--- _id: '3184' abstract: - lang: eng text: 'Algorithms for discrete energy minimization play a fundamental role for low-level vision. Known techniques include graph cuts, belief propagation (BP) and recently introduced tree-reweighted message passing (TRW). So far, the standard benchmark for their comparison has been a 4-connected grid-graph arising in pixel-labelling stereo. This minimization problem, however, has been largely solved: recent work shows that for many scenes TRW finds the global optimum. Furthermore, it is known that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions into account. We propose the problem of stereo with occlusions as a new test bed for minimization algorithms. This is a more challenging graph since it has much larger connectivity, and it also serves as a better stereo model. An attractive feature of this problem is that increased connectivity does not result in increased complexity of message passing algorithms. Indeed, one contribution of this paper is to show that sophisticated implementations of BP and TRW have the same time and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion of our experimental study is that for our problem graph cut outperforms both TRW and BP considerably. TRW achieves consistently a lower energy than BP. However, as connectivity increases the speed of convergence of TRW becomes slower. Unlike 4-connected grids, the difference between the energy of the best optimization method and the lower bound of TRW appears significant. This shows the hardness of the problem and motivates future research.' alternative_title: - LNCS author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1' apa: 'Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1' chicago: Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1. ieee: 'V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms for highly connected graphs,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952 LNCS, pp. 1–15.' ista: 'Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS, vol. 3952 LNCS, 1–15.' mla: Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp. 1–15, doi:10.1007/11744047_1. short: V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:52Z date_published: 2006-05-03T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '03' doi: 10.1007/11744047_1 extern: 1 main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf month: '05' page: 1 - 15 publication_status: published publisher: Springer publist_id: '3498' quality_controlled: 0 status: public title: Comparison of energy minimization algorithms for highly connected graphs type: conference volume: 3952 LNCS year: '2006' ... --- _id: '3185' abstract: - lang: eng text: This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193 apa: Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006). Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193 chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193. ieee: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492, 2006. ista: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492. mla: Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193. short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492. date_created: 2018-12-11T12:01:53Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '01' doi: 10.1109/TPAMI.2006.193 extern: 1 intvolume: ' 28' issue: '9' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf month: '09' page: 1480 - 1492 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '3496' quality_controlled: 0 status: public title: Probabilistic fusion of stereo with color and contrast for bilayer segmentation type: journal_article volume: 28 year: '2006' ... --- _id: '3186' abstract: - lang: eng text: We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion. alternative_title: - LNCS author: - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Daniel full_name: Cremers, Daniel last_name: Cremers - first_name: Andrew full_name: Delong, Andrew last_name: Delong citation: ama: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32' apa: 'Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32' chicago: Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer, 2006. https://doi.org/10.1007/11744078_32. ieee: 'Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3953, pp. 409–422.' ista: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision, LNCS, vol. 3953, 409–422.' mla: Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32. short: Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp. 409–422. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:53Z date_published: 2006-04-28T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '28' doi: 10.1007/11744078_32 extern: 1 intvolume: ' 3953' month: '04' page: 409 - 422 publication_status: published publisher: Springer publist_id: '3497' quality_controlled: 0 status: public title: An integral solution to surface evolution PDEs via geo cuts type: conference volume: 3953 year: '2006' ... --- _id: '3404' alternative_title: - Manuals in Biomedical Research author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Ravi full_name: Sawhney, Ravi K last_name: Sawhney - first_name: Martin full_name: Stark, Martin last_name: Stark - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing; 2006:213-284.' apa: Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force microscopy. In Techniques in Microscopy for Biomedical Applications (Vol. 2, pp. 213–284). World Scientific Publishing. chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic Force Microscopy.” In Techniques in Microscopy for Biomedical Applications, 2:213–84. World Scientific Publishing, 2006. ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,” in Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–284. ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical Research, vol. 2, 213–284.' mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–84. short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284. date_created: 2018-12-11T12:03:09Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:43:15Z day: '28' extern: 1 intvolume: ' 2' month: '09' page: 213 - 284 publication: Techniques in Microscopy for Biomedical Applications publication_status: published publisher: World Scientific Publishing publist_id: '2998' quality_controlled: 0 status: public title: Atomic force microscopy type: book_chapter volume: 2 year: '2006' ... --- _id: '3413' abstract: - lang: eng text: |- Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids. Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded. We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state. author: - first_name: Max full_name: Kessler, Max last_name: Kessler - first_name: Kay full_name: Gottschalk, Kay E last_name: Gottschalk - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Hermann full_name: Gaub, Hermann last_name: Gaub citation: ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065 apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006). Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065 chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065. ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin folds into the membrane against an external force,” Journal of Molecular Biology, vol. 357, no. 2. Elsevier, pp. 644–654, 2006. ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 357(2), 644–654. mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier, 2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065. short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of Molecular Biology 357 (2006) 644–654. date_created: 2018-12-11T12:03:12Z date_published: 2006-03-24T00:00:00Z date_updated: 2021-01-12T07:43:18Z day: '24' doi: 10.1016/j.jmb.2005.12.065 extern: 1 intvolume: ' 357' issue: '2' month: '03' page: 644 - 654 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '2988' quality_controlled: 0 status: public title: Bacteriorhodopsin folds into the membrane against an external force type: journal_article volume: 357 year: '2006' ... --- _id: '3414' abstract: - lang: eng text: Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter. author: - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Christine full_name: Ziegler, Christine last_name: Ziegler - first_name: Werner full_name: Kühlbrandt, Werner last_name: Kühlbrandt - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028 apa: Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., & Mueller, D. (2006). Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.10.028 chicago: Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt, and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.10.028. ieee: A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli,” Journal of Molecular Biology, vol. 355, no. 1. Elsevier, pp. 2–8, 2006. ista: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 355(1), 2–8. mla: Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology, vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:10.1016/j.jmb.2005.10.028. short: A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 355 (2006) 2–8. date_created: 2018-12-11T12:03:12Z date_published: 2006-01-06T00:00:00Z date_updated: 2021-01-12T07:43:19Z day: '06' doi: 10.1016/j.jmb.2005.10.028 extern: 1 intvolume: ' 355' issue: '1' month: '01' page: 2 - 8 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '2987' quality_controlled: 0 status: public title: Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli type: journal_article volume: 355 year: '2006' ... --- _id: '3415' author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: David full_name: Cisneros, David last_name: Cisneros - first_name: Tanuj full_name: Sapra, Tanuj K last_name: Sapra - first_name: Jens full_name: Struckmeier, Jens last_name: Struckmeier - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031 apa: Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., & Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031 chicago: Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier, and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031. ieee: H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller, “Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology of Aging, vol. 27. Elsevier, pp. 546–561, 2006. ista: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 27, 546–561. mla: Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging, vol. 27, Elsevier, 2006, pp. 546–61, doi:10.1016/j.neurobiolaging.2005.03.031. short: H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller, Neurobiology of Aging 27 (2006) 546–561. date_created: 2018-12-11T12:03:12Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:27Z day: '01' doi: 10.1016/j.neurobiolaging.2005.03.031 extern: 1 intvolume: ' 27' month: '01' page: 546 - 561 publication: Neurobiology of Aging publication_status: published publisher: Elsevier publist_id: '2986' quality_controlled: 0 status: public title: Imaging and detecting molecular interactions of single membrane proteins type: review volume: 27 year: '2006' ... --- _id: '3437' abstract: - lang: eng text: The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models. author: - first_name: Andrea full_name: Betancourt, Andrea J last_name: Betancourt - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006' apa: 'Betancourt, A., & Bollback, J. P. (2006). Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006' chicago: 'Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development. Elsevier, 2006. https://doi.org/10.1016/j.gde.2006.10.006.' ieee: 'A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution,” Current Opinion in Genetics & Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.' ista: 'Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 16(6), 618–623.' mla: 'Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp. 618–23, doi:10.1016/j.gde.2006.10.006.' short: A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development 16 (2006) 618–623. date_created: 2018-12-11T12:03:19Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:43:27Z day: '01' doi: 10.1016/j.gde.2006.10.006 extern: 1 intvolume: ' 16' issue: '6' month: '12' page: 618 - 623 publication: Current Opinion in Genetics & Development publication_status: published publisher: Elsevier publist_id: '2963' quality_controlled: 0 status: public title: 'Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution' type: journal_article volume: 16 year: '2006' ... --- _id: '3431' abstract: - lang: eng text: Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses. author: - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: E. full_name: Schneidman, E. last_name: Schneidman - first_name: M. full_name: Berry, M. J. last_name: Berry - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4. apa: Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models for networks of real neurons. ArXiv. ArXiv. chicago: Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006. ieee: G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006. ista: Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks of real neurons. ArXiv, 1–4, . mla: Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4. short: G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4. date_created: 2018-12-11T12:03:18Z date_published: 2006-11-22T00:00:00Z date_updated: 2021-01-12T07:43:25Z day: '22' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/q-bio/0611072 month: '11' oa: 1 page: 1 - 4 publication: ArXiv publication_status: published publisher: ArXiv publist_id: '2969' quality_controlled: 0 status: public title: Ising models for networks of real neurons type: preprint year: '2006' ... --- _id: '3449' abstract: - lang: eng text: We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rhada full_name: Jagadeesan, Rhada last_name: Jagadeesan - first_name: Corin full_name: Pitcher, Corin last_name: Pitcher citation: ama: 'Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82. doi:10.1109/CSFW.2006.14' apa: 'Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls (pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14' chicago: Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14. ieee: 'K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented at the CSF: Computer Security Foundations, 2006, pp. 70–82.' ista: 'Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer Security Foundations, 70–82.' mla: Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82, doi:10.1109/CSFW.2006.14. short: K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82. conference: name: 'CSF: Computer Security Foundations' date_created: 2018-12-11T12:03:23Z date_published: 2006-07-31T00:00:00Z date_updated: 2021-01-12T07:43:32Z day: '31' doi: 10.1109/CSFW.2006.14 extern: 1 month: '07' page: 70 - 82 publication_status: published publisher: IEEE publist_id: '2938' quality_controlled: 0 status: public title: Games for controls type: conference year: '2006' ... --- _id: '3463' abstract: - lang: eng text: It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network. author: - first_name: Joseph full_name: Bischofberger, Joseph last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2' apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2' chicago: 'Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology. Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.' ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review),” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–372, 2006.' ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 453(3), 361–372.' mla: 'Bischofberger, Joseph, et al. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.' short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 361–372.' date_created: 2018-12-11T12:03:28Z date_published: 2006-12-01T00:00:00Z date_updated: 2019-04-26T07:22:28Z day: '01' doi: 10.1007/s00424-006-0093-2 extern: 1 intvolume: ' 453' issue: '3' month: '12' page: 361 - 372 publication: 'Pflugers Archiv : European Journal of Physiology' publication_status: published publisher: Springer publist_id: '2924' quality_controlled: 0 status: public title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review) type: review volume: 453 year: '2006' ... --- _id: '3499' abstract: - lang: eng text: 'We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. ' acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR- 0234690, and by the SNSF under the Indo-Swiss Joint Research Programme. alternative_title: - 'LNCS ' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207. Springer; 2006:271-286. doi:10.1007/11874683_18' apa: 'Chatterjee, K. (2006). Nash equilibrium for upward-closed objectives (Vol. 4207, pp. 271–286). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_18' chicago: Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,” 4207:271–86. Springer, 2006. https://doi.org/10.1007/11874683_18. ieee: 'K. Chatterjee, “Nash equilibrium for upward-closed objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 271–286.' ista: 'Chatterjee K. 2006. Nash equilibrium for upward-closed objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 271–286.' mla: Chatterjee, Krishnendu. Nash Equilibrium for Upward-Closed Objectives. Vol. 4207, Springer, 2006, pp. 271–86, doi:10.1007/11874683_18. short: K. Chatterjee, in:, Springer, 2006, pp. 271–286. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:03:39Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:43:52Z day: '28' doi: 10.1007/11874683_18 extern: 1 intvolume: ' 4207' month: '09' page: 271 - 286 publication_status: published publisher: Springer publist_id: '2888' quality_controlled: 0 status: public title: Nash equilibrium for upward-closed objectives type: conference volume: 4207 year: '2006' ... --- _id: '3500' abstract: - lang: eng text: The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n). acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610 and the SNSF under the Indo-Swiss Joint Research Programme. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Chatterjee K, Henzinger TA, Piterman N. Algorithms for Büchi Games. In: ACM; 2006.' apa: 'Chatterjee, K., Henzinger, T. A., & Piterman, N. (2006). Algorithms for Büchi Games. Presented at the GDV: Games in Design and Verification, ACM.' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms for Büchi Games.” ACM, 2006. ieee: 'K. Chatterjee, T. A. Henzinger, and N. Piterman, “Algorithms for Büchi Games,” presented at the GDV: Games in Design and Verification, 2006.' ista: 'Chatterjee K, Henzinger TA, Piterman N. 2006. Algorithms for Büchi Games. GDV: Games in Design and Verification.' mla: Chatterjee, Krishnendu, et al. Algorithms for Büchi Games. ACM, 2006. short: K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006. conference: name: 'GDV: Games in Design and Verification' date_created: 2018-12-11T12:03:39Z date_published: 2006-08-21T00:00:00Z date_updated: 2021-01-12T07:43:53Z day: '21' extern: 1 main_file_link: - open_access: '0' url: http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf month: '08' publication_status: published publisher: ACM publist_id: '2887' quality_controlled: 0 status: public title: Algorithms for Büchi Games type: conference year: '2006' ... --- _id: '3510' abstract: - lang: eng text: Embodiments automatically generate an accurate network of watertight NURBS patches from polygonal models of objects while automatically detecting and preserving character lines thereon. These embodiments generate from an initial triangulation of the surface, a hierarchy of progressively coarser triangulations of the surface by performing a sequence of edge contractions using a greedy algorithm that selects edge contractions by their numerical properties. Operations are also performed to connect the triangulations in the hierarchy using homeomorphisms that preserve the topology of the initial triangulation in the coarsest triangulation. A desired quadrangulation of the surface can then be generated by homeomorphically mapping edges of a coarsest triangulation in the hierarchy back to the initial triangulation. This quadrangulation is topologically consistent with the initial triangulation and is defined by a plurality of quadrangular patches. These quadrangular patches are linked together by a (U, V) mesh that is guaranteed to be continuous at patch boundaries. A grid is then preferably fit to each of the quadrangles in the resulting quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles. A watertight NURBS model may be generated from the resulting quadrangulation. applicant: - Raindrop Geomagic, Inc. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu - first_name: Dmitry full_name: Nekhayev, Dmitry last_name: Nekhayev - first_name: Michael full_name: Facello, Michael last_name: Facello - first_name: Steven full_name: Williams, Steven last_name: Williams citation: ama: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. 2006. apa: Edelsbrunner, H., Fu, P., Nekhayev, D., Facello, M., & Williams, S. (2006). Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. chicago: Edelsbrunner, Herbert, Ping Fu, Dmitry Nekhayev, Michael Facello, and Steven Williams. “Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism,” 2006. ieee: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, and S. Williams, “Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.” 2006. ista: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. 2006. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. mla: Edelsbrunner, Herbert, et al. Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism. 2006. short: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006). date_created: 2018-12-11T12:03:42Z date_published: 2006-02-07T00:00:00Z date_updated: 2022-01-05T12:58:26Z day: '07' extern: '1' ipc: G06F 7/60 ; G06F 17/10 ; G06F 101/00 ipn: US6996505B1 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US6996505 month: '02' oa: 1 oa_version: Published Version publication_date: 2006-02-07 publist_id: '2877' status: public title: Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3511' abstract: - lang: eng text: 'Methods, apparatus and computer program products provide efficient techniques for designing and printing shells of hearing-aid devices with a high degree of quality assurance and reliability and with a reduced number of manual and time consuming production steps and operations. These techniques also preferably provide hearing-aid shells having internal volumes that can approach a maximum allowable ratio of internal volume relative to external volume. These high internal volumes facilitate the inclusion of hearing-aid electrical components having higher degrees of functionality and/or the use of smaller and less conspicuous hearing-aid shells. A preferred method includes operations to generate a watertight digital model of a hearing-aid shell by thickening a three-dimensional digital model of a shell surface in a manner that eliminates self-intersections and results in a thickened model having an internal volume that is a high percentage of an external volume of the model. ' acknowledgement: sold to Siemens and Phonak applicant: - Phonak AG article_processing_charge: No author: - first_name: Ping full_name: Fu, Ping last_name: Fu - first_name: Dmitry full_name: Nekhayev, Dmitry last_name: Nekhayev - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Fu P, Nekhayev D, Edelsbrunner H. Manufacturing methods and systems for rapid production of hearing-aid shells. 2006. apa: Fu, P., Nekhayev, D., & Edelsbrunner, H. (2006). Manufacturing methods and systems for rapid production of hearing-aid shells. chicago: Fu, Ping, Dmitry Nekhayev, and Herbert Edelsbrunner. “Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells,” 2006. ieee: P. Fu, D. Nekhayev, and H. Edelsbrunner, “Manufacturing methods and systems for rapid production of hearing-aid shells.” 2006. ista: Fu P, Nekhayev D, Edelsbrunner H. 2006. Manufacturing methods and systems for rapid production of hearing-aid shells. mla: Fu, Ping, et al. Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells. 2006. short: P. Fu, D. Nekhayev, H. Edelsbrunner, (2006). date_created: 2018-12-11T12:03:43Z date_published: 2006-05-23T00:00:00Z date_updated: 2022-01-05T13:03:56Z day: '23' extern: '1' ipc: G06F 9/00 ipn: US7050876B1 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US7050876B1 month: '05' oa: 1 oa_version: Published Version publication_date: 2006-05-23 publist_id: '2876' status: public title: Manufacturing methods and systems for rapid production of hearing-aid shells type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3512' abstract: - lang: eng text: Methods, apparatus and computer program products provide efficient techniques for reconstructing surfaces from data point sets. These techniques include reconstructing surfaces from sets of scanned data points that have preferably undergone preprocessing operations to improve their quality by, for example, reducing noise and removing outliers. These techniques include reconstructing a dense and locally two-dimensionally distributed 3D point set (e.g., point cloud) by merging stars in two-dimensional weighted Delaunay triangulations within estimated tangent planes. The techniques include determining a plurality of stars from a plurality of points p.sub.i in a 3D point set S that at least partially describes the 3D surface, by projecting the plurality of points p.sub.i onto planes T.sub.i that are each estimated to be tangent about a respective one of the plurality of points p.sub.i. The plurality of stars are then merged into a digital model of the 3D surface. applicant: - Geomagic Inc. article_processing_charge: No author: - first_name: Yates full_name: Fletcher, Yates last_name: Fletcher - first_name: Tobias full_name: Gloth, Tobias last_name: Gloth - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu citation: ama: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. Method, apparatus and computer products that reconstruct surfaces from data points. 2006. apa: Fletcher, Y., Gloth, T., Edelsbrunner, H., & Fu, P. (2006). Method, apparatus and computer products that reconstruct surfaces from data points. chicago: Fletcher, Yates, Tobias Gloth, Herbert Edelsbrunner, and Ping Fu. “Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points,” 2006. ieee: Y. Fletcher, T. Gloth, H. Edelsbrunner, and P. Fu, “Method, apparatus and computer products that reconstruct surfaces from data points.” 2006. ista: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. 2006. Method, apparatus and computer products that reconstruct surfaces from data points. mla: Fletcher, Yates, et al. Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points. 2006. short: Y. Fletcher, T. Gloth, H. Edelsbrunner, P. Fu, (2006). date_created: 2018-12-11T12:03:43Z date_published: 2006-04-04T00:00:00Z date_updated: 2022-01-05T14:00:00Z day: '04' extern: '1' ipc: ' G06T17/20 ; B33Y50/00' ipn: US7023432B2 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US7023432B2 month: '04' oa: 1 oa_version: Published Version publication_date: 2006-04-04 publist_id: '2875' status: public title: Method, apparatus and computer products that reconstruct surfaces from data points type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3545' abstract: - lang: eng text: The functional organization of the basal ganglia ( BG) is often defined according to one of two opposing schemes. The first proposes multiple, essentially independent channels of information processing. The second posits convergence and lateral integration of striatal channels at the level of the globus pallidus ( GP). We tested the hypothesis that these proposed aspects of functional connectivity within the striatopallidal axis are dynamic and related to brain state. Local field potentials ( LFPs) were simultaneously recorded from multiple sites in striatum and GP in anesthetized rats during slow-wave activity( SWA) and during global activation evoked by sensory stimulation. Functional connectivity was inferred from comparative analyses of the internuclear and intranuclear coherence between bipolar derivations of LFPs. During prominent SWA, as shown in the electrocorticogram and local field potentials in the basal ganglia, intranuclear coherence, and, thus, lateral functional connectivity within striatum or globus pallidus was relatively weak. Furthermore, the temporal coupling of LFPs recorded across these two nuclei involved functional convergence at the level of GP. Global activation, indicated by a loss of SWA, was accompanied by a rapid functional reorganization of the striatopallidal axis. Prominent lateral functional connectivity developed within GP and, to a significantly more constrained spatial extent, striatum. Additionally, functional convergence on GP was no longer apparent, despite increased internuclear coherence. These data demonstrate that functional connectivity within the BG is highly dynamic and suggest that the relative expression of organizational principles, such as parallel, independent processing channels, striatopallidal convergence, and lateral integration within BG nuclei, is dependent on brain state. author: - first_name: Peter full_name: Magill,Peter J last_name: Magill - first_name: Alek full_name: Pogosyan,Alek last_name: Pogosyan - first_name: Andrew full_name: Sharott,Andrew last_name: Sharott - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: John full_name: Bolam, John Paul last_name: Bolam - first_name: Peter full_name: Brown,Peter last_name: Brown citation: ama: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. 2006;26(23):6318-6329. doi:10.1523/​JNEUROSCI.0620-06.2006 apa: Magill, P., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., & Brown, P. (2006). Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/​JNEUROSCI.0620-06.2006 chicago: Magill, Peter, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John Bolam, and Peter Brown. “Changes in Functional Connectivity within the Rat Striatopallidal Axis during Global Brain Activation in Vivo.” Journal of Neuroscience. Society for Neuroscience, 2006. https://doi.org/10.1523/​JNEUROSCI.0620-06.2006. ieee: P. Magill, A. Pogosyan, A. Sharott, J. L. Csicsvari, J. Bolam, and P. Brown, “Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo,” Journal of Neuroscience, vol. 26, no. 23. Society for Neuroscience, pp. 6318–6329, 2006. ista: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. 2006. Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. 26(23), 6318–6329. mla: Magill, Peter, et al. “Changes in Functional Connectivity within the Rat Striatopallidal Axis during Global Brain Activation in Vivo.” Journal of Neuroscience, vol. 26, no. 23, Society for Neuroscience, 2006, pp. 6318–29, doi:10.1523/​JNEUROSCI.0620-06.2006. short: P. Magill, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, Journal of Neuroscience 26 (2006) 6318–6329. date_created: 2018-12-11T12:03:53Z date_published: 2006-06-07T00:00:00Z date_updated: 2021-01-12T07:44:13Z day: '07' doi: 10.1523/​JNEUROSCI.0620-06.2006 extern: 1 intvolume: ' 26' issue: '23' month: '06' page: 6318 - 6329 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '2840' quality_controlled: 0 status: public title: Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo type: journal_article volume: 26 year: '2006' ... --- _id: '3559' abstract: - lang: eng text: Persistent homology is the mathematical core of recent work on shape, including reconstruction, recognition, and matching. Its per- tinent information is encapsulated by a pairing of the critical values of a function, visualized by points forming a diagram in the plane. The original algorithm in [10] computes the pairs from an ordering of the simplices in a triangulation and takes worst-case time cubic in the number of simplices. The main result of this paper is an algorithm that maintains the pairing in worst-case linear time per transposition in the ordering. A side-effect of the algorithm’s anal- ysis is an elementary proof of the stability of persistence diagrams [7] in the special case of piecewise-linear functions. We use the algorithm to compute 1-parameter families of diagrams which we apply to the study of protein folding trajectories. acknowledgement: Partially supported by NSF under grant CCR- 00-86013, by DARPA under grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under grant B543154. author: - first_name: David full_name: Cohen-Steiner, David last_name: Cohen Steiner - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov citation: ama: 'Cohen Steiner D, Edelsbrunner H, Morozov D. Vines and vineyards by updating persistence in linear time. In: ACM; 2006:119-126. doi:10.1145/1137856.1137877' apa: 'Cohen Steiner, D., Edelsbrunner, H., & Morozov, D. (2006). Vines and vineyards by updating persistence in linear time (pp. 119–126). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137877' chicago: Cohen Steiner, David, Herbert Edelsbrunner, and Dmitriy Morozov. “Vines and Vineyards by Updating Persistence in Linear Time,” 119–26. ACM, 2006. https://doi.org/10.1145/1137856.1137877. ieee: 'D. Cohen Steiner, H. Edelsbrunner, and D. Morozov, “Vines and vineyards by updating persistence in linear time,” presented at the SCG: Symposium on Computational Geometry, 2006, pp. 119–126.' ista: 'Cohen Steiner D, Edelsbrunner H, Morozov D. 2006. Vines and vineyards by updating persistence in linear time. SCG: Symposium on Computational Geometry, 119–126.' mla: Cohen Steiner, David, et al. Vines and Vineyards by Updating Persistence in Linear Time. ACM, 2006, pp. 119–26, doi:10.1145/1137856.1137877. short: D. Cohen Steiner, H. Edelsbrunner, D. Morozov, in:, ACM, 2006, pp. 119–126. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:03:58Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:44:18Z day: '01' doi: 10.1145/1137856.1137877 extern: 1 month: '06' page: 119 - 126 publication_status: published publisher: ACM publist_id: '2826' quality_controlled: 0 status: public title: Vines and vineyards by updating persistence in linear time type: conference year: '2006' ... --- _id: '3560' abstract: - lang: eng text: We continue the study of topological persistence [5] by investigat- ing the problem of simplifying a function f in a way that removes topological noise as determined by its persistence diagram [2]. To state our results, we call a function g an ε-simplification of another function f if ∥f − g∥∞ ≤ ε, and the persistence diagrams of g are the same as those of f except all points within L1-distance at most ε from the diagonal have been removed. We prove that for func- tions f on a 2-manifold such ε-simplification exists, and we give an algorithm to construct them in the piecewise linear case. acknowledgement: Partially supported by NSF under grant CCR-00-86013, by DARPA under grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under grant B543154. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Edelsbrunner H, Morozov D, Pascucci V. Persistence-sensitive simplification of functions on 2-manifolds. In: ACM; 2006:127-134. doi:10.1145/1137856.1137878' apa: 'Edelsbrunner, H., Morozov, D., & Pascucci, V. (2006). Persistence-sensitive simplification of functions on 2-manifolds (pp. 127–134). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137878' chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Valerio Pascucci. “Persistence-Sensitive Simplification of Functions on 2-Manifolds,” 127–34. ACM, 2006. https://doi.org/10.1145/1137856.1137878. ieee: 'H. Edelsbrunner, D. Morozov, and V. Pascucci, “Persistence-sensitive simplification of functions on 2-manifolds,” presented at the SCG: Symposium on Computational Geometry, 2006, pp. 127–134.' ista: 'Edelsbrunner H, Morozov D, Pascucci V. 2006. Persistence-sensitive simplification of functions on 2-manifolds. SCG: Symposium on Computational Geometry, 127–134.' mla: Edelsbrunner, Herbert, et al. Persistence-Sensitive Simplification of Functions on 2-Manifolds. ACM, 2006, pp. 127–34, doi:10.1145/1137856.1137878. short: H. Edelsbrunner, D. Morozov, V. Pascucci, in:, ACM, 2006, pp. 127–134. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:03:58Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:44:19Z day: '01' doi: 10.1145/1137856.1137878 extern: 1 main_file_link: - open_access: '0' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.4465 month: '06' page: 127 - 134 publication_status: published publisher: ACM publist_id: '2825' quality_controlled: 0 status: public title: Persistence-sensitive simplification of functions on 2-manifolds type: conference year: '2006' ... --- _id: '3594' author: - first_name: Josephine full_name: Pemberton, Josephine M last_name: Pemberton - first_name: Graeme full_name: Swanson, Graeme M last_name: Swanson - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Suzanne full_name: Livingstone, Suzanne R last_name: Livingstone - first_name: Helen full_name: Senn, Helen V last_name: Senn citation: ama: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. Hybridisation between red and sika deer in Scotland. Deer. 2006;13(9):22-26. apa: Pemberton, J., Swanson, G., Barton, N. H., Livingstone, S., & Senn, H. (2006). Hybridisation between red and sika deer in Scotland. Deer. BDS . chicago: Pemberton, Josephine, Graeme Swanson, Nicholas H Barton, Suzanne Livingstone, and Helen Senn. “Hybridisation between Red and Sika Deer in Scotland.” Deer. BDS , 2006. ieee: J. Pemberton, G. Swanson, N. H. Barton, S. Livingstone, and H. Senn, “Hybridisation between red and sika deer in Scotland,” Deer, vol. 13, no. 9. BDS , pp. 22–26, 2006. ista: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. 2006. Hybridisation between red and sika deer in Scotland. Deer. 13(9), 22–26. mla: Pemberton, Josephine, et al. “Hybridisation between Red and Sika Deer in Scotland.” Deer, vol. 13, no. 9, BDS , 2006, pp. 22–26. short: J. Pemberton, G. Swanson, N.H. Barton, S. Livingstone, H. Senn, Deer 13 (2006) 22–26. date_created: 2018-12-11T12:04:08Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:31Z day: '01' extern: 1 intvolume: ' 13' issue: '9' month: '01' page: 22 - 26 publication: Deer publication_status: published publisher: 'BDS ' publist_id: '2789' quality_controlled: 0 status: public title: Hybridisation between red and sika deer in Scotland type: review volume: 13 year: '2006' ...