[{"day":"03","month":"05","doi":"10.1007/11744047_1","date_published":"2006-05-03T00:00:00Z","conference":{"name":"ECCV: European Conference on Computer Vision"},"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf"}],"citation":{"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.","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.","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.","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.","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","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"},"page":"1 - 15","quality_controlled":0,"publist_id":"3498","abstract":[{"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.","lang":"eng"}],"extern":1,"type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"volume":"3952 LNCS","date_updated":"2021-01-12T07:41:39Z","date_created":"2018-12-11T12:01:52Z","_id":"3184","year":"2006","publisher":"Springer","status":"public","publication_status":"published","title":"Comparison of energy minimization algorithms for highly connected graphs"},{"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"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.","short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 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.","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.","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","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.","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"},"main_file_link":[{"url":"http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf","open_access":"0"}],"quality_controlled":0,"page":"1480 - 1492","date_published":"2006-09-01T00:00:00Z","doi":"10.1109/TPAMI.2006.193","month":"09","day":"01","year":"2006","_id":"3185","status":"public","publication_status":"published","title":"Probabilistic fusion of stereo with color and contrast for bilayer segmentation","intvolume":" 28","publisher":"IEEE","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"first_name":"Antonio","last_name":"Criminisi","full_name":"Criminisi, Antonio"},{"full_name":"Blake, Andrew","last_name":"Blake","first_name":"Andrew"},{"first_name":"Geoffrey","last_name":"Cross","full_name":"Cross, Geoffrey"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"}],"date_created":"2018-12-11T12:01:53Z","date_updated":"2021-01-12T07:41:39Z","volume":28,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"9","publist_id":"3496","extern":1},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"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.","lang":"eng"}],"publist_id":"3497","extern":1,"_id":"3186","year":"2006","title":"An integral solution to surface evolution PDEs via geo cuts","publication_status":"published","status":"public","intvolume":" 3953","publisher":"Springer","author":[{"full_name":"Boykov, Yuri","last_name":"Boykov","first_name":"Yuri"},{"full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"},{"full_name":"Cremers, Daniel","last_name":"Cremers","first_name":"Daniel"},{"first_name":"Andrew","last_name":"Delong","full_name":"Delong, Andrew"}],"date_created":"2018-12-11T12:01:53Z","date_updated":"2021-01-12T07:41:39Z","volume":3953,"month":"04","day":"28","citation":{"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.","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.","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","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.","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.","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"},"quality_controlled":0,"page":"409 - 422","conference":{"name":"ECCV: European Conference on Computer Vision"},"doi":"10.1007/11744078_32","date_published":"2006-04-28T00:00:00Z"},{"date_published":"2006-09-28T00:00:00Z","citation":{"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.","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.","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.","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.","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.","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."},"publication":"Techniques in Microscopy for Biomedical Applications","page":"213 - 284","quality_controlled":0,"day":"28","month":"09","author":[{"full_name":"Harald Janovjak","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sawhney, Ravi K","last_name":"Sawhney","first_name":"Ravi"},{"full_name":"Stark, Martin","last_name":"Stark","first_name":"Martin"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"}],"volume":2,"date_created":"2018-12-11T12:03:09Z","date_updated":"2021-01-12T07:43:15Z","year":"2006","_id":"3404","publisher":"World Scientific Publishing","intvolume":" 2","publication_status":"published","title":"Atomic force microscopy","status":"public","publist_id":"2998","extern":1,"type":"book_chapter","alternative_title":["Manuals in Biomedical Research"]},{"day":"24","month":"03","publication":"Journal of Molecular Biology","citation":{"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.","short":"M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of Molecular Biology 357 (2006) 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.","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.","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","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.","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"},"quality_controlled":0,"page":"644 - 654","doi":"10.1016/j.jmb.2005.12.065","date_published":"2006-03-24T00:00:00Z","type":"journal_article","abstract":[{"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.\n\nHere 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.\n\nWe 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.","lang":"eng"}],"issue":"2","publist_id":"2988","extern":1,"year":"2006","_id":"3413","title":"Bacteriorhodopsin folds into the membrane against an external force","publication_status":"published","status":"public","publisher":"Elsevier","intvolume":" 357","author":[{"last_name":"Kessler","first_name":"Max","full_name":"Kessler, Max"},{"full_name":"Gottschalk, Kay E","first_name":"Kay","last_name":"Gottschalk"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","full_name":"Harald Janovjak"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"},{"full_name":"Gaub, Hermann","last_name":"Gaub","first_name":"Hermann"}],"date_created":"2018-12-11T12:03:12Z","date_updated":"2021-01-12T07:43:18Z","volume":357},{"extern":1,"abstract":[{"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.","lang":"eng"}],"issue":"1","publist_id":"2987","type":"journal_article","date_updated":"2021-01-12T07:43:19Z","date_created":"2018-12-11T12:03:12Z","volume":355,"author":[{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"full_name":"Harald Janovjak","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"full_name":"Ziegler, Christine","last_name":"Ziegler","first_name":"Christine"},{"full_name":"Kühlbrandt, Werner","last_name":"Kühlbrandt","first_name":"Werner"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"publication_status":"published","status":"public","title":"Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli","intvolume":" 355","publisher":"Elsevier","year":"2006","_id":"3414","month":"01","day":"06","date_published":"2006-01-06T00:00:00Z","doi":"10.1016/j.jmb.2005.10.028","quality_controlled":0,"page":"2 - 8","publication":"Journal of Molecular Biology","citation":{"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.","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.","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","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.","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","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."}},{"publication":"Neurobiology of Aging","citation":{"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.","short":"H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller, Neurobiology of Aging 27 (2006) 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.","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.","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","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.","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"},"quality_controlled":0,"page":"546 - 561","doi":"10.1016/j.neurobiolaging.2005.03.031","date_published":"2006-01-01T00:00:00Z","month":"01","day":"01","_id":"3415","year":"2006","publication_status":"published","title":"Imaging and detecting molecular interactions of single membrane proteins","status":"public","intvolume":" 27","publisher":"Elsevier","author":[{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"last_name":"Cisneros","first_name":"David","full_name":"Cisneros, David"},{"full_name":"Sapra, Tanuj K","last_name":"Sapra","first_name":"Tanuj"},{"last_name":"Struckmeier","first_name":"Jens","full_name":"Struckmeier, Jens"},{"last_name":"Mueller","first_name":"Daniel","full_name":"Mueller, Daniel J"}],"date_created":"2018-12-11T12:03:12Z","date_updated":"2019-04-26T07:22:27Z","volume":27,"type":"review","publist_id":"2986","extern":1},{"extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2963","issue":"6","type":"journal_article","date_updated":"2021-01-12T07:43:27Z","date_created":"2018-12-11T12:03:19Z","volume":16,"author":[{"full_name":"Betancourt, Andrea J","first_name":"Andrea","last_name":"Betancourt"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Jonathan Bollback"}],"status":"public","publication_status":"published","title":"Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution","publisher":"Elsevier","intvolume":" 16","year":"2006","_id":"3437","month":"12","day":"01","doi":"10.1016/j.gde.2006.10.006","date_published":"2006-12-01T00:00:00Z","quality_controlled":0,"page":"618 - 623","publication":"Current Opinion in Genetics & Development","citation":{"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.","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.","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.","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.","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","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"}},{"title":"Ising models for networks of real neurons","publication_status":"published","status":"public","publisher":"ArXiv","_id":"3431","year":"2006","date_created":"2018-12-11T12:03:18Z","date_updated":"2021-01-12T07:43:25Z","author":[{"full_name":"Gasper Tkacik","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schneidman, E.","last_name":"Schneidman","first_name":"E."},{"last_name":"Berry","first_name":"M.","full_name":"Berry, M. J."},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William S"}],"type":"preprint","extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2969","quality_controlled":0,"page":"1 - 4","publication":"ArXiv","citation":{"ieee":"G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006.","apa":"Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models for networks of real neurons. ArXiv. ArXiv.","ista":"Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks of real neurons. ArXiv, 1–4, .","ama":"Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.","chicago":"Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006.","short":"G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.","mla":"Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4."},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/q-bio/0611072","open_access":"1"}],"date_published":"2006-11-22T00:00:00Z","month":"11","day":"22"},{"conference":{"name":"CSF: Computer Security Foundations"},"doi":"10.1109/CSFW.2006.14","date_published":"2006-07-31T00:00:00Z","quality_controlled":0,"page":"70 - 82","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","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.","short":"K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82.","mla":"Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82, doi: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."},"month":"07","day":"31","date_updated":"2021-01-12T07:43:32Z","date_created":"2018-12-11T12:03:23Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee"},{"full_name":"Jagadeesan, Rhada","last_name":"Jagadeesan","first_name":"Rhada"},{"first_name":"Corin","last_name":"Pitcher","full_name":"Pitcher, Corin"}],"publication_status":"published","status":"public","title":"Games for controls","publisher":"IEEE","year":"2006","_id":"3449","extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2938","type":"conference"},{"page":"361 - 372","quality_controlled":0,"citation":{"short":"J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 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.","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.","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","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."},"publication":"Pflugers Archiv : European Journal of Physiology","date_published":"2006-12-01T00:00:00Z","doi":"10.1007/s00424-006-0093-2","month":"12","day":"01","intvolume":" 453","publisher":"Springer","title":"Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review)","status":"public","publication_status":"published","_id":"3463","year":"2006","volume":453,"date_created":"2018-12-11T12:03:28Z","date_updated":"2019-04-26T07:22:28Z","author":[{"full_name":"Bischofberger, Joseph","last_name":"Bischofberger","first_name":"Joseph"},{"full_name":"Engel, Dominique","first_name":"Dominique","last_name":"Engel"},{"full_name":"Frotscher, Michael","first_name":"Michael","last_name":"Frotscher"},{"full_name":"Peter Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"type":"review","extern":1,"issue":"3","publist_id":"2924","abstract":[{"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.","lang":"eng"}]},{"year":"2006","_id":"3499","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.","publisher":"Springer","intvolume":" 4207","status":"public","publication_status":"published","title":"Nash equilibrium for upward-closed objectives","author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"volume":4207,"date_updated":"2021-01-12T07:43:52Z","date_created":"2018-12-11T12:03:39Z","type":"conference","alternative_title":["LNCS "],"publist_id":"2888","abstract":[{"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. ","lang":"eng"}],"extern":1,"citation":{"chicago":"Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,” 4207:271–86. Springer, 2006. https://doi.org/10.1007/11874683_18.","short":"K. Chatterjee, in:, Springer, 2006, pp. 271–286.","mla":"Chatterjee, Krishnendu. Nash Equilibrium for Upward-Closed Objectives. Vol. 4207, Springer, 2006, pp. 271–86, 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","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.","ama":"Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207. Springer; 2006:271-286. doi:10.1007/11874683_18"},"page":"271 - 286","quality_controlled":0,"doi":"10.1007/11874683_18","date_published":"2006-09-28T00:00:00Z","conference":{"name":"CSL: Computer Science Logic"},"month":"09","day":"28"},{"date_published":"2006-08-21T00:00:00Z","conference":{"name":"GDV: Games in Design and Verification"},"citation":{"short":"K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006.","mla":"Chatterjee, Krishnendu, et al. Algorithms for Büchi Games. ACM, 2006.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms for Büchi Games.” ACM, 2006.","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.","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."},"main_file_link":[{"open_access":"0","url":"http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf"}],"quality_controlled":0,"day":"21","month":"08","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Krishnendu Chatterjee"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"},{"last_name":"Piterman","first_name":"Nir","full_name":"Piterman, Nir"}],"date_updated":"2021-01-12T07:43:53Z","date_created":"2018-12-11T12:03:39Z","year":"2006","_id":"3500","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.","publisher":"ACM","status":"public","publication_status":"published","title":"Algorithms for Büchi Games","publist_id":"2887","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)."}],"extern":1,"type":"conference"},{"type":"patent","publist_id":"2877","abstract":[{"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.","lang":"eng"}],"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"3510","year":"2006","applicant":["Raindrop Geomagic, Inc."],"title":"Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism","status":"public","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Fu, Ping","first_name":"Ping","last_name":"Fu"},{"full_name":"Nekhayev, Dmitry","last_name":"Nekhayev","first_name":"Dmitry"},{"full_name":"Facello, Michael","first_name":"Michael","last_name":"Facello"},{"first_name":"Steven","last_name":"Williams","full_name":"Williams, Steven"}],"ipc":"G06F 7/60 ; G06F 17/10 ; G06F 101/00","oa_version":"Published Version","date_updated":"2022-01-05T12:58:26Z","date_created":"2018-12-11T12:03:42Z","article_processing_charge":"No","day":"07","month":"02","publication_date":"2006-02-07","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.","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.","short":"H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006).","mla":"Edelsbrunner, Herbert, et al. Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism. 2006.","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."},"main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/US6996505"}],"oa":1,"ipn":"US6996505B1","date_published":"2006-02-07T00:00:00Z"},{"month":"05","day":"23","article_processing_charge":"No","date_published":"2006-05-23T00:00:00Z","ipn":"US7050876B1","publication_date":"2006-05-23","citation":{"chicago":"Fu, Ping, Dmitry Nekhayev, and Herbert Edelsbrunner. “Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells,” 2006.","short":"P. Fu, D. Nekhayev, H. Edelsbrunner, (2006).","mla":"Fu, Ping, et al. 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.","apa":"Fu, P., Nekhayev, D., & Edelsbrunner, H. (2006). Manufacturing methods and systems for rapid production of hearing-aid shells.","ista":"Fu P, Nekhayev D, Edelsbrunner H. 2006. Manufacturing methods and systems for rapid production of hearing-aid shells.","ama":"Fu P, Nekhayev D, Edelsbrunner H. Manufacturing methods and systems for rapid production of hearing-aid shells. 2006."},"main_file_link":[{"url":"https://patents.google.com/patent/US7050876B1","open_access":"1"}],"oa":1,"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. "}],"publist_id":"2876","extern":"1","type":"patent","author":[{"last_name":"Fu","first_name":"Ping","full_name":"Fu, Ping"},{"full_name":"Nekhayev, Dmitry","first_name":"Dmitry","last_name":"Nekhayev"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"date_created":"2018-12-11T12:03:43Z","date_updated":"2022-01-05T13:03:56Z","oa_version":"Published Version","ipc":"G06F 9/00","_id":"3511","year":"2006","acknowledgement":"sold to Siemens and Phonak","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Manufacturing methods and systems for rapid production of hearing-aid shells","status":"public","applicant":["Phonak AG"]},{"author":[{"last_name":"Fletcher","first_name":"Yates","full_name":"Fletcher, Yates"},{"full_name":"Gloth, Tobias","first_name":"Tobias","last_name":"Gloth"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Fu, Ping","last_name":"Fu","first_name":"Ping"}],"ipc":" G06T17/20 ; B33Y50/00","oa_version":"Published Version","date_updated":"2022-01-05T14:00:00Z","date_created":"2018-12-11T12:03:43Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"3512","year":"2006","applicant":["Geomagic Inc."],"title":"Method, apparatus and computer products that reconstruct surfaces from data points","status":"public","publist_id":"2875","abstract":[{"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.","lang":"eng"}],"extern":"1","type":"patent","date_published":"2006-04-04T00:00:00Z","publication_date":"2006-04-04","citation":{"ieee":"Y. Fletcher, T. Gloth, H. Edelsbrunner, and P. Fu, “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.","ista":"Fletcher Y, Gloth T, Edelsbrunner H, Fu P. 2006. Method, apparatus and computer products that reconstruct surfaces from data points.","ama":"Fletcher Y, Gloth T, Edelsbrunner H, Fu P. Method, apparatus and computer products that reconstruct surfaces from data points. 2006.","chicago":"Fletcher, Yates, Tobias Gloth, Herbert Edelsbrunner, and Ping Fu. “Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points,” 2006.","short":"Y. Fletcher, T. Gloth, H. Edelsbrunner, P. Fu, (2006).","mla":"Fletcher, Yates, et al. Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points. 2006."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/US7023432B2"}],"ipn":"US7023432B2","article_processing_charge":"No","day":"04","month":"04"},{"volume":26,"date_created":"2018-12-11T12:03:53Z","date_updated":"2021-01-12T07:44:13Z","author":[{"first_name":"Peter","last_name":"Magill","full_name":"Magill,Peter J"},{"first_name":"Alek","last_name":"Pogosyan","full_name":"Pogosyan,Alek"},{"first_name":"Andrew","last_name":"Sharott","full_name":"Sharott,Andrew"},{"full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"},{"full_name":"Bolam, John Paul","first_name":"John","last_name":"Bolam"},{"last_name":"Brown","first_name":"Peter","full_name":"Brown,Peter"}],"intvolume":" 26","publisher":"Society for Neuroscience","title":"Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo","publication_status":"published","status":"public","year":"2006","_id":"3545","extern":1,"issue":"23","publist_id":"2840","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2006-06-07T00:00:00Z","doi":"10.1523/JNEUROSCI.0620-06.2006","page":"6318 - 6329","quality_controlled":0,"citation":{"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.","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.","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","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","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.","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."},"publication":"Journal of Neuroscience","month":"06","day":"07"},{"month":"06","day":"01","conference":{"name":"SCG: Symposium on Computational Geometry"},"date_published":"2006-06-01T00:00:00Z","doi":"10.1145/1137856.1137877","quality_controlled":0,"page":"119 - 126","citation":{"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.","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","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.","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","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.","short":"D. Cohen Steiner, H. Edelsbrunner, D. Morozov, in:, ACM, 2006, pp. 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."},"extern":1,"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."}],"publist_id":"2826","type":"conference","date_updated":"2021-01-12T07:44:18Z","date_created":"2018-12-11T12:03:58Z","author":[{"last_name":"Cohen Steiner","first_name":"David","full_name":"Cohen-Steiner, David"},{"full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"first_name":"Dmitriy","last_name":"Morozov","full_name":"Morozov, Dmitriy"}],"status":"public","publication_status":"published","title":"Vines and vineyards by updating persistence in linear time","publisher":"ACM","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.","_id":"3559","year":"2006"},{"main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.4465","open_access":"0"}],"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","ista":"Edelsbrunner H, Morozov D, Pascucci V. 2006. Persistence-sensitive simplification of functions on 2-manifolds. SCG: Symposium on Computational Geometry, 127–134.","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","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.","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.","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."},"page":"127 - 134","quality_controlled":0,"doi":"10.1145/1137856.1137878","date_published":"2006-06-01T00:00:00Z","conference":{"name":"SCG: Symposium on Computational Geometry"},"day":"01","month":"06","year":"2006","_id":"3560","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.","publisher":"ACM","status":"public","publication_status":"published","title":"Persistence-sensitive simplification of functions on 2-manifolds","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner"},{"first_name":"Dmitriy","last_name":"Morozov","full_name":"Morozov, Dmitriy"},{"full_name":"Pascucci, Valerio","first_name":"Valerio","last_name":"Pascucci"}],"date_created":"2018-12-11T12:03:58Z","date_updated":"2021-01-12T07:44:19Z","type":"conference","publist_id":"2825","abstract":[{"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.","lang":"eng"}],"extern":1},{"date_published":"2006-01-01T00:00:00Z","page":"22 - 26","quality_controlled":0,"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.","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.","apa":"Pemberton, J., Swanson, G., Barton, N. H., Livingstone, S., & Senn, H. (2006). Hybridisation between red and sika deer in Scotland. Deer. BDS .","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.","short":"J. Pemberton, G. Swanson, N.H. Barton, S. Livingstone, H. Senn, Deer 13 (2006) 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.","chicago":"Pemberton, Josephine, Graeme Swanson, Nicholas H Barton, Suzanne Livingstone, and Helen Senn. “Hybridisation between Red and Sika Deer in Scotland.” Deer. BDS , 2006."},"publication":"Deer","day":"01","month":"01","volume":13,"date_created":"2018-12-11T12:04:08Z","date_updated":"2019-04-26T07:22:31Z","author":[{"full_name":"Pemberton, Josephine M","first_name":"Josephine","last_name":"Pemberton"},{"last_name":"Swanson","first_name":"Graeme","full_name":"Swanson, Graeme M"},{"full_name":"Nicholas Barton","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"first_name":"Suzanne","last_name":"Livingstone","full_name":"Livingstone, Suzanne R"},{"first_name":"Helen","last_name":"Senn","full_name":"Senn, Helen V"}],"publisher":"BDS ","intvolume":" 13","status":"public","publication_status":"published","title":"Hybridisation between red and sika deer in Scotland","_id":"3594","year":"2006","extern":1,"publist_id":"2789","issue":"9","type":"review"}]