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At least 523 records · Page 29Linked to original sources

PubMed2001

What do computer models of cognition explain: a reply to Gobet.

The differences between Gobet's views and ours call attention to some points concerning the argumentative status of computational models. If we have two fundamentally different models which reasonably accurately simulate a phenomenon, we must ask, what is the argumentative status of the models in psychological terms. Moreover, if it is possible to present different models of same phenomena, what is the general argumentative power of models in psychology? As the kind of differences between our views and the ones of Gobet's are common in modelling, we briefly call attention to these foundational issues in our paper.

Cognition↗

PubMedDate not supplied

A high frequency resonance in the responses of retinal ganglion cells to rapidly modulated stimuli: a computer model.

Brisk Y-type ganglion cells in the cat retina exhibit a high frequency resonance (HFR) in their responses to large, rapidly modulated stimuli. We used a computer model to test whether negative feedback mediated by axon-bearing amacrine cells onto ganglion cells could account for the experimentally observed properties of HFRs. Temporal modulation transfer functions (tMTFs) recorded from model ganglion cells exhibited HFR peaks whose amplitude, width, and locations were qualitatively consistent with experimental data. Moreover, the wide spatial distribution of axon-mediated feedback accounted for the observed increase in HFR amplitude with stimulus size. Model phase plots were qualitatively similar to those recorded from Y ganglion cells, including an anomalous phase advance that in our model coincided with the amplification of low-order harmonics that overlapped the HFR peak. When axon-mediated feedback in the model was directed primarily to bipolar cells, whose synaptic output was graded, or else when the model was replaced with a simple cascade of linear filters, it was possible to produce large HFR peaks but the region of anomalous phase advance was always eliminated, suggesting the critical involvement of strongly non-linear feedback loops. To investigate whether HFRs might contribute to visual processing, we simulated high frequency ocular tremor by rapidly modulating a naturalistic image. Visual signals riding on top of the imposed jitter conveyed an enhanced representation of large objects. We conclude that by amplifying responses to ocular tremor, HFRs may selectively enhance the processing of large image features.

Action Potentials↗

PubMed2006

Evaluating computational models in cognitive neuropsychology: the case from the consonant/vowel distinction.

Caramazza et al. [Caramazza, A., Chialant, D., Capasso, R., & Miceli, G. (2000). Separable processing of consonants and vowels. Nature, 403(6768), 428-430.] report two patients who exhibit a double dissociation between consonants and vowels in speech production. The patterning of this double dissociation cannot be explained by appealing to sub-phonemic distinctions, such as sonority level or damage to specific phonological features. They argue that consonant/vowel status is an autonomous level of representation. Monaghan and Shillcock [Monaghan, P., & Shillcock, R. (2003). Connectionist modelling of the separable processing of consonants and vowels. Brain and Language, 86(1), 83-98.] present computational models which supposedly exhibit a similar double dissociation. They contend that these models can explain the patient data, without appeal to such supra-phonemic distinctions as consonant/vowel status. Here we argue that their claim fails to meet two necessary criteria. Their models do not fit the pattern of the patient data, either quantitatively or qualitatively. Furthermore, the motivation for these models is unclear beyond just being an attempt to explain this specific phenomenon. We conclude that these models, in their current form, do not provide an alternative explanation to the representation of consonants and vowels.

Aphasia↗

PubMed2006

Computational modeling of extracellular mechanotransduction.

Mechanotransduction may occur through numerous mechanisms, including potentially through autocrine signaling in a dynamically changing extracellular space. We developed a computational model to analyze how alterations in the geometry of an epithelial lateral intercellular space (LIS) affect the concentrations of constitutively shed ligands inside and below the LIS. The model employs the finite element method to solve for the concentration of ligands based on the governing ligand diffusion-convection equations inside and outside of the LIS, and assumes idealized parallel plate geometry and an impermeable tight junction at the apical surface. Using the model, we examined the temporal relationship between geometric changes and ligand concentration, and the dependence of this relationship on system characteristics such as ligand diffusivity, shedding rate, and rate of deformation. Our results reveal how the kinetics of mechanical deformation can be translated into varying rates of ligand accumulation, a potentially important mechanism for cellular discrimination of varying rate-mechanical processes. Furthermore, our results demonstrate that rapid changes in LIS geometry can transiently increase ligand concentrations in underlying media or tissues, suggesting a mechanism for communication of mechanical state between epithelial and subepithelial cells. These results underscore both the plausibility and complexity of the proposed extracellular mechanotransduction mechanism.

Animals↗

PubMed1997

Annular dilatation increases stress in the mitral valve and delays coaptation: a finite element computer model.

The purpose of this study was to examine the effects of annular dilatation on coaptation, and leaflet and chordal stresses, using a three dimensional finite element computer model. To do this, the whole mitral valve was simulated using ANSYS 4.4A software. Normal model geometry, collagen fiber orientation, tissue thickness, and material properties were determined from fresh porcine valves. For annular dilatation, the annular circumference was increased by 18% versus normal. Isovolumic contraction and rapid ventricular ejection were simulated. Data showed that, in the annular dilatation model, the stress magnitudes increased more than two-fold compared with normal in both the anterior leaflet and posterior leaflet. Coaptation was greatly delayed in the dilatation model, and the leaflets never fully coapted. Chordal stresses were also greatly increased in the dilatation model. In conclusion, increased stress due to annular dilatation may lead to tissue disruption, further dilatation, delayed coaptation, and increased regurgitation, in a 'closed-loop' degenerative process.

Animals↗

PubMed2004

Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction.

Heterotrimeric G protein signaling is regulated by signaling modules composed of heterotrimeric G proteins, active G protein-coupled receptors (Rs), which activate G proteins, and GTPase-activating proteins (GAPs), which deactivate G proteins. We term these modules GTPase-cycle modules. The local concentrations of these proteins are spatially regulated between plasma membrane microdomains and between the plasma membrane and cytosol, but no data or models are available that quantitatively explain the effect of such regulation on signaling. We present a computational model of the GTPase-cycle module that predicts that the interplay of local G protein, R, and GAP concentrations gives rise to 16 distinct signaling regimes and numerous intermediate signaling phenomena. The regimes suggest alternative modes of the GTPase-cycle module that occur based on defined local concentrations of the component proteins. In one mode, signaling occurs while G protein and receptor are unclustered and GAP eliminates signaling; in another, G protein and receptor are clustered and GAP can rapidly modulate signaling but does not eliminate it. Experimental data from multiple GTPase-cycle modules is interpreted in light of these predictions. The latter mode explains previously paradoxical data in which GAP does not alter maximal current amplitude of G protein-activated ion channels, but hastens signaling. The predictions indicate how variations in local concentrations of the component proteins create GTPase-cycle modules with distinctive phenotypes. They provide a quantitative framework for investigating how regulation of local concentrations of components of the GTPase-cycle module affects signaling.

GTP Phosphohydrolases↗

PubMed2002

Toward a method of selecting among computational models of cognition.

The question of how one should decide among competing explanations of data is at the heart of the scientific enterprise. Computational models of cognition are increasingly being advanced as explanations of behavior. The success of this line of inquiry depends on the development of robust methods to guide the evaluation and selection of these models. This article introduces a method of selecting among mathematical models of cognition known as minimum description length, which provides an intuitive and theoretically well-grounded understanding of why one model should be chosen. A central but elusive concept in model selection, complexity, can also be derived with the method. The adequacy of the method is demonstrated in 3 areas of cognitive modeling: psychophysics, information integration, and categorization.

Cognition↗

PubMed2003

Computational model of the pregnant occupant: predicting the risk of injury in automobile crashes.

OBJECTIVE: The goal of this study was to create a computational model of the pregnant occupant of a motor vehicle to predict fetal outcome in crashes. STUDY DESIGN: A finite element uterine model of a 7-month pregnant woman was created and integrated into a multibody human model. Unrestrained, three-point belt, and three-point belt plus airbag tests were simulated at speeds that ranged from 13 to 55 km per hour. RESULTS: Peak uterine strain, as determined by the model, correlated well with the risk of fetal death, as determined by investigations of car crashes. The strain in the uterine wall exceeded the limits of the tissue in simulations of no restraint at 35 km per hour and three-point belt tests at 45 and 55 km per hour. The safest restraint for the pregnant driver is the combination three-point belt and airbag. CONCLUSION: The model is a good first step toward the prediction of the risk of fetal death and verified experimental findings that note the importance of proper restraint use for the pregnant occupant.

Accidents, Traffic↗

PubMed1989

A hydrogen bonded chain in bacteriorhodopsin by computer modelling approach.

The seven alpha-helical segments of Bacteriorhodopsin (BR) passing through the membrane are investigated for a continuous Hydrogen Bonded Chain (HBC). The study is carried out by computer modelling approach. It is assumed that the seven helices are placed as (AGFEDCB), which has been accepted as the best model by several groups. Helices A, D, E and G are considered to be present in right handed alpha-helical conformation. The inter-orientation of these helices are represented by Eulerian angles alpha, beta and gamma. For the helices B, C and F which contain Proline in the middle, several conformational possibilities were considered. In these cases apart from the Eulerian angles alpha, beta and gamma, the dihedral angles phi p-1 and psi p-1 of the residues that are succeeded by Proline residue in the helical regions were also used in fixing the position of the helices with respect to each other. All these parameters were varied to fit with the top, middle and bottom distances reported by electron diffraction studies. Good fit was obtained for all right handed alpha-helical conformations and also for helices B, C and F with a left handed turn at the residue preceeding proline. Hence two structures were analysed for continuous HBC. Structure I which contained all the seven helices in right handed alpha-helical conformation and Structure II, which had the helices A, D, E and G in right handed conformation and the helices B, C and F in right handed alpha-helical conformation with a left handed turn at the residue preceeding proline. All possible staggered conformations were considered for the side chains and the inter atomic distances were analysed for Hydrogen bonds. It was possible to obtain a continuous chain in both the structures which includes most of the residues found to be important by the experiments. However Lys-216 has to be considered in two different conformations to connect the cytoplasmic side with the extra cellular side. The overall height spanned by HBC is about 25A. The chains obtained by both the structures I and II are analysed in terms of the conformational parameters. It has also been possible to place the retinal in the region as predicted by the experiments. The Tryptophan residues which affect the spectral characteristics can be aligned on either side of the retinal.

Bacteriorhodopsins↗

PubMed2006

A computational model of oxygen transport in skeletal muscle for sprouting and splitting modes of angiogenesis.

Oxygen transport from capillary networks in muscle at a high oxygen consumption rate was simulated using a computational model to assess the relative efficacies of sprouting and splitting modes of angiogenesis. Efficacy was characterized by the volumetric fraction of hypoxic tissue and overall heterogeneity of oxygen distribution at steady state. Oxygen transport was simulated for a three-dimensional vascular network using parameters for rat extensor digitorum longus (EDL) muscle when oxygen consumption by tissue reached 6, 12, and 18 times basal consumption. First, a control network was generated by using straight non-anastomosed capillaries to establish baseline capillarity. Two networks were then constructed simulating either abluminal lateral sprouting or intraluminal splitting angiogenesis such that capillary surface area was equal in both networks. The sprouting network was constructed by placing anastomosed capillaries between straight capillaries of the control network with a higher probability of placement near hypoxic tissue. The splitting network was constructed by splitting capillaries from the control network into two branches at randomly chosen branching points. Under conditions of moderate oxygen consumption (6 times basal), only minor differences in oxygen delivery resulted between the sprouting and splitting networks. At higher consumption levels (12 and 18 times basal), the splitting network had the lowest volume of hypoxic tissue of the three networks. However, when total blood flow in all three networks was made equal, the sprouting network had the lowest volume of hypoxic tissue. This study also shows that under the steady-state conditions the effect of myoglobin (Mb) on oxygen transport was small.

Animals↗

PubMed1991

A computational model of approximate Bayesian inference for associating clinical algorithms with decision analyses.

The lack of rationale or explanation is a major deficiency of clinical algorithms. To address this issue, the authors present a computational model for associating decision analyses with clinical algorithms. Automata theory is used to model categorical reasoning with approximate Bayesian inference based on probability intervals. This approximation reduces the number of computations to linear-order instead of the exponential-order combinations of clinical findings in exact Bayes. The linkage of decision analyses and clinical algorithms by means of this model exploits a new concept of "regular" clinical algorithms and their equivalency in theory and provides valuable perspectives in practice for developers of clinical algorithms.

Algorithms↗

PubMed2006

Determinants of flow along arterio-arterial anastomoses in monochorionic placentae by dynamic computer modelling of chorionic plate vasculature.

OBJECTIVES: To investigate anatomical and physiological determinants of inter-fetal transfusion along arterio-arterial (AA) anastomoses in monochorionic placentae. METHODS: A computer model of chorionic arterial vasculature was constructed in QuickBASIC using data collected from experimentation and the published literature. After validating the model, the influence of various physiological and anatomical variables on anastomotic flow rates was examined. RESULTS: AA anastomotic flow rates were significantly related to changes in fetal mean arterial pressure (p < 0.0001) and heart rate (p < 0.0005). AA flow rates were also related to the imbalance in number of arterio-venous (AV) anastomoses, to placental territory share, and to the branch number of the AA anastomosis (AAAs) from the chorionic arterial tree. CONCLUSIONS: Net blood flow and direction along AA anastomoses are influenced by fetal cardiac output, by the presence of compensatory AV anastomoses, and by the branch number of the chorionic arteries connected by the anastomosis. This study provides insight into the determinants of chronic transfusional imbalance as well as acute inter-fetal transfusion.

Arterio-Arterial Fistula↗

PubMedDate not supplied

[Computer modeling of enzymatic hydrolysis of a linear polysaccharide by endoglycanases].

The kinetics of linear polysaccharide hydrolysis with endoglycanases was studied with the help of computer modelling. Simple hydrolysis of a substrate (polymerization degree 30) -- analogous to beta-1,3-glucan -- laminarin was considered. The theoretical action patterns of several enzymes having active centres with known subsite maps were compared with experimental data for endolaminarinase LIV from Spisula sachalinensis. Analysis of the data obtained revealed some characteristic features in the course of the reaction and showed how to achieve information on the active centres of endoglycanases on the basis of such an action pattern. The method of evaluating maximum distance from the catalytic site to the boundary of the active centre was proposed.

Computers↗

PubMed2006

Numbers and space: a computational model of the SNARC effect.

The SNARC (spatial numerical associations of response codes) effect reflects the tendency to respond faster with the left hand to relatively small numbers and with the right hand to relatively large numbers (S. Dehaene, S. Bossini, & P. Giraux, 1993). Using computational modeling, the present article aims to provide a framework for conceptualizing the SNARC effect. In line with models of spatial stimulus-response congruency, the authors modeled the SNARC effect as the result of parallel activation of preexisting links between magnitude and spatial representation and short-term links created on the basis of task instructions. This basic dual-route model simulated all characteristics associated with the SNARC effect. In addition, 2 experiments tested and confirmed new predictions derived from the model.

Adult↗

PubMed1998

A computational model of depth perception based on headcentric disparity.

It is now well established that depth is coded by local horizontal disparity and global vertical disparity. We present a computational model which explains how depth is extracted from these two types of disparities. The model uses the two (one for each eye) headcentric directions of binocular targets, derived from retinal signals and oculomotor signals. Headcentric disparity is defined as the difference between headcentric directions of corresponding features in the left and right eye's images. Using Helmholtz's coordinate systems we decompose headcentric disparity into azimuthal and elevational disparity. Elevational disparities of real objects are zero if the signals which contribute to headcentric disparity do not contain any errors. Azimuthal headcentric disparity is a 1D quantity from which an exact equation relating distance and disparity can be derived. The equation is valid for all headcentric directions and for all binocular fixation positions. Such an equation does not exist if disparity is expressed in retinal coordinates. Possible types of errors in oculomotor signals (six) produce global elevational disparity fields which are characterised by different gradients in the azimuthal and elevational directions. Computations show that the elevational disparity fields uniquely characterise both the type and size of the errors in oculomotor signals. Our model uses a measure of the global elevational disparity field together with local azimuthal disparity to accurately derive headcentric distance throughout the visual field. The model explains existing data on whole-field disparity transformations as well as hitherto unexplained aspects of stereoscopic depth perception.

Computational Biology↗

PubMed2002

Interaction of the cardiovascular system with an implanted rotary assist device: simulation study with a refined computer model.

In recent years, implanted rotary pumps have achieved the level of extended clinical application including complete mobilization and physical exercise of the recipients. A computer model was developed to study the interaction between a continuous-flow pump and the recovering cardiovascular system, the effects of changing pre- and afterloads, and the possibilities for indirect estimation of hemodynamic parameters and pump control. A numerical model of the cardiovascular system using Matlab Simulink simulation software was established. Data of circulatory system modules were derived from patients, our own in vitro and in vivo experiments, and the literature. Special care was taken to simulate properly the dynamic pressure-volume characteristics of both left and right ventricle, the Frank-Starling behavior, and the impedance of the proximal vessels. Excellent correlation with measured data was achieved including pressure and flow patterns within the time domain, response to varying loads, and effects of previously observed pressure-flow hysteresis in rotary pumps. Potential energy, external work, pressure-volume area, and other derived heart work parameters could be calculated. The model offers the possibility to perform parameter variations to study the effects of changing patient condition and therapy and to display them with three-dimensional graphics (demonstrated with the effects on right ventricular work and efficiency). The presented model gives an improved understanding of the interaction between the pump and both ventricles. It can be used for the investigation of various clinical and control questions in normal and pathological conditions of the left ventricular assist device recipient.

Computer Simulation↗

PubMedDate not supplied

[Electron computer modeling of membrane structure and distribution of admixture particles in the lipid bilayer].

A simple molecular model of double lipid layer of the membrane is proposed. Equilibrium distribution of small hydrophilic particles between bilayer and contacting solution was studied by computer modeling. Connection between the concentration profile of the particles and its structural organization was considered. Special role of the bilayer central region was found. The results obtained qualitatively agree with the known experimental data.

Computers↗

PubMedDate not supplied

DNA computation model to solve 0-1 programming problem.

0-1 programming problem is an important problem in opsearch with very widespread applications. In this paper, a new DNA computation model utilizing solution-based and surface-based methods is presented to solve the 0-1 programming problem. This model contains the major benefits of both solution-based and surface-based methods; including vast parallelism, extraordinary information density and ease of operation. The result, verified by biological experimentation, revealed the potential of DNA computation in solving complex programming problem.

Algorithms↗