--- _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' ... --- _id: '3609' abstract: - lang: eng text: Bombina bombina and B. variegata are two anciently diverged toad taxa that have adapted to different breeding habitats yet hybridize freely in zones of overlap where their parapatric distributions meet. Here, we report on a joint genetic and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine. We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency clines with a sharp central step occur across a sharp ecotone, where transitions in aquatic habitat, elevation, and terrestrial vegetation coincide. The width of the hybrid zone, estimated as the inverse of the maximum gradient in allele frequency, is 2.3 km. This is the smallest of four estimates derived from different clinal transects across Europe. We argue that the narrow cline near Stryi is mainly due to a combination of habitat distribution and habitat preference. Adult toads show a preference for either ponds (B. bombina) or puddles (B. variegata), which is known to affect the distribution of genotypes within the hybrid zones. At Stryi, it should cause a reduction of the dispersal rate across the ecotone and thus narrow the cline. A detailed comparison of all five intensively studied Bombina transects lends support to the hypothesis that habitat distribution plus habitat preference can jointly affect the structure of hybrid zones and, ultimately, the resulting barriers to gene flow between differentiated gene pools. This study also represents a resampling of an area that was last studied more than 70 years ago. Our allele-frequency clines largely coincide with those that were described then on the basis of morphological variation. However, we found asymmetrical introgression of B. variegata genes into B. bombina territory along the bank of a river. author: - first_name: Alexey full_name: Yanchukov, Alexey last_name: Yanchukov - first_name: Sebastian full_name: Hofman, Sebastian last_name: Hofman - first_name: Jacek full_name: Szymura, Jacek M last_name: Szymura - first_name: Sergey full_name: Mezhzherin, Sergey V last_name: Mezhzherin - first_name: Sviatoslav full_name: Morozov-Leonov, Sviatoslav last_name: Morozov Leonov - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger citation: ama: 'Yanchukov A, Hofman S, Szymura J, et al. Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time. Evolution; International Journal of Organic Evolution. 2006;60(3):583-600. doi:10.1111/j.0014-3820.2006.tb01139.x' apa: 'Yanchukov, A., Hofman, S., Szymura, J., Mezhzherin, S., Morozov Leonov, S., Barton, N. H., & Nürnberger, B. (2006). Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb01139.x' chicago: 'Yanchukov, Alexey, Sebastian Hofman, Jacek Szymura, Sergey Mezhzherin, Sviatoslav Morozov Leonov, Nicholas H Barton, and Beate Nürnberger. “Hybridization of Bombina Bombina and B. Variegata (Anura, Discoglossidae) at a Sharp Ecotone in Western Ukraine: Comparisons across Transects and over Time.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb01139.x.' ieee: 'A. Yanchukov et al., “Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time,” Evolution; International Journal of Organic Evolution, vol. 60, no. 3. Wiley-Blackwell, pp. 583–600, 2006.' ista: 'Yanchukov A, Hofman S, Szymura J, Mezhzherin S, Morozov Leonov S, Barton NH, Nürnberger B. 2006. Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time. Evolution; International Journal of Organic Evolution. 60(3), 583–600.' mla: 'Yanchukov, Alexey, et al. “Hybridization of Bombina Bombina and B. Variegata (Anura, Discoglossidae) at a Sharp Ecotone in Western Ukraine: Comparisons across Transects and over Time.” Evolution; International Journal of Organic Evolution, vol. 60, no. 3, Wiley-Blackwell, 2006, pp. 583–600, doi:10.1111/j.0014-3820.2006.tb01139.x.' short: A. Yanchukov, S. Hofman, J. Szymura, S. Mezhzherin, S. Morozov Leonov, N.H. Barton, B. Nürnberger, Evolution; International Journal of Organic Evolution 60 (2006) 583–600. date_created: 2018-12-11T12:04:13Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:44:38Z day: '01' doi: 10.1111/j.0014-3820.2006.tb01139.x extern: 1 intvolume: ' 60' issue: '3' month: '03' page: 583 - 600 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2774' quality_controlled: 0 status: public title: 'Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time' type: journal_article volume: 60 year: '2006' ... --- _id: '3608' abstract: - lang: eng text: 'We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests. ' author: - first_name: Mark full_name: Kirkpatrick, Mark last_name: Kirkpatrick - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Kirkpatrick M, Barton NH. Chromosome inversions, local adaptation, and speciation. Genetics. 2006;173(1):419-434. doi:10.1534/genetics.105.047985 apa: Kirkpatrick, M., & Barton, N. H. (2006). Chromosome inversions, local adaptation, and speciation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.105.047985 chicago: Kirkpatrick, Mark, and Nicholas H Barton. “Chromosome Inversions, Local Adaptation, and Speciation.” Genetics. Genetics Society of America, 2006. https://doi.org/10.1534/genetics.105.047985. ieee: M. Kirkpatrick and N. H. Barton, “Chromosome inversions, local adaptation, and speciation,” Genetics, vol. 173, no. 1. Genetics Society of America, pp. 419–434, 2006. ista: Kirkpatrick M, Barton NH. 2006. Chromosome inversions, local adaptation, and speciation. Genetics. 173(1), 419–434. mla: Kirkpatrick, Mark, and Nicholas H. Barton. “Chromosome Inversions, Local Adaptation, and Speciation.” Genetics, vol. 173, no. 1, Genetics Society of America, 2006, pp. 419–34, doi:10.1534/genetics.105.047985. short: M. Kirkpatrick, N.H. Barton, Genetics 173 (2006) 419–434. date_created: 2018-12-11T12:04:13Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T07:44:37Z day: '01' doi: 10.1534/genetics.105.047985 extern: 1 intvolume: ' 173' issue: '1' month: '05' page: 419 - 434 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '2775' quality_controlled: 0 status: public title: Chromosome inversions, local adaptation, and speciation type: journal_article volume: 173 year: '2006' ... --- _id: '3610' abstract: - lang: eng text: For a model of diallelic loci with arbitrary epistasis, Barton and Turelli [2004. Effects of genetic drift on variance components under a general model of epistasis. Evolution 58, 2111–2132] gave results for variances among and within replicate lines obtained by inbreeding without selection. Here, we discuss the relation between their population genetic methods and classical quantitative genetic arguments. In particular, we consider the case of no dominance using classical identity by descent arguments, which generalizes their results from two alleles to multiple alleles. To clarify the connections between the alternative methods, we obtain the same results using an intermediate method, which explicitly identifies the statistical effects of sets of loci. We also discuss the effects of population bottlenecks on covariances among relatives. author: - first_name: William full_name: Hill, William G last_name: Hill - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Hill W, Barton NH, Turelli M. Prediction of effects of genetic drift on variance components under a general model of epistasis. Theoretical Population Biology. 2006;70(1):56-62. doi:10.1016/j.tpb.2005.10.001 apa: Hill, W., Barton, N. H., & Turelli, M. (2006). Prediction of effects of genetic drift on variance components under a general model of epistasis. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2005.10.001 chicago: Hill, William, Nicholas H Barton, and Michael Turelli. “Prediction of Effects of Genetic Drift on Variance Components under a General Model of Epistasis.” Theoretical Population Biology. Academic Press, 2006. https://doi.org/10.1016/j.tpb.2005.10.001. ieee: W. Hill, N. H. Barton, and M. Turelli, “Prediction of effects of genetic drift on variance components under a general model of epistasis,” Theoretical Population Biology, vol. 70, no. 1. Academic Press, pp. 56–62, 2006. ista: Hill W, Barton NH, Turelli M. 2006. Prediction of effects of genetic drift on variance components under a general model of epistasis. Theoretical Population Biology. 70(1), 56–62. mla: Hill, William, et al. “Prediction of Effects of Genetic Drift on Variance Components under a General Model of Epistasis.” Theoretical Population Biology, vol. 70, no. 1, Academic Press, 2006, pp. 56–62, doi:10.1016/j.tpb.2005.10.001. short: W. Hill, N.H. Barton, M. Turelli, Theoretical Population Biology 70 (2006) 56–62. date_created: 2018-12-11T12:04:14Z date_published: 2006-08-01T00:00:00Z date_updated: 2021-01-12T07:44:39Z day: '01' doi: 10.1016/j.tpb.2005.10.001 extern: 1 intvolume: ' 70' issue: '1' month: '08' page: 56 - 62 publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '2773' quality_controlled: 0 status: public title: Prediction of effects of genetic drift on variance components under a general model of epistasis type: journal_article volume: 70 year: '2006' ... --- _id: '3679' abstract: - lang: eng text: This paper describes a new system for "Finding Satellite Tracks” in astronomical images based on the modern geometric approach. There is an increasing need of using methods with solid mathematical and statistical foundation in astronomical image processing. Where the computational methods are serving in all disciplines of science, they are becoming popular in the field of astronomy as well. Currently different computational systems are required to be numerically optimized before to get applied on astronomical images. So at present there is no single system which solves the problems of astronomers using computational methods based on modern approaches. The system "Finding Satellite Tracks” is based on geometric matching method "Recognition by Adaptive Subdivision of Transformation Space (RAST)". alternative_title: - LNCS author: - first_name: Haider full_name: Ali,Haider last_name: Ali - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Ali H, Lampert C, Breuel T. Satellite tracks removal in astronomical images. In: Vol 4225. Springer; 2006:892-901. doi:10.1007/11892755_92' apa: 'Ali, H., Lampert, C., & Breuel, T. (2006). Satellite tracks removal in astronomical images (Vol. 4225, pp. 892–901). Presented at the CIARP: Iberoamerican Congress in Pattern Recognition, Springer. https://doi.org/10.1007/11892755_92' chicago: Ali, Haider, Christoph Lampert, and Thomas Breuel. “Satellite Tracks Removal in Astronomical Images,” 4225:892–901. Springer, 2006. https://doi.org/10.1007/11892755_92. ieee: 'H. Ali, C. Lampert, and T. Breuel, “Satellite tracks removal in astronomical images,” presented at the CIARP: Iberoamerican Congress in Pattern Recognition, 2006, vol. 4225, pp. 892–901.' ista: 'Ali H, Lampert C, Breuel T. 2006. Satellite tracks removal in astronomical images. CIARP: Iberoamerican Congress in Pattern Recognition, LNCS, vol. 4225, 892–901.' mla: Ali, Haider, et al. Satellite Tracks Removal in Astronomical Images. Vol. 4225, Springer, 2006, pp. 892–901, doi:10.1007/11892755_92. short: H. Ali, C. Lampert, T. Breuel, in:, Springer, 2006, pp. 892–901. conference: name: 'CIARP: Iberoamerican Congress in Pattern Recognition' date_created: 2018-12-11T12:04:35Z date_published: 2006-10-31T00:00:00Z date_updated: 2021-01-12T07:45:05Z day: '31' doi: 10.1007/11892755_92 extern: 1 intvolume: ' 4225' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/ali-ciarp2006.pdf month: '10' page: 892 - 901 publication_status: published publisher: Springer publist_id: '2700' quality_controlled: 0 status: public title: Satellite tracks removal in astronomical images type: conference volume: 4225 year: '2006' ... --- _id: '3677' abstract: - lang: eng text: We propose a video retrieval framework based on a novel combination of spatiograms and the Jensen-Shannon divergence, and validate its performance in two quantitative experiments on TRECVID BBC Rushes data. In the first experiment, color-based methods are tested by grouping redundant shots in an unsupervised clustering. Results of the second experiment show that motion-based spatiograms make a promising fast, compressed-domain descriptor for the detection of interview scenes. alternative_title: - TRECVID Notebook Papers and Slides author: - first_name: Adrian full_name: Ulges, Adrian last_name: Ulges - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Daniel full_name: Keysers,Daniel last_name: Keysers citation: ama: 'Ulges A, Lampert C, Keysers D. Spatiogram-based shot distances for video retrieval. In: NIST (National Institute of Standards and Technology, US Department of Commerce); 2006:1-10.' apa: Ulges, A., Lampert, C., & Keysers, D. (2006). Spatiogram-based shot distances for video retrieval (pp. 1–10). Presented at the TRECVID Workshop, NIST (National Institute of Standards and Technology, US Department of Commerce). chicago: Ulges, Adrian, Christoph Lampert, and Daniel Keysers. “Spatiogram-Based Shot Distances for Video Retrieval,” 1–10. NIST (National Institute of Standards and Technology, US Department of Commerce), 2006. ieee: A. Ulges, C. Lampert, and D. Keysers, “Spatiogram-based shot distances for video retrieval,” presented at the TRECVID Workshop, 2006, pp. 1–10. ista: Ulges A, Lampert C, Keysers D. 2006. Spatiogram-based shot distances for video retrieval. TRECVID Workshop, TRECVID Notebook Papers and Slides, , 1–10. mla: Ulges, Adrian, et al. Spatiogram-Based Shot Distances for Video Retrieval. NIST (National Institute of Standards and Technology, US Department of Commerce), 2006, pp. 1–10. short: A. Ulges, C. Lampert, D. Keysers, in:, NIST (National Institute of Standards and Technology, US Department of Commerce), 2006, pp. 1–10. conference: name: TRECVID Workshop date_created: 2018-12-11T12:04:34Z date_published: 2006-11-14T00:00:00Z date_updated: 2021-01-12T07:45:04Z day: '14' extern: 1 main_file_link: - open_access: '0' url: http://www-nlpir.nist.gov/projects/tvpubs/tv6.papers/dfki.pdf month: '11' page: 1 - 10 publication_status: published publisher: NIST (National Institute of Standards and Technology, US Department of Commerce) publist_id: '2702' quality_controlled: 0 status: public title: Spatiogram-based shot distances for video retrieval type: conference year: '2006' ... --- _id: '3680' abstract: - lang: eng text: The detection of counterfeit in printed documents is currently based mainly on built-in security features or on human expertise. We propose a classification system that supports non-expert users to distinguish original documents from PC-made forgeries by analyzing the printing technique used. Each letter in a document is classified using a support vector machine that has been trained to distinguish laser from inkjet printouts. A color-coded visualization helps the user to interpret the per-letter classification results author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Lin full_name: Mei,Lin last_name: Mei - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Lampert C, Mei L, Breuel T. Printing technique classification for document counterfeit detection. In: Vol 1. IEEE; 2006:639-634. doi:10.1109/ICCIAS.2006.294214' apa: 'Lampert, C., Mei, L., & Breuel, T. (2006). Printing technique classification for document counterfeit detection (Vol. 1, pp. 639–634). Presented at the CIS: Computational Intelligence and Security, IEEE. https://doi.org/10.1109/ICCIAS.2006.294214' chicago: Lampert, Christoph, Lin Mei, and Thomas Breuel. “Printing Technique Classification for Document Counterfeit Detection,” 1:639–634. IEEE, 2006. https://doi.org/10.1109/ICCIAS.2006.294214. ieee: 'C. Lampert, L. Mei, and T. Breuel, “Printing technique classification for document counterfeit detection,” presented at the CIS: Computational Intelligence and Security, 2006, vol. 1, pp. 639–634.' ista: 'Lampert C, Mei L, Breuel T. 2006. Printing technique classification for document counterfeit detection. CIS: Computational Intelligence and Security vol. 1, 639–634.' mla: Lampert, Christoph, et al. Printing Technique Classification for Document Counterfeit Detection. Vol. 1, IEEE, 2006, pp. 639–634, doi:10.1109/ICCIAS.2006.294214. short: C. Lampert, L. Mei, T. Breuel, in:, IEEE, 2006, pp. 639–634. conference: name: 'CIS: Computational Intelligence and Security' date_created: 2018-12-11T12:04:35Z date_published: 2006-11-03T00:00:00Z date_updated: 2021-01-12T07:45:06Z day: '03' doi: 10.1109/ICCIAS.2006.294214 extern: 1 intvolume: ' 1' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/lampert-cis2006.pdf month: '11' page: 639 - 634 publication_status: published publisher: IEEE publist_id: '2698' quality_controlled: 0 status: public title: Printing technique classification for document counterfeit detection type: conference volume: 1 year: '2006' ... --- _id: '3695' abstract: - lang: eng text: We give an analytical and geometrical treatment of what it means to separate a Gaussian kernel along arbitrary axes in Ropfn, and we present a separation scheme that allows us to efficiently implement anisotropic Gaussian convolution filters for data of arbitrary dimensionality. Based on our previous analysis we show that this scheme is optimal with regard to the number of memory accesses and interpolation operations needed. The proposed method relies on nonorthogonal convolution axes and works completely in image space. Thus, it avoids the need for a fast Fourier transform (FFT)-subroutine. Depending on the accuracy and speed requirements, different interpolation schemes and methods to implement the one-dimensional Gaussian (finite impulse response and infinite impulse response) can be integrated. Special emphasis is put on analyzing the performance and accuracy of the new method. In particular, we show that without any special optimization of the source code, it can perform anisotropic Gaussian filtering faster than methods relying on the FFT. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Oliver full_name: Wirjadi,Oliver last_name: Wirjadi citation: ama: Lampert C, Wirjadi O. An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter. IEEE Transactions on Image Processing (TIP). 2006;15(11):3501-3513. doi: 10.1109/TIP.2006.877501 apa: Lampert, C., & Wirjadi, O. (2006). An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter. IEEE Transactions on Image Processing (TIP). IEEE. https://doi.org/ 10.1109/TIP.2006.877501 chicago: Lampert, Christoph, and Oliver Wirjadi. “An Optimal Non-Orthogonal Separation of the Anisotropic Gaussian Convolution Filter.” IEEE Transactions on Image Processing (TIP). IEEE, 2006. https://doi.org/ 10.1109/TIP.2006.877501 . ieee: C. Lampert and O. Wirjadi, “An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter,” IEEE Transactions on Image Processing (TIP), vol. 15, no. 11. IEEE, pp. 3501–3513, 2006. ista: Lampert C, Wirjadi O. 2006. An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter. IEEE Transactions on Image Processing (TIP). 15(11), 3501–3513. mla: Lampert, Christoph, and Oliver Wirjadi. “An Optimal Non-Orthogonal Separation of the Anisotropic Gaussian Convolution Filter.” IEEE Transactions on Image Processing (TIP), vol. 15, no. 11, IEEE, 2006, pp. 3501–13, doi: 10.1109/TIP.2006.877501 . short: C. Lampert, O. Wirjadi, IEEE Transactions on Image Processing (TIP) 15 (2006) 3501–3513. date_created: 2018-12-11T12:04:40Z date_published: 2006-11-01T00:00:00Z date_updated: 2021-01-12T07:49:01Z day: '01' doi: ' 10.1109/TIP.2006.877501 ' extern: 1 intvolume: ' 15' issue: '11' main_file_link: - open_access: '1' url: http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:386-kluedo-14003 month: '11' oa: 1 page: 3501 - 3513 publication: IEEE Transactions on Image Processing (TIP) publication_status: published publisher: IEEE publist_id: '2669' quality_controlled: 0 status: public title: An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter type: journal_article volume: 15 year: '2006' ... --- _id: '3693' abstract: - lang: eng text: Gaussian filtering in one, two or three dimensions is among the most commonly needed tasks in signal and image processing. Finite impulse response filters in the time domain with Gaussian masks are easy to implement in either floating or fixed point arithmetic, because Gaussian kernels are strictly positive and bounded. But these implementations are slow for large images or kernels. With the recursive IIR-filters and FFT-based methods, there are at least two alternative methods to perform Gaussian filtering in a faster way, but so far they are only applicable when floating-point hardware is available. In this paper, a fixed-point implementation of recursive Gaussian filtering is discussed and applied to isotropic and anisotropic image filtering by making use of a non-orthogonal separation scheme of the Gaussian filter. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Oliver full_name: Wirjadi,Oliver last_name: Wirjadi citation: ama: 'Lampert C, Wirjadi O. Anisotropic Gaussian filtering using fixed point arithmetic. In: IEEE; 2006:1565-1568. doi:10.1109/ICIP.2006.312606' apa: 'Lampert, C., & Wirjadi, O. (2006). Anisotropic Gaussian filtering using fixed point arithmetic (pp. 1565–1568). Presented at the ICIP: IEEE International Conference on Image Processing, IEEE. https://doi.org/10.1109/ICIP.2006.312606' chicago: Lampert, Christoph, and Oliver Wirjadi. “Anisotropic Gaussian Filtering Using Fixed Point Arithmetic,” 1565–68. IEEE, 2006. https://doi.org/10.1109/ICIP.2006.312606. ieee: 'C. Lampert and O. Wirjadi, “Anisotropic Gaussian filtering using fixed point arithmetic,” presented at the ICIP: IEEE International Conference on Image Processing, 2006, pp. 1565–1568.' ista: 'Lampert C, Wirjadi O. 2006. Anisotropic Gaussian filtering using fixed point arithmetic. ICIP: IEEE International Conference on Image Processing, 1565–1568.' mla: Lampert, Christoph, and Oliver Wirjadi. Anisotropic Gaussian Filtering Using Fixed Point Arithmetic. IEEE, 2006, pp. 1565–68, doi:10.1109/ICIP.2006.312606. short: C. Lampert, O. Wirjadi, in:, IEEE, 2006, pp. 1565–1568. conference: name: 'ICIP: IEEE International Conference on Image Processing' date_created: 2018-12-11T12:04:39Z date_published: 2006-10-08T00:00:00Z date_updated: 2021-01-12T07:49:00Z day: '08' doi: 10.1109/ICIP.2006.312606 extern: 1 month: '10' page: 1565 - 1568 publication_status: published publisher: IEEE publist_id: '2670' quality_controlled: 0 status: public title: Anisotropic Gaussian filtering using fixed point arithmetic type: conference year: '2006' ... --- _id: '3692' author: - first_name: Daniel full_name: Keysers,Daniel last_name: Keysers - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Keysers D, Lampert C, Breuel T. Color image dequantization by constrained diffusion. In: Vol 6058. SPIE; 2006. doi:10.1117/12.648713' apa: Keysers, D., Lampert, C., & Breuel, T. (2006). Color image dequantization by constrained diffusion (Vol. 6058). Presented at the SPIE Electronic Imaging, SPIE. https://doi.org/10.1117/12.648713 chicago: Keysers, Daniel, Christoph Lampert, and Thomas Breuel. “Color Image Dequantization by Constrained Diffusion,” Vol. 6058. SPIE, 2006. https://doi.org/10.1117/12.648713. ieee: D. Keysers, C. Lampert, and T. Breuel, “Color image dequantization by constrained diffusion,” presented at the SPIE Electronic Imaging, 2006, vol. 6058. ista: Keysers D, Lampert C, Breuel T. 2006. Color image dequantization by constrained diffusion. SPIE Electronic Imaging vol. 6058. mla: Keysers, Daniel, et al. Color Image Dequantization by Constrained Diffusion. Vol. 6058, SPIE, 2006, doi:10.1117/12.648713. short: D. Keysers, C. Lampert, T. Breuel, in:, SPIE, 2006. conference: name: SPIE Electronic Imaging date_created: 2018-12-11T12:04:39Z date_published: 2006-01-15T00:00:00Z date_updated: 2019-05-10T12:19:52Z day: '15' doi: 10.1117/12.648713 extern: 1 intvolume: ' 6058' month: '01' publication_status: published publisher: SPIE publist_id: '2674' quality_controlled: 0 status: public title: Color image dequantization by constrained diffusion type: conference volume: 6058 year: '2006' ... --- _id: '3729' abstract: - lang: eng text: Measuring the visco-elastic properties of biological macromolecules constitutes an important step towards the understanding of dynamic biological processes, such as cell adhesion, muscle function, or plant cell wall stability. Force spectroscopy techniques based on the atomic force microscope (AFM) are increasingly used to study the complex visco-elastic response of (bio-)molecules on a single-molecule level. These experiments either require that the AFM cantilever is actively oscillated or that the molecule is clamped at constant force to monitor thermal cantilever motion. Here we demonstrate that the visco-elasticity of single bio-molecules can readily be extracted from the Brownian cantilever motion during conventional force-extension measurements. It is shown that the characteristics of the cantilever determine the signal-to-noise (S/N) ratio and time resolution. Using a small cantilever, the visco-elastic properties of single dextran molecules were resolved with a time resolution of 8.3 ms. The presented approach can be directly applied to probe the dynamic response of complex bio-molecular systems or proteins in force-extension experiments. author: - first_name: Christian full_name: Bippes, Christian A last_name: Bippes - first_name: Andrew full_name: Humphris, Andrew D last_name: Humphris - first_name: Martin full_name: Stark, Martin last_name: Stark - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Bippes C, Humphris A, Stark M, Mueller D, Janovjak HL. Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments. European Biophysics Journal. 2006;35(3):287-292. doi:10.1007/s00249-005-0023-9 apa: Bippes, C., Humphris, A., Stark, M., Mueller, D., & Janovjak, H. L. (2006). Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments. European Biophysics Journal. Springer. https://doi.org/10.1007/s00249-005-0023-9 chicago: Bippes, Christian, Andrew Humphris, Martin Stark, Daniel Mueller, and Harald L Janovjak. “Direct Measurement of Single-Molecule Visco-Elasticity in Atomic Force Microscope Force-Extension Experiments.” European Biophysics Journal. Springer, 2006. https://doi.org/10.1007/s00249-005-0023-9. ieee: C. Bippes, A. Humphris, M. Stark, D. Mueller, and H. L. Janovjak, “Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments,” European Biophysics Journal, vol. 35, no. 3. Springer, pp. 287–292, 2006. ista: Bippes C, Humphris A, Stark M, Mueller D, Janovjak HL. 2006. Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments. European Biophysics Journal. 35(3), 287–292. mla: Bippes, Christian, et al. “Direct Measurement of Single-Molecule Visco-Elasticity in Atomic Force Microscope Force-Extension Experiments.” European Biophysics Journal, vol. 35, no. 3, Springer, 2006, pp. 287–92, doi:10.1007/s00249-005-0023-9. short: C. Bippes, A. Humphris, M. Stark, D. Mueller, H.L. Janovjak, European Biophysics Journal 35 (2006) 287–292. date_created: 2018-12-11T12:04:51Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:51:46Z day: '01' doi: 10.1007/s00249-005-0023-9 extern: 1 intvolume: ' 35' issue: '3' month: '02' page: 287 - 292 publication: European Biophysics Journal publication_status: published publisher: Springer publist_id: '2500' quality_controlled: 0 status: public title: Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments type: journal_article volume: 35 year: '2006' ... --- _id: '3728' abstract: - lang: eng text: Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard–Jones contact interactions is applied to model the protein–membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins. author: - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak - first_name: Sławomir full_name: Filipek, Sławomir last_name: Filipek - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Krystiana full_name: Krzysko, Krystiana A last_name: Krzysko citation: ama: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2006;1758(4):537-544. doi:10.1016/j.bbamem.2006.03.028' apa: 'Cieplak, M., Filipek, S., Janovjak, H. L., & Krzysko, K. (2006). Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2006.03.028' chicago: 'Cieplak, Marek, Sławomir Filipek, Harald L Janovjak, and Krystiana Krzysko. “Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier, 2006. https://doi.org/10.1016/j.bbamem.2006.03.028.' ieee: 'M. Cieplak, S. Filipek, H. L. Janovjak, and K. Krzysko, “Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment,” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4. Elsevier, pp. 537–544, 2006.' ista: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. 2006. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1758(4), 537–544.' mla: 'Cieplak, Marek, et al. “Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4, Elsevier, 2006, pp. 537–44, doi:10.1016/j.bbamem.2006.03.028.' short: M. Cieplak, S. Filipek, H.L. Janovjak, K. Krzysko, Biochimica et Biophysica Acta (BBA) - Biomembranes 1758 (2006) 537–544. date_created: 2018-12-11T12:04:50Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:51:46Z day: '01' doi: 10.1016/j.bbamem.2006.03.028 extern: 1 intvolume: ' 1758' issue: '4' month: '04' page: 537 - 544 publication: Biochimica et Biophysica Acta (BBA) - Biomembranes publication_status: published publisher: Elsevier publist_id: '2502' quality_controlled: 0 status: public title: 'Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment' type: journal_article volume: 1758 year: '2006' ... --- _id: '3722' 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: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: 'Janovjak HL, Mueller D. Rastersondenmikroskopie. In: Bioanalytik. Spektrum Akademischer Verlag; 2006.' apa: Janovjak, H. L., & Mueller, D. (2006). Rastersondenmikroskopie. In Bioanalytik. Spektrum Akademischer Verlag. chicago: Janovjak, Harald L, and Daniel Mueller. “Rastersondenmikroskopie.” In Bioanalytik. Spektrum Akademischer Verlag, 2006. ieee: H. L. Janovjak and D. Mueller, “Rastersondenmikroskopie,” in Bioanalytik, Spektrum Akademischer Verlag, 2006. ista: 'Janovjak HL, Mueller D. 2006.Rastersondenmikroskopie. In: Bioanalytik. .' mla: Janovjak, Harald L., and Daniel Mueller. “Rastersondenmikroskopie.” Bioanalytik, Spektrum Akademischer Verlag, 2006. short: H.L. Janovjak, D. Mueller, in:, Bioanalytik, Spektrum Akademischer Verlag, 2006. date_created: 2018-12-11T12:04:48Z date_published: 2006-06-16T00:00:00Z date_updated: 2021-01-12T07:51:44Z day: '16' extern: 1 month: '06' publication: Bioanalytik publication_status: published publisher: Spektrum Akademischer Verlag publist_id: '2508' quality_controlled: 0 status: public title: Rastersondenmikroskopie type: book_chapter year: '2006' ... --- _id: '3755' abstract: - lang: eng text: A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems. author: - first_name: Thuc full_name: Le,Thuc T. last_name: Le - first_name: Thierry full_name: Emonet,Thierry last_name: Emonet - first_name: Sébastien full_name: Harlepp, Sébastien last_name: Harlepp - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Philippe full_name: Cluzel,Philippe last_name: Cluzel citation: ama: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 2006;90(9):3315-3321. doi:10.1529/biophysj.105.073353 apa: Le, T., Emonet, T., Harlepp, S., Guet, C. C., & Cluzel, P. (2006). Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.073353 chicago: Le, Thuc, Thierry Emonet, Sébastien Harlepp, Calin C Guet, and Philippe Cluzel. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal. Biophysical Society, 2006. https://doi.org/10.1529/biophysj.105.073353. ieee: T. Le, T. Emonet, S. Harlepp, C. C. Guet, and P. Cluzel, “Dynamical determinants of drug-inducible gene expression in a single bacterium,” Biophysical Journal, vol. 90, no. 9. Biophysical Society, pp. 3315–3321, 2006. ista: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. 2006. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 90(9), 3315–3321. mla: Le, Thuc, et al. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal, vol. 90, no. 9, Biophysical Society, 2006, pp. 3315–21, doi:10.1529/biophysj.105.073353. short: T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90 (2006) 3315–3321. date_created: 2018-12-11T12:04:59Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:51:58Z day: '01' doi: 10.1529/biophysj.105.073353 extern: 1 intvolume: ' 90' issue: '9' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/ month: '01' oa: 1 page: 3315 - 3321 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2472' quality_controlled: 0 status: public title: Dynamical determinants of drug-inducible gene expression in a single bacterium type: journal_article volume: 90 year: '2006' ... --- _id: '3758' abstract: - lang: eng text: Control of physical simulation has become a popular topic in the field of computer graphics. Keyframe control has been applied to simulations of rigid bodies, smoke, liquid, flocks, and finite element-based elastic bodies. In this paper, we create a framework for controlling systems of interacting particles -- paying special attention to simulations of cloth and flocking behavior. We introduce a novel integrator-swapping approximation in order to apply the adjoint method to linearized implicit schemes appropriate for cloth simulation. This allows the control of cloth while avoiding computationally infeasible derivative calculations. Meanwhile, flocking control using the adjoint method is significantly more efficient than currently-used methods for constraining group behaviors, allowing the controlled simulation of greater numbers of agents in fewer optimization iterations. article_processing_charge: No author: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Peter full_name: Mucha, Peter last_name: Mucha - first_name: Greg full_name: Turk, Greg last_name: Turk citation: ama: 'Wojtan C, Mucha P, Turk G. Keyframe control of complex particle systems using the adjoint method. In: ACM; 2006:15-23.' apa: 'Wojtan, C., Mucha, P., & Turk, G. (2006). Keyframe control of complex particle systems using the adjoint method (pp. 15–23). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, ACM.' chicago: Wojtan, Chris, Peter Mucha, and Greg Turk. “Keyframe Control of Complex Particle Systems Using the Adjoint Method,” 15–23. ACM, 2006. ieee: 'C. Wojtan, P. Mucha, and G. Turk, “Keyframe control of complex particle systems using the adjoint method,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 2006, pp. 15–23.' ista: 'Wojtan C, Mucha P, Turk G. 2006. Keyframe control of complex particle systems using the adjoint method. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 15–23.' mla: Wojtan, Chris, et al. Keyframe Control of Complex Particle Systems Using the Adjoint Method. ACM, 2006, pp. 15–23. short: C. Wojtan, P. Mucha, G. Turk, in:, ACM, 2006, pp. 15–23. conference: name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation' date_created: 2018-12-11T12:05:00Z date_published: 2006-09-01T00:00:00Z date_updated: 2023-02-23T11:41:22Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://www.amath.unc.edu/Faculty/mucha/Reprints/SCAclothcontrolpreprint.pdf month: '09' oa_version: None page: 15 - 23 publication_status: published publisher: ACM publist_id: '2469' status: public title: Keyframe control of complex particle systems using the adjoint method type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '3818' abstract: - lang: eng text: Rigorous analysis of synaptic transmission in the central nervous system requires access to presynaptic terminals. However, cortical terminals have been largely inaccessible to presynaptic patch-clamp recording, due to their small size. Using improved patch-clamp techniques in brain slices, we recorded from mossy fiber terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm. The major steps of improvement were the enhanced visibility provided by high-numerical aperture objectives and infrared illumination, the development of vibratomes with minimal vertical blade vibrations and the use of sucrose-based solutions for storage and cutting. Based on these improvements, we describe a protocol that allows us to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings can be obtained in slices from both rats and mice. Presynaptic recordings can be also obtained in slices from transgenic mice in which terminals are labeled with enhanced green fluorescent protein. author: - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Liyi full_name: Li, Liyi last_name: Li - first_name: Jörg full_name: Geiger, Jörg R last_name: Geiger - 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, Li L, Geiger J, Jonas PM. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 2006;1(4):2075-2081. doi:10.1038/nprot.2006.312 apa: Bischofberger, J., Engel, D., Li, L., Geiger, J., & Jonas, P. M. (2006). Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.312 chicago: Bischofberger, Josef, Dominique Engel, Liyi Li, Jörg Geiger, and Peter M Jonas. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.312 . ieee: J. Bischofberger, D. Engel, L. Li, J. Geiger, and P. M. Jonas, “Patch-clamp recording from mossy fiber terminals in hippocampal slices,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 2075–81, 2006. ista: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. 2006. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 1(4), 2075–81. mla: Bischofberger, Josef, et al. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 2075–81, doi:10.1038/nprot.2006.312 . short: J. Bischofberger, D. Engel, L. Li, J. Geiger, P.M. Jonas, Nature Protocols 1 (2006) 2075–81. date_created: 2018-12-11T12:05:20Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:25Z day: '01' doi: '10.1038/nprot.2006.312 ' extern: 1 intvolume: ' 1' issue: '4' month: '01' page: 2075 - 81 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '2392' quality_controlled: 0 status: public title: Patch-clamp recording from mossy fiber terminals in hippocampal slices type: journal_article volume: 1 year: '2006' ... --- _id: '3890' abstract: - lang: eng text: We consider two-player infinite games played on graphs. The games are concurrent, in that at each state the players choose their moves simultaneously and independently, and stochastic, in that the moves determine a probability distribution for the successor state. The value of a game is the maximal probability with which a player can guarantee the satisfaction of her objective. We show that the values of concurrent games with w-regular objectives expressed as parity conditions can be decided in NP boolean AND coNP. This result substantially improves the best known previous bound of 3EXPTIME. It also shows that the full class of concurrent parity games is no harder than the special case of turn-based stochastic reachability games, for which NP boolean AND coNP is the best known bound. While the previous, more restricted NP boolean AND coNP results for graph games relied on the existence of particularly simple (pure memoryless) optimal strategies, in concurrent games with parity objectives optimal strategies may not exist, and epsilon-optimal strategies (which achieve the value of the game within a parameter epsilon > 0) require in general both randomization and infinite memory. Hence our proof must rely on a more detailed analysis of strategies and, in addition to the main result, yields two results that are interesting on their own. First, we show that there exist epsilon-optimal strategies that in the limit coincide with memoryless strategies; this parallels the celebrated result of Mertens-Neyman for concurrent games with limit-average objectives. Second, we complete the characterization of the memory requirements for epsilon-optimal strategies for concurrent games with parity conditions, by showing that memoryless strategies suffice for epsilon-optimality for coBachi conditions. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, De Alfaro L, Henzinger TA. The complexity of quantitative concurrent parity games. In: SIAM; 2006:678-687. doi:10.1145/1109557.1109631' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). The complexity of quantitative concurrent parity games (pp. 678–687). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1145/1109557.1109631' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity of Quantitative Concurrent Parity Games,” 678–87. SIAM, 2006. https://doi.org/10.1145/1109557.1109631. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of quantitative concurrent parity games,” presented at the SODA: Symposium on Discrete Algorithms, 2006, pp. 678–687.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative concurrent parity games. SODA: Symposium on Discrete Algorithms, 678–687.' mla: Chatterjee, Krishnendu, et al. The Complexity of Quantitative Concurrent Parity Games. SIAM, 2006, pp. 678–87, doi:10.1145/1109557.1109631. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2006, pp. 678–687. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T12:05:43Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:59Z day: '01' doi: 10.1145/1109557.1109631 extern: 1 month: '01' page: 678 - 687 publication_status: published publisher: SIAM publist_id: '2273' quality_controlled: 0 status: public title: The complexity of quantitative concurrent parity games type: conference year: '2006' ... --- _id: '3889' abstract: - lang: eng text: We study observation-based strategies for two-player turn-based games on graphs with omega-regular objectives. An observation-based strategy relies on imperfect information about the history of a play, namely, on the past sequence of observations. Such games occur in the synthesis of a controller that does not see the private state of the plant. Our main results are twofold. First, we give a fixed-point algorithm for computing the set of states from which a player can win with a deterministic observation-based strategy for any omega-regular objective. The fixed point is computed in the lattice of antichains of state sets. This algorithm has the advantages of being directed by the objective and of avoiding an explicit subset construction on the game graph. Second, we give an algorithm for computing the set of states from which a player can win with probability 1 with a randomized observation-based strategy for a Buchi objective. This set is of interest because in the absence of perfect information, randomized strategies are more powerful than deterministic ones. We show that our algorithms are optimal by proving matching lower bounds. acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR-0234690, by the SNSF under the Indo-Swiss Joint Research Programme, and by the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant 2.4530.02. 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 - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean-François last_name: Raskin citation: ama: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular games with imperfect information. In: Vol 4207. Springer; 2006:287-302. doi:10.1007/11874683_19' apa: 'Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Algorithms for omega-regular games with imperfect information (Vol. 4207, pp. 287–302). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_19' chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Algorithms for Omega-Regular Games with Imperfect Information,” 4207:287–302. Springer, 2006. https://doi.org/10.1007/11874683_19. ieee: 'K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for omega-regular games with imperfect information,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 287–302.' ista: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2006. Algorithms for omega-regular games with imperfect information. CSL: Computer Science Logic, LNCS, vol. 4207, 287–302.' mla: Chatterjee, Krishnendu, et al. Algorithms for Omega-Regular Games with Imperfect Information. Vol. 4207, Springer, 2006, pp. 287–302, doi:10.1007/11874683_19. short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp. 287–302. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:43Z date_published: 2006-11-13T00:00:00Z date_updated: 2021-01-12T07:52:59Z day: '13' doi: 10.1007/11874683_19 extern: 1 intvolume: ' 4207' month: '11' page: 287 - 302 publication_status: published publisher: Springer publist_id: '2276' quality_controlled: 0 status: public title: Algorithms for omega-regular games with imperfect information type: conference volume: 4207 year: '2006' ... --- _id: '3891' abstract: - lang: eng text: 'We study infinite stochastic games played by two-players over a finite state space, with objectives specified by sets of infinite traces. The games are concurrent (players make moves simultaneously and independently), stochastic (the next state is determined by a probability distribution that depends on the current state and chosen moves of the players) and infinite (proceeds for infinite number of rounds). The analysis of concurrent stochastic games can be classified into: quantitative analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing the set of states with optimum value 1. We consider concurrent games with tail objectives, i.e., objectives that are independent of the finite-prefix of traces, and show that the class of tail objectives are strictly richer than the omega-regular objectives. We develop new proof techniques to extend several properties of concurrent games with omega-regular objectives to concurrent games with tail objectives. We prove the positive limit-one property for tail objectives, that states for all concurrent games if the optimum value for a player is positive for a tail objective Phi at some state, then there is a state where the optimum value is 1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly conflicting objectives) games with tail objectives can be related to equilibrium values of nonzero-sum (not strictly conflicting objectives) games with simpler reachability objectives. A consequence of our analysis presents a polynomial time reduction of the quantitative analysis of tail objectives to the qualitative analysis for the sub-class of one-player stochastic games (Markov decision processes).' 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. Concurrent games with tail objectives. In: Vol 4207. Springer; 2006:256-270. doi:10.1007/11874683_17' apa: 'Chatterjee, K. (2006). Concurrent games with tail objectives (Vol. 4207, pp. 256–270). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_17' chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives,” 4207:256–70. Springer, 2006. https://doi.org/10.1007/11874683_17. ieee: 'K. Chatterjee, “Concurrent games with tail objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 256–270.' ista: 'Chatterjee K. 2006. Concurrent games with tail objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 256–270.' mla: Chatterjee, Krishnendu. Concurrent Games with Tail Objectives. Vol. 4207, Springer, 2006, pp. 256–70, doi:10.1007/11874683_17. short: K. Chatterjee, in:, Springer, 2006, pp. 256–270. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:44Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:53:00Z day: '28' doi: 10.1007/11874683_17 extern: 1 intvolume: ' 4207' month: '09' page: 256 - 270 publication_status: published publisher: Springer publist_id: '2272' quality_controlled: 0 status: public title: Concurrent games with tail objectives type: conference volume: 4207 year: '2006' ... --- _id: '3888' abstract: - lang: eng text: A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with omega-regular winning conditions specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete, respectively. The value of the game for a player at a state s given an objective Phi is the maximal probability with which the player can guarantee the satisfaction of Phi from s. We present a strategy-improvement algorithm to compute values in stochastic Rabin games, where an improvement step involves solving Markov decision processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values for stochastic Streett games but does not directly yield an optimal strategy for Streett objectives. We then show how to obtain an optimal strategy for Streett objectives by solving certain nonstochastic Streett games. 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 - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Henzinger TA. Strategy improvement for stochastic Rabin and Streett games. In: Vol 4137. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2006:375-389. doi:10.1007/11817949_25' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement for stochastic Rabin and Streett games (Vol. 4137, pp. 375–389). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11817949_25' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement for Stochastic Rabin and Streett Games,” 4137:375–89. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006. https://doi.org/10.1007/11817949_25. ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement for stochastic Rabin and Streett games,” presented at the CONCUR: Concurrency Theory, 2006, vol. 4137, pp. 375–389.' ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement for stochastic Rabin and Streett games. CONCUR: Concurrency Theory, LNCS, vol. 4137, 375–389.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement for Stochastic Rabin and Streett Games. Vol. 4137, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–89, doi:10.1007/11817949_25. short: K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–389. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:05:43Z date_published: 2006-08-10T00:00:00Z date_updated: 2021-01-12T07:52:58Z day: '10' doi: 10.1007/11817949_25 extern: 1 intvolume: ' 4137' month: '08' page: 375 - 389 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2278' quality_controlled: 0 status: public title: Strategy improvement for stochastic Rabin and Streett games type: conference volume: 4137 year: '2006' ... --- _id: '3908' abstract: - lang: eng text: 'It is commonly believed that both the average length and the frequency of microsatellites correlate with genome size. We have estimated the frequency and the average length for 69 perfect dinucleotide microsatellites in an insect with an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae). Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat arrays are 1.4 to 2 times longer than in other insect species. The average repeat number in C. biguttulus lies in the range of higher vertebrates. Natural populations are highly variable. At least 30 alleles per locus were found and the expected heterozygosity is above 0.95 at all three loci studied. In contrast, the observed heterozygosity is much lower (≤0.51), which could be caused by long null alleles.' author: - first_name: Jana full_name: Ustinova, Jana last_name: Ustinova - first_name: Roland full_name: Achmann, Roland last_name: Achmann - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Frieder full_name: Mayer, Frieder last_name: Mayer citation: ama: 'Ustinova J, Achmann R, Cremer S, Mayer F. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 2006;62(2):158-167. doi:10.1007/s00239-005-0022-6' apa: 'Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-005-0022-6' chicago: 'Ustinova, Jana, Roland Achmann, Sylvia Cremer, and Frieder Mayer. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution. Springer, 2006. https://doi.org/10.1007/s00239-005-0022-6.' ieee: 'J. Ustinova, R. Achmann, S. Cremer, and F. Mayer, “Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus,” Journal of Molecular Evolution, vol. 62, no. 2. Springer, pp. 158–167, 2006.' ista: 'Ustinova J, Achmann R, Cremer S, Mayer F. 2006. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 62(2), 158–167.' mla: 'Ustinova, Jana, et al. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution, vol. 62, no. 2, Springer, 2006, pp. 158–67, doi:10.1007/s00239-005-0022-6.' short: J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution 62 (2006) 158–167. date_created: 2018-12-11T12:05:49Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:53:07Z day: '01' doi: 10.1007/s00239-005-0022-6 extern: '1' intvolume: ' 62' issue: '2' language: - iso: eng month: '02' oa_version: None page: 158 - 167 publication: Journal of Molecular Evolution publication_status: published publisher: Springer publist_id: '2242' status: public title: 'Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2006' ... --- _id: '3934' abstract: - lang: eng text: T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla. author: - first_name: Mihaela full_name: Drumea-Mirancea, Mihaela last_name: Drumea Mirancea - first_name: Johannes full_name: Wessels, Johannes T last_name: Wessels - first_name: Claudia full_name: Müller, Claudia A last_name: Müller - first_name: Mike full_name: Essl, Mike last_name: Essl - first_name: Johannes full_name: Eble, Johannes A last_name: Eble - first_name: Eva full_name: Tolosa, Eva last_name: Tolosa - first_name: Manuel full_name: Koch, Manuel last_name: Koch - first_name: Dieter full_name: Reinhardt, Dieter P last_name: Reinhardt - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin - first_name: York full_name: Stierhof, York-Dieter last_name: Stierhof - first_name: Heinz full_name: Schwarz, Heinz last_name: Schwarz - first_name: Gerd full_name: Klein, Gerd last_name: Klein citation: ama: 'Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405. doi:10.1242/​jcs.02840' apa: 'Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa, E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/​jcs.02840' chicago: 'Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl, Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/​jcs.02840.' ieee: 'M. Drumea Mirancea et al., “Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules,” Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp. 1396–1405, 2006.' ista: 'Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M, Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.' mla: 'Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006, pp. 1396–405, doi:10.1242/​jcs.02840.' short: M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M. Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein, Journal of Cell Science 119 (2006) 1396–1405. date_created: 2018-12-11T12:05:58Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '01' doi: 10.1242/​jcs.02840 extern: 1 intvolume: ' 119' issue: Pt 7 month: '04' page: 1396 - 1405 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '2192' quality_controlled: 0 status: public title: 'Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules' type: journal_article volume: 119 year: '2006' ... --- _id: '3935' abstract: - lang: eng text: Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis. author: - first_name: Haiyan full_name: Chu, Haiyan last_name: Chu - first_name: Ingo full_name: Thievessen, Ingo last_name: Thievessen - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Ari full_name: Waisman, Ari last_name: Waisman - first_name: Attila full_name: Braun, Attila last_name: Braun - first_name: Angelika full_name: Noegel, Angelika A last_name: Noegel - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006 apa: Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A., … Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006 chicago: Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman, Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology. American Society for Microbiology, 2006. https://doi.org/10.1128/MCB.26.5.1817-1825.2006. ieee: H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response,” Molecular and Cellular Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825, 2006. ista: Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A, Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5), 1817–1825. mla: Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology, vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006. short: H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A. Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825. date_created: 2018-12-11T12:05:58Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '01' doi: 10.1128/MCB.26.5.1817-1825.2006 extern: 1 intvolume: ' 26' issue: '5' month: '03' page: 1817 - 1825 publication: Molecular and Cellular Biology publication_status: published publisher: American Society for Microbiology publist_id: '2193' quality_controlled: 0 status: public title: γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response type: journal_article volume: 26 year: '2006' ... --- _id: '3936' abstract: - lang: eng text: At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials. author: - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Martina full_name: Bauer, Martina last_name: Bauer - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490. doi:10.1016/j.ceb.2006.08.007' apa: 'Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007' chicago: 'Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.' ieee: 'M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes and signaling relay for blood cells,” Current Opinion in Cell Biology, vol. 18, no. 5. Elsevier, pp. 482–490, 2006.' ista: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490.' mla: 'Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier, 2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.' short: M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology 18 (2006) 482–490. date_created: 2018-12-11T12:05:59Z date_published: 2006-10-01T00:00:00Z date_updated: 2021-01-12T07:53:19Z day: '01' doi: 10.1016/j.ceb.2006.08.007 extern: 1 intvolume: ' 18' issue: '5' month: '10' page: 482 - 490 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '2191' quality_controlled: 0 status: public title: 'β1 integrins: zip codes and signaling relay for blood cells' type: journal_article volume: 18 year: '2006' ... --- _id: '4140' abstract: - lang: eng text: Wnt11 is a key signal, determining cell polarization and migration during vertebrate gastrulation. It is known that Wnt11 functionally interacts with several signaling components, the homologues of which control planar cell polarity in Drosophila melanogaster. Although in D. melanogaster these components are thought to polarize cells by asymmetrically localizing at the plasma membrane, it is not yet clear whether their subcellular localization plays a similarly important role in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation. article_processing_charge: No author: - first_name: Sabine full_name: Witzel, Sabine last_name: Witzel - first_name: Vitaly full_name: Zimyanin, Vitaly last_name: Zimyanin - first_name: Filipa full_name: Carreira Barbosa, Filipa last_name: Carreira Barbosa - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 2006;175(5):791-802. doi:10.1083/jcb.200606017 apa: Witzel, S., Zimyanin, V., Carreira Barbosa, F., Tada, M., & Heisenberg, C.-P. J. (2006). Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200606017 chicago: Witzel, Sabine, Vitaly Zimyanin, Filipa Carreira Barbosa, Masazumi Tada, and Carl-Philipp J Heisenberg. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology. Rockefeller University Press, 2006. https://doi.org/10.1083/jcb.200606017. ieee: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, and C.-P. J. Heisenberg, “Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane,” Journal of Cell Biology, vol. 175, no. 5. Rockefeller University Press, pp. 791–802, 2006. ista: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. 2006. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 175(5), 791–802. mla: Witzel, Sabine, et al. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology, vol. 175, no. 5, Rockefeller University Press, 2006, pp. 791–802, doi:10.1083/jcb.200606017. short: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg, Journal of Cell Biology 175 (2006) 791–802. date_created: 2018-12-11T12:07:11Z date_published: 2006-12-04T00:00:00Z date_updated: 2021-01-12T07:54:48Z day: '04' doi: 10.1083/jcb.200606017 extern: '1' intvolume: ' 175' issue: '5' language: - iso: eng month: '12' oa_version: None page: 791 - 802 publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '1980' status: public title: Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 175 year: '2006' ... --- _id: '4145' abstract: - lang: eng text: The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development. article_processing_charge: No author: - first_name: Davide full_name: Tonelli, Davide last_name: Tonelli - first_name: Frederico full_name: Calegari, Frederico last_name: Calegari - first_name: Ji full_name: Fei, Ji last_name: Fei - first_name: Tadashi full_name: Nomura, Tadashi last_name: Nomura - first_name: Noriko full_name: Osumi, Noriko last_name: Osumi - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Wieland full_name: Huttner, Wieland last_name: Huttner citation: ama: Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 2006;41(6):727-732. doi:10.2144/000112296 apa: Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P. J., & Huttner, W. (2006). Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. Informa Healthcare. https://doi.org/10.2144/000112296 chicago: Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi, Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques. Informa Healthcare, 2006. https://doi.org/10.2144/000112296. ieee: D. Tonelli et al., “Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid,” Biotechniques, vol. 41, no. 6. Informa Healthcare, pp. 727–732, 2006. ista: Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 41(6), 727–732. mla: Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:10.2144/000112296. short: D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg, W. Huttner, Biotechniques 41 (2006) 727–732. date_created: 2018-12-11T12:07:12Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:54:50Z day: '01' doi: 10.2144/000112296 extern: '1' intvolume: ' 41' issue: '6' language: - iso: eng month: '12' oa_version: None page: 727 - 732 publication: Biotechniques publication_status: published publisher: Informa Healthcare publist_id: '1974' status: public title: Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2006' ... --- _id: '4176' abstract: - lang: eng text: 'During vertebrate gastrulation, a well-orchestrated series of morphogenetic changes leads to the formation of the three germ layers: the ectoderm, mesoderm and endoderm. The analysis of gene expression patterns during gastrulation has been central to the identification of genes involved in germ layer formation. However, many proteins are regulated on a translational or post-translational level and are thus undetectable by gene expression analysis. Therefore, we developed a 2D-gel-based comparative proteomic approach to target proteins involved in germ layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and mesendodermal progenitor cells were compared and 35 significantly regulated proteins were identified by mass spectrometry, including several proteins with predicted functions in cytoskeletal organization. A comparison of our proteomic results with data obtained in an accompanying microarray-based gene expression analysis revealed no significant overlap, confirming the complementary nature of proteomics and transcriptomics. The regulation of ezrin2, which was identified based on a reduction in spot intensity in mesendodermal cells, was independently validated. Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal cells and is required for proper germ layer morphogenesis. We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development.' article_processing_charge: No author: - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Petra full_name: Stockinger, Petra last_name: Stockinger - first_name: Andrej full_name: Shevchenko, Andrej last_name: Shevchenko - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 2006;119(10):2073-2083. doi:10.1242/jcs.02928 apa: Link, V., Carvalho, L., Castanon, I., Stockinger, P., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02928 chicago: Link, Vinzenz, Lara Carvalho, Irinka Castanon, Petra Stockinger, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02928. ieee: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, and C.-P. J. Heisenberg, “Identification of regulators of germ layer morphogenesis using proteomics in zebrafish,” Journal of Cell Science, vol. 119, no. 10. Company of Biologists, pp. 2073–2083, 2006. ista: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. 2006. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 119(10), 2073–2083. mla: Link, Vinzenz, et al. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science, vol. 119, no. 10, Company of Biologists, 2006, pp. 2073–83, doi:10.1242/jcs.02928. short: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, C.-P.J. Heisenberg, Journal of Cell Science 119 (2006) 2073–2083. date_created: 2018-12-11T12:07:24Z date_published: 2006-05-15T00:00:00Z date_updated: 2021-01-12T07:55:04Z day: '15' doi: 10.1242/jcs.02928 extern: '1' intvolume: ' 119' issue: '10' language: - iso: eng month: '05' oa_version: None page: 2073 - 2083 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '1944' status: public title: Identification of regulators of germ layer morphogenesis using proteomics in zebrafish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2006' ... --- _id: '4173' abstract: - lang: eng text: 'Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.' article_processing_charge: No author: - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Andrej full_name: Shevchenko, Andrej last_name: Shevchenko - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos. BMC Developmental Biology. 2006;6:1-9. doi:10.1186/1471-213X-6-1 apa: Link, V., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Proteomics of early zebrafish embryos. BMC Developmental Biology. BioMed Central. https://doi.org/10.1186/1471-213X-6-1 chicago: Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology. BioMed Central, 2006. https://doi.org/10.1186/1471-213X-6-1. ieee: V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish embryos,” BMC Developmental Biology, vol. 6. BioMed Central, pp. 1–9, 2006. ista: Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish embryos. BMC Developmental Biology. 6, 1–9. mla: Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology, vol. 6, BioMed Central, 2006, pp. 1–9, doi:10.1186/1471-213X-6-1. short: V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006) 1–9. date_created: 2018-12-11T12:07:23Z date_published: 2006-01-13T00:00:00Z date_updated: 2021-01-12T07:55:02Z day: '13' doi: 10.1186/1471-213X-6-1 extern: '1' intvolume: ' 6' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: http://www.biomedcentral.com/1471-213X/6/1 month: '01' oa: 1 oa_version: None page: 1 - 9 publication: BMC Developmental Biology publication_status: published publisher: BioMed Central publist_id: '1945' status: public title: Proteomics of early zebrafish embryos tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2006' ... --- _id: '4178' abstract: - lang: eng text: Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools. article_processing_charge: No author: - first_name: Tobias full_name: Langenberg, Tobias last_name: Langenberg - first_name: Tadeusz full_name: Dracz, Tadeusz last_name: Dracz - first_name: Andrew full_name: Oates, Andrew last_name: Oates - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Michael full_name: Brand, Michael last_name: Brand citation: ama: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 2006;235(4):928-933. doi:10.1002/dvdy.20692 apa: Langenberg, T., Dracz, T., Oates, A., Heisenberg, C.-P. J., & Brand, M. (2006). Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. Wiley-Blackwell. https://doi.org/10.1002/dvdy.20692 chicago: Langenberg, Tobias, Tadeusz Dracz, Andrew Oates, Carl-Philipp J Heisenberg, and Michael Brand. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics. Wiley-Blackwell, 2006. https://doi.org/10.1002/dvdy.20692. ieee: T. Langenberg, T. Dracz, A. Oates, C.-P. J. Heisenberg, and M. Brand, “Analysis and visualization of cell movement in the developing zebrafish brain,” Developmental Dynamics, vol. 235, no. 4. Wiley-Blackwell, pp. 928–933, 2006. ista: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. 2006. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 235(4), 928–933. mla: Langenberg, Tobias, et al. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics, vol. 235, no. 4, Wiley-Blackwell, 2006, pp. 928–33, doi:10.1002/dvdy.20692. short: T. Langenberg, T. Dracz, A. Oates, C.-P.J. Heisenberg, M. Brand, Developmental Dynamics 235 (2006) 928–933. date_created: 2018-12-11T12:07:25Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:55:04Z day: '01' doi: 10.1002/dvdy.20692 extern: '1' intvolume: ' 235' issue: '4' language: - iso: eng month: '04' oa_version: None page: 928 - 933 publication: Developmental Dynamics publication_status: published publisher: Wiley-Blackwell publist_id: '1940' status: public title: Analysis and visualization of cell movement in the developing zebrafish brain type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 235 year: '2006' ... --- _id: '4184' abstract: - lang: eng text: Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis. article_processing_charge: No author: - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - first_name: Beatriz full_name: Fernández, Beatriz last_name: Fernández - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: António full_name: Jacinto, António last_name: Jacinto - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 2006;133(14):2671-2681. doi:doi: 10.1242/dev.02439' apa: 'Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., & Heisenberg, C.-P. J. (2006). Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. Company of Biologists. https://doi.org/doi: 10.1242/dev.02439' chicago: 'Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development. Company of Biologists, 2006. https://doi.org/doi: 10.1242/dev.02439.' ieee: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila,” Development, vol. 133, no. 14. Company of Biologists, pp. 2671–2681, 2006. ista: Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2006. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 133(14), 2671–2681. mla: 'Köppen, Mathias, et al. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development, vol. 133, no. 14, Company of Biologists, 2006, pp. 2671–81, doi:doi: 10.1242/dev.02439.' short: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Development 133 (2006) 2671–2681. date_created: 2018-12-11T12:07:27Z date_published: 2006-07-15T00:00:00Z date_updated: 2021-01-12T07:55:08Z day: '15' doi: 'doi: 10.1242/dev.02439' extern: '1' intvolume: ' 133' issue: '14' language: - iso: eng month: '07' oa_version: None page: 2671 - 2681 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1935' status: public title: Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 133 year: '2006' ... --- _id: '4218' abstract: - lang: eng text: The molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration. article_processing_charge: No author: - first_name: Heiko full_name: Blaser, Heiko last_name: Blaser - first_name: Michal full_name: Reichman Fried, Michal last_name: Reichman Fried - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Karin full_name: Dumstrei, Karin last_name: Dumstrei - first_name: Florence full_name: Marlow, Florence last_name: Marlow - first_name: Koichi full_name: Kawakami, Koichi last_name: Kawakami - first_name: Lilianna full_name: Solnica Krezel, Lilianna last_name: Solnica Krezel - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Erez full_name: Raz, Erez last_name: Raz citation: ama: 'Blaser H, Reichman Fried M, Castanon I, et al. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 2006;11(5):613-627. doi:10.1016/j.devcel.2006.09.023' apa: 'Blaser, H., Reichman Fried, M., Castanon, I., Dumstrei, K., Marlow, F., Kawakami, K., … Raz, E. (2006). Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2006.09.023' chicago: 'Blaser, Heiko, Michal Reichman Fried, Irinka Castanon, Karin Dumstrei, Florence Marlow, Koichi Kawakami, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg, and Erez Raz. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell. Cell Press, 2006. https://doi.org/10.1016/j.devcel.2006.09.023.' ieee: 'H. Blaser et al., “Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow,” Developmental Cell, vol. 11, no. 5. Cell Press, pp. 613–627, 2006.' ista: 'Blaser H, Reichman Fried M, Castanon I, Dumstrei K, Marlow F, Kawakami K, Solnica Krezel L, Heisenberg C-PJ, Raz E. 2006. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 11(5), 613–627.' mla: 'Blaser, Heiko, et al. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell, vol. 11, no. 5, Cell Press, 2006, pp. 613–27, doi:10.1016/j.devcel.2006.09.023.' short: H. Blaser, M. Reichman Fried, I. Castanon, K. Dumstrei, F. Marlow, K. Kawakami, L. Solnica Krezel, C.-P.J. Heisenberg, E. Raz, Developmental Cell 11 (2006) 613–627. date_created: 2018-12-11T12:07:39Z date_published: 2006-11-06T00:00:00Z date_updated: 2021-01-12T07:55:23Z day: '06' doi: 10.1016/j.devcel.2006.09.023 extern: '1' intvolume: ' 11' issue: '5' language: - iso: eng month: '11' oa_version: None page: 613 - 627 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '1898' status: public title: 'Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2006' ...