SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

An internationally recognized leader in visualization, scientific computing, and image analysis

SCI Publications

2008


G. Adluru, E.V.R. DiBella, C.J. McGann. “Data Acquisition and Reconstruction of Undersampled Radial MR Myocardial Perfusion,” In Proceedings of the 11th Annual Scientific Sessions of the Society for Cardiovascular Magnetic Resonance (SCMR) 2008, pp. 215. 2008.


G. Adluru, E.V.R. DiBella. “A Comparison of L1 and L2 Norms as Temporal Constraints for Reconstruction of Undersampled Dynamic Contrast Enhanced Cardiac Scans with Respiratory Motion,” In Proceedings of the 16th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM) 2008, pp. 340. 2008.


G. Adluru, E.V.R. DiBella. “Data Reordering for Improved Constrained Reconstruction from Undersampled k-space Data,” In Proceedings of the 16th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM) 2008, pp. 3153. 2008.


A.E. Anderson, B.J. Ellis, C.L. Peters, J.A. Weiss. “Cartilage Thickness: Factors Influencing Multidetector CT Measurements in a Phantom Study,” In Radiology, Vol. 246, No. 1, pp. 133-141. 2008.
PubMed ID: 18982614


A.E. Anderson, B.J. Ellis, S.A. Maas, C.L. Peters, J.A. Weiss. “Validation of Finite Element Predictions of Cartilage Contact Pressure in the Human Hip Joint,” In ASME Journal of Biomechanical Engineering, Vol. 130, No. 3, pp. 051008-1--10. May, 2008.


E.W. Anderson, J. Ahrens, K. Heitmann, S. Habib, C.T. Silva. “Provenance in Comparative Analysis: A Study in Cosmology,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 30--37. 2008.


A.E. Anderson, B.J. Ellis, C.L. Peters, J.A. Weiss. “Factors Influencing Cartilage Thickness Measurements with Multi-Detector CT: A Phantom Study,” In Radiology, Vol. 246, No. 1, pp. 144-141. 2008.


A. Baptista, B. Howe, J. Freire, D. Maier, C.T. Silva. “Scientific Exploration in the Era of Ocean Observatories,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 53--58. 2008.


L. Bavoil, S.P. Callahan, and C.T. Silva. “Robust Soft Shadow Mapping with Depth Peeling,” In Journal of Graphics Tools, Vol. 13, No. 1, pp. 19--30. 2008.


E.W. Bethel, H. Childs, A. Mascarenhas, V. Pascucci, Prabhat. “Scientific Data Management Challenges in High Performance Visual Data Analysis,” In Scientific Data Management: Challenges, Existing Technology, and Deployment, Chapman Hall/CRC Press, 2008.


D. Brayford, M. Turner, W.T. Hewitt. “A Physical Model for the Polarized Scattering of Light,” In Proceedings of The sixth Theory and Practice of Computer Graphics 2008 Conference (TPCG08), University of Manchester, UK, Note: Best Paper Award, June, 2008.


K. Buerger, P. Kondratieva, J. Krüger, R. Westermann. “Importance-Driven Particle Techniques for Flow Visualization,” In Proceedings of IEEE VGTC PacificVis 2008, pp. 71--78. 2008.


C.R. Butson, G.A. Clark. “Mechanisms of noise-induced improvement in light-intensity encoding in Hermissenda photoreceptor network,” In Journal of Neurophysiology, Vol. 99, No. 1, pp. 155--165. January, 2008.
ISSN: 0022-3077
DOI: 10.1152/jn.01250.2006
PubMed ID: 18003872

ABSTRACT

In a companion paper we showed that random channel and synaptic noise improve the ability of a biologically realistic, GENESIS-based computational model of the Hermissenda eye to encode light intensity. In this paper we explore mechanisms for noise-induced improvement by examining contextual spike-timing relationships among neurons in the photoreceptor network. In other systems, synaptically connected pairs of spiking cells can develop phase-locked spike-timing relationships at particular, well-defined frequencies. Consequently, domains of stability (DOS) emerge in which an increase in the frequency of inhibitory postsynaptic potentials can paradoxically increase, rather than decrease, the firing rate of the postsynaptic cell. We have extended this analysis to examine DOS as a function of noise amplitude in the exclusively inhibitory Hermissenda photoreceptor network. In noise-free simulations, DOS emerge at particular firing frequencies of type B and type A photoreceptors, thus producing a nonmonotonic relationship between their firing rates and light intensity. By contrast, in the noise-added conditions, an increase in noise amplitude leads to an increase in the variance of the interspike interval distribution for a given cell; in turn, this blocks the emergence of phase locking and DOS. These noise-induced changes enable the eye to better perform one of its basic tasks: encoding light intensity. This effect is independent of stochastic resonance, which is often used to describe perithreshold stimuli. The constructive role of noise in biological signal processing has implications both for understanding the dynamics of the nervous system and for the design of neural interface devices.

Keywords: Action Potentials, Action Potentials: physiology, Animals, Artifacts, Computer Simulation, Eye, Eye: cytology, Hermissenda, Hermissenda: physiology, Invertebrate, Invertebrate: physiology, Nerve Net, Nerve Net: physiology, Neurons, Neurons: physiology, Ocular, Ocular Physiological Phenomena, Ocular: physiology, Photic Stimulation, Photoreceptor Cells, Reaction Time, Reaction Time: physiology, Sensory Thresholds, Sensory Thresholds: physiology, Synaptic Transmission, Synaptic Transmission: physiology, Vision


C.R. Butson, G.A. Clark. “Random noise paradoxically improves light-intensity encoding in Hermissenda photoreceptor network,” In Journal of Neurophysiology, Vol. 99, No. 1, pp. 146--154. January, 2008.
ISSN: 0022-3077
DOI: 10.1152/jn.01247.2006
PubMed ID: 18003873

ABSTRACT

×
Neurons are notoriously noisy devices. Although the traditional view posits that noise degrades system performance, recent evidence suggests that noise may instead enhance neural information processing under certain conditions. Here we report that random channel and synaptic noise improve the ability of a biologically realistic computational model of the Hermissenda eye to encode light intensity. The model was created in GENESIS and is based on a previous model used to examine effects of changes in type B photoreceptor excitability, synaptic strength, and network architecture. The network consists of two type A and three type B multicompartmental photoreceptors. Each compartment contains a population of Hodgkin-Huxley-type ion channels and each cell is stimulated via artificial light currents. We found that the addition of random channel and synaptic noise yielded a significant improvement in the accuracy of the network's encoding of light intensity across eight light levels spanning 3.5 log units (P

Keywords: Action Potentials, Action Potentials: physiology, Animals, Artifacts, Computer Simulation, Eye, Eye: cytology, Hermissenda, Hermissenda: physiology, Invertebrate, Invertebrate: physiology, Nerve Net, Nerve Net: physiology, Neurons, Neurons: physiology, Ocular, Ocular Physiological Phenomena, Ocular: physiology, Photic Stimulation, Photoreceptor Cells, Reaction Time, Reaction Time: physiology, Sensory Thresholds, Sensory Thresholds: physiology, Synaptic Transmission, Synaptic Transmission: physiology, Vision


C.R. Butson, C.C. McIntyre. “Current Steering to Control the Volume of Tissue Activated During Deep Brain Stimulation,” In Brain Stimulation, Vol. 1, No. 1, pp. 7--15. January, 2008.
DOI: 10.1016/j.brs.2007.08.004
PubMed ID: 19142235

ABSTRACT

×
BACKGROUND: Over the last two decades, deep brain stimulation (DBS) has become a recognized and effective clinical therapy for numerous neurological conditions. Since its inception, clinical DBS technology has progressed at a relatively slow rate; however, advances in neural engineering research have the potential to improve DBS systems. One such advance is the concept of current steering, or the use of multiple stimulation sources to direct current flow through targeted regions of brain tissue.

OBJECTIVE: The goals of this study were to develop a theoretical understanding of the effects of current steering in the context of DBS, and use that information to evaluate the potential utility of current steering during stimulation of the subthalamic nucleus.

METHODS: We used finite element electric field models, coupled to multi-compartment cable axon models, to predict the volume of tissue activated (VTA) by DBS as a function of the stimulation parameter settings.

RESULTS: Balancing current flow through adjacent cathodes increased the VTA magnitude, relative to monopolar stimulation, and current steering enabled us to sculpt the shape of the VTA to fit a given anatomical target.

CONCLUSIONS: These results provide motivation for the integration of current steering technology into clinical DBS systems, thereby expanding opportunities to customize DBS to individual patients, and potentially enhancing therapeutic efficacy.


S.P. Callahan, J.H. Callahan, C.E. Scheidegger, C.T. Silva. “Direct Volume Rendering: A 3D Plotting Technique for Scientific Data,” In Computing in Science and Engineering, Vol. 10, No. 1, pp. 88--92. 2008.


S.P. Callahan. “Adaptive Visualization of Dynamic Unstructured Meshes,” SCI Technical Report, No. UUSCI-2008-003, Note: Ph.D. Thesis, University of Utah School of Computing, 2008.


S.P. Callahan, C.T. Silva. “Image-Space Acceleration for Direct Volume Rendering of Unstructured Grids using Joint Bilateral Upsampling,” SCI Technical Report, No. UUSCI-2008-002, University of Utah, 2008.


S.P. Callahan, J. Freire, C.E. Scheidegger, C.T. Silva, and H.T. Vo. “Towards a Provenance-Enabling ParaView,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 120--127. 2008.


J. Cates, P.T. Fletcher, Z. Warnock, R.T. Whitaker. “A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11,” In Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 512--516. 2008.
DOI: 10.1109/ISBI.2008.4541045