. Second, we assume that the output stage of the basal ganglia, the internal segment of the globus pallidus (Gpi), selects a single action from several competing actions via lateral interactions. Third, we propose that a form of local working memory exists in the form of reciprocal connections between the external globus pallidus (Gpe) and the subthalamic nucleus (STN). As a test of the model, the system was trained to learn a sequence of states that required the context of previous actions. The striatum, which was assumed to represent a conjunction of cortical states, directly selected the action in the GP during training. The STN-to-GP connection strengths were modified by an associative learning rule and came to encode the sequence after 20 to 40 iterations through the sequence. Subsequently, the system automatically reproduced the sequence when cued to the first action. The behavior of the model was found to be sensitive to the ratio of the striatal-nigral learning rate to the STN-GP learning rate. Additionally, the degree of striatal inhibition of the globus pallidus had a significant influence on both learning and the ability to select an action. Low learning rates, which would be hypothesized to reflect low levels of dopamine, as in Parkinson's disease, led to slow acquisition of contextual information. However, this could be partially offset by modeling a lesion of the globus pallidus that resulted in an increase in the gain of the STN units. The parameter sensitivity of the model is discussed within the framework of existing behavioral and lesion data.

Basal Ganglia↗
PubMed1994

Interface for the documentation and compilation of a library of computer models in physiology.

A software interface for the documentation and compilation of a library of computer models in physiology was developed. The interface is an interactive program built within a word processing template in order to provide ease and flexibility of documentation. A model editor within the interface directs the model builder as to standardized requirements for incorporating models into the library and provides the user with an index to the levels of documentation. The interface and accompanying library are intended to facilitate model development, preservation and distribution and will be available for public use.

Computer Simulation↗
PubMed2000

Selective inhibitors and computer modelling of the active site of monoamine oxidase.

MAO inhibitors can be employed for computer modelling of the active site of MAO A and B. Competitive fully reversible MAO inhibitors with rigid structure and limited number of conformers are preferential compounds for these studies. Among various isatin analogues with nearllanar structure selective MAO B inhibitors fit to 3D box of 8.5x5.1x1.8 A, whereas 3D box of 14.2x5.6x1.8 A accommodates selective MAO A inhibitors. Validity of these data was tested using a series of pyrazinocarbazoles, analogues of short-acting antidepressant pirlindole. Rigid analogues exhibiting potent and selective inhibition of MAO A have 3D size limits of 13x7x4.4 A. Flexible analogues also demonstrated potent inhibition of MAO B and in contrast to rigid analogues their inhibitory activity did not show any dependence on 3D sizes. 3D-QSAR with CoMFA of isatin and pirlindole analogues of MAO A and B revealed differences in the models of MAO A and B.

Amino Acid Sequence↗
PubMedDate not supplied

AUR Memorial Award. Two computer models for selection of optimal magnetic resonance imaging (MRI) pulse sequence timing.

Two computer modeling techniques have been developed that aid in the selection of optimal magnetic resonance imaging (MRI) pulse sequences and timing intervals for specific clinical situations. The "parameter sensitivity" technique provides a means of selecting three separate MRI scans which are individually sensitive to changes in each of the three NMR tissue parameters N, T1, and T2. The "contrast" technique allows selection of a single optimal MRI sequence using the expected changes in all three tissue parameters simultaneously. Excellent correlation is demonstrated between the models and images obtained in a normal volunteer and in a patient with multiple sclerosis. The two methods compliment each other; the parameter sensitivity method is most useful in situations where subtle changes in tissue parameters are expected, whereas the contrast method is suited to circumstances where large differences in tissue parameters are anticipated and the magnitude and direction of these changes are known.

Computers↗
PubMed1998

Computer model of antiepileptic effects mediated by alterations in GABA(A)-mediated inhibition.

Results from a computer model of a thalamic network predict that agents augmenting GABA(A)-mediated inhibition in the reticular thalamic (RE) nucleus will be antiepileptic or desynchronizing. This provides support for the hypothesis that antiepileptics like benzodiazepines may exert their effects through an isolated increase of inhibition in the RE nucleus. When desynchronized, the model thalamocortical neurons showed a decreased probability of firing a low threshold spike, a decreased secondary inhibitory postsynaptic potential and a higher frequency of oscillations. The transition to desynchrony was also accompanied by an increased frequency in the firing of the model RE neurons.

Anticonvulsants↗
PubMed1987

Comparison of computer modelling and X-ray results of the binding of a pyrazole derivative to liver alcohol dehydrogenase.

The binding to liver alcohol dehydrogenase of the inhibitor 2,4-(4-pyrazolyl)-butylisothiourea has been studied both by modelling experiments using computer graphics with interactive energy minimization and by X-ray crystallographic structure determination. For the modelling experiments, we used the program system TOM, which was developed in our laboratory as an extension of the program FRODO. Different strategies for using computer graphics with interactive energy minimization were tested. Two essentially different binding modes were found. One of these was favoured from energy minimizations using a potential energy function which was the sum of a Coulomb interaction term and two different van der Waals' interaction terms for non-bonded and torsional interactions. This binding mode was close to the crystallographic observed structure. The results show that flexibility of both ligand and receptor side-chains as well as main-chain conformations are important for docking to the active site of liver alcohol dehydrogenase.

Alcohol Dehydrogenase↗
PubMed1994

A computational model of information retrieval with UMLS.

A high level representation of data would clarify the complex collection of medical concepts, terms and relationships derived from standard classifications that the Unified Medical Language System contains. A conceptual model is described which represents the data structure. A second objective of this conceptual model is to provide users with the capability to build queries to information databases as easily as possible on the basis of this data structure. The methods used to build this model are semantic networks and conceptual graphs. The object-oriented computational model which implements this conceptual model is detailed. It reuses part of the generic C++ classes of the National Institutes of Health library. New classes are added to this library to implement the needed functionalities.

Information Storage and Retrieval↗
PubMed2002

Reaching to grasp with a multi-jointed arm. I. Computational model.

The generation of goal-directed movements requires the solution of many difficult computational problems. Among these are transformations from extrinsic to intrinsic reference frames, specifying solution paths, removing under-specification due to excess degrees of freedom and path multiplicity, constraint satisfaction, and error correction. There are no current motor-control computational models that address these issues in the context of realistic arm movement with redundant degrees of freedom. In this paper, we conjecture there is a geometric stage between sensory input and physical execution. The geometric stage determines movement trajectories independently of forces. It uses a gradient technique that relies on the metric of the space of postures to resolve endpoint path selection, posture-change specification, error correction, and multiple constraint satisfaction on-line without preplanning. The model is instantiated in an arm with seven degrees of freedom that moves in three-dimensional space. Simulated orientation-matching movements are compared with actual human movement data to assess the validity of several of the model's behavioral predictions.

Algorithms↗
PubMed1991

A computational model of afferent neural activity from the cochlea to the dorsal acoustic stria.

The first comprehensive computational model of the precortical mammalian auditory system to include afferent neural processing up to the level of the dorsal acoustic stria (DAS) is described. The model consists of two scissile stages simulating (1) the cochlea and auditory nerve (AN) and (2) the dorsal cochlear nucleus (DCN). The model derives its input from a 128-channel cochlear filterbank. Cochlear transduction, rectification, logarithmic compression, and two-tone suppression functions are performed at the first stage of the simulation. The 512 artificial neurons employed model the cell at the level of transmembrane potential and have interconnections that follow closely those reported in recent anatomical and physiological studies of the cat AN and DCN. The responses of the model to pure-tone stimuli (at various sound-pressure levels) and noise stimuli (at various levels and bandwidths) are reported in detail and compare well with published results. The model is being used to investigate the representation of initial English stop consonants (differing in voice-onset time) in the DAS; this work is briefly described.

Acoustics↗
PubMed2004

Computational model of flow-tissue interactions in intussusceptive angiogenesis.

Angiogenesis, the growth of vascular structures, is a complex biological process which has long puzzled scientists. Better physiological understanding of this phenomenon could result in many useful medical applications such as the development of new methods for cancer therapy. We report on the development of a simple computational model of micro-vascular structure formation in intussusceptive angiogenesis observed in vivo. The tissue is represented by a discrete set of basic structural entities and flow conditions within the resulting domain are obtained by solving the Navier-Stokes equations. The tissue is then remodelled according to the tangential shear stress while approximating advection by means of simple non-diffusive heuristics. The updated tissue geometry then becomes the input for the next remodelling step. The model, consisting of steady-state flow and a simple mechanistic tissue response, successfully predicts bifurcation formation and micro-vessel separation in a porous cellular medium. This opens new modelling possibilities in computational studies of the cellular transport involved in micro-vascular growth.

Capillaries↗
PubMed2006

A computer model to simulate control of parasitic gastroenteritis in sheep on UK farms.

A computer model that simulates the population dynamics and epidemiology of three major species of parasitic nematodes of sheep found in the UK (Telodorsagia [Ostertagia] spp., Haemonchus spp. and Trichostrongylus spp.) is described. The model has been developed as a tool for veterinarians and advisors to aid in the implementation of integrated parasite control strategies designed to optimise anthelmintic usage and delay the development of resistance on UK farms. The model represents the parasite life cycle, flock dynamics and the response of individuals with different susceptible and resistant genotypes to the major broad-spectrum classes of anthelmintic available in the UK. Where possible, UK data have been used for the model parameters. The model allows worm control simulations on individual UK farms. Inputs include environmental and farm management variables which impact on the epidemiology of the disease, e.g. regional weather data; flock stocking rates; initial pasture larval contamination levels and species proportions; lambing dates; timing of flock movements to clean pastures; and removal of lambs during the year. Farm management data, as well as nematode egg outputs and grass larval counts, were collected from eight UK farms over a 1-year period for initial validation of the model outputs. The management data for each farm were used as inputs for each model run and model outputs for nematode egg counts from ewes and lambs were compared to the observed data for each farm. Statistical analysis of results shows a positive correlation for observed and simulated counts and regression analysis suggests an acceptable fit between the data. Comparison of observed and simulated outputs for resistance were possible for only one farm due to low numbers of worms developing in the laboratory tests. Additional studies will be necessary before resistance data can be reliably compared. Further validation studies are proposed to ensure that the model is robust and applicable across a diverse range of farm types. The model will be used to demonstrate the advantage, in terms of delaying resistance development, of current guidelines for anthelmintic use and management practices for worm control in sheep.

Animals↗
PubMed2005

Computational modeling and exploration of contour integration for visual saliency.

We propose a computational model of contour integration for visual saliency. The model uses biologically plausible devices to simulate how the representations of elements aligned collinearly along a contour in an image are enhanced. Our model adds such devices as a dopamine-like fast plasticity, local GABAergic inhibition and multi-scale processing of images. The fast plasticity addresses the problem of how neurons in visual cortex seem to be able to influence neurons they are not directly connected to, for instance, as observed in contour closure effect. Local GABAergic inhibition is used to control gain in the system without using global mechanisms which may be non-plausible given the limited reach of axonal arbors in visual cortex. The model is then used to explore not only its validity in real and artificial images, but to discover some of the mechanisms involved in processing of complex visual features such as junctions and end-stops as well as contours. We present evidence for the validity of our model in several phases, starting with local enhancement of only a few collinear elements. We then test our model on more complex contour integration images with a large number of Gabor elements. Sections of the model are also extracted and used to discover how the model might relate contour integration neurons to neurons that process end-stops and junctions. Finally, we present results from real world images. Results from the model suggest that it is a good current approximation of contour integration in human vision. As well, it suggests that contour integration mechanisms may be strongly related to mechanisms for detecting end-stops and junction points. Additionally, a contour integration mechanism may be involved in finding features for objects such as faces. This suggests that visual cortex may be more information efficient and that neural regions may have multiple roles.

Form Perception↗
PubMed1985

Application of a computable model of human spatial vision to phase discrimination.

We have used a computable model of human spatial vision to make predictions for phase-discrimination experiments. This model is being developed to deal with a broad range of problems in vision and was not specifically formulated to deal with phase discrimination. In the model, cross correlation of the stimuli with an array of sensors produces feature vectors that are operated on by a position-uncertain ideal observer to simulate detection and discrimination experiments. In this report the stimuli are compound sinusoidal gratings composed of a fundamental and a higher-frequency component added in various phases. We compare model predictions with three key results from the literature: the effect of the contrast of the fundamental on phase discrimination, threshold phase difference as a function of the fundamental frequency, and the contrast required for phase discrimination as a function of the frequency ratio of the two grating components. In the first two cases, the predictions capture the main features of the data, although quantitative discrepancies remain. In the third case, the model fails, and this failure suggests additional restrictions on the combination of information across sensors.

Discrimination Learning↗
PubMed2005

NMDA/AMPA ratio impacts state transitions and entrainment to oscillations in a computational model of the nucleus accumbens medium spiny projection neuron.

We describe a computational model of the principal cell in the nucleus accumbens (NAcb), the medium spiny projection (MSP) neuron. The model neuron, constructed in NEURON, includes all of the known ionic currents in these cells and receives synaptic input from simulated spike trains via NMDA, AMPA, and GABAA receptors. After tuning the model by adjusting maximal current conductances in each compartment, the model cell closely matched whole-cell recordings from an adult rat NAcb slice preparation. Synaptic inputs in the range of 1000-1300 Hz are required to maintain an "up" state in the model. Cell firing in the model required concurrent depolarization of several dendritic branches, which responded independently to afferent input. Depolarization from action potentials traveled to the tips of the dendritic branches and increased Ca2+ influx through voltage-gated Ca2+ channels. As NMDA/AMPA current ratios were increased, the membrane showed an increase in hysteresis of "up" and "down" state dwell times, but intrinsic bistability was not observed. The number of oscillatory inputs required to entrain the model cell was determined to be approximately 20% of the "up" state inputs. Altering the NMDA/AMPA ratio had a profound effect on processing of afferent input, including the ability to entrain to oscillations in afferent input in the theta range (4-12 Hz). These results suggest that afferent information integration by the NAcb MSP cell may be compromised by pathology in which the NMDA current is altered or modulated, as has been proposed in both schizophrenia and addiction.

Animals↗
PubMed1987

Computer modeling of DDD pacemakers for use in prophylaxis of junctional reentry tachycardia.

A computer simulation model of cardiac rhythm and heart-pacemaker interactions has been used to examine the response of short AV delay DDD pacing to an atrial premature depolarization in patients with a potential junctional reentry circuit. Special attention was given to the possibility of using the pacemaker to prevent atrioventricular reentry tachycardia mediated by a bidirectional accessory pathway. The computational experiments examined: (a) the differences between pacing modes with constant and quasi-Wenckebach prolongation of AV delay; (b) the effects of imposing the restrictions of a pacemaker atrial refractory period and upper rate limit; and (c) the effects of varying the ventricular refractory period so that it was either the same or longer than that of the atria. The computational results prove that some possible modes of initiation of junctional reentry tachycardia are beyond the prophylactic capabilities of current DDD pacemakers. Future possibilities involving the use of computer modeling to develop more sophisticated pacemaker modes are briefly discussed.

Cardiac Complexes, Premature↗