[{"month":"12","day":"01","publication":"Discrete & Computational Geometry","citation":{"ama":"Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8","ista":"Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 36(4), 553–572.","ieee":"P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer, pp. 553–572, 2006.","apa":"Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8","mla":"Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8.","short":"P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational Geometry 36 (2006) 553–572.","chicago":"Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer, 2006. https://doi.org/10.1007/s00454-006-1265-8."},"quality_controlled":0,"page":"553 - 572","date_published":"2006-12-01T00:00:00Z","doi":"10.1007/s00454-006-1265-8","type":"journal_article","abstract":[{"lang":"eng","text":"Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking."}],"publist_id":"2148","issue":"4","extern":1,"year":"2006","_id":"3980","title":"Extreme elevation on a 2-manifold","publication_status":"published","status":"public","intvolume":" 36","publisher":"Springer","author":[{"last_name":"Agarwal","first_name":"Pankaj","full_name":"Agarwal, Pankaj K"},{"full_name":"Herbert Edelsbrunner","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"},{"last_name":"Wang","first_name":"Yusu","full_name":"Wang, Yusu"}],"date_updated":"2021-01-12T07:53:38Z","date_created":"2018-12-11T12:06:15Z","volume":36},{"day":"01","month":"01","doi":"424","date_published":"2006-01-01T00:00:00Z","main_file_link":[{"url":"http://www.zlb.de/aktivitaeten/bd_neu/heftinhalte2006/DigitaleBib011106.pdf","open_access":"0"}],"citation":{"ama":"Danowski P, Heller L. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 2006;40(11):1250-1271. doi:424","ista":"Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 40(11), 1250–1271.","apa":"Danowski, P., & Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. Zentral- und Landesbibliothek Berlin. https://doi.org/424","ieee":"P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,” Bibliotheksdienst, vol. 40, no. 11. Zentral- und Landesbibliothek Berlin, pp. 1250–1271, 2006.","mla":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst, vol. 40, no. 11, Zentral- und Landesbibliothek Berlin, 2006, pp. 1250–71, doi:424.","short":"P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271.","chicago":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst. Zentral- und Landesbibliothek Berlin, 2006. https://doi.org/424."},"publication":"Bibliotheksdienst","page":"1250 - 1271","quality_controlled":0,"publist_id":"1229","issue":"11","abstract":[{"lang":"eng","text":"Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert."}],"extern":1,"type":"journal_article","author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","first_name":"Patrick","last_name":"Danowski","full_name":"Patrick Danowski"},{"full_name":"Heller,Lambert","last_name":"Heller","first_name":"Lambert"}],"volume":40,"date_created":"2018-12-11T12:08:23Z","date_updated":"2021-01-12T07:56:17Z","_id":"4345","year":"2006","intvolume":" 40","publisher":"Zentral- und Landesbibliothek Berlin","publication_status":"published","title":"Bibliothek 2.0 - Die Bibliothek der Zukunft?","status":"public"},{"type":"journal_article","publist_id":"1108","issue":"5","abstract":[{"lang":"eng","text":"Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance."}],"extern":1,"year":"2006","_id":"4352","publisher":"American Society of Tropical Medicine and Hygiene","intvolume":" 74","publication_status":"published","status":"public","title":"Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil","author":[{"last_name":"Conn","first_name":"Jan","full_name":"Conn, Jan E"},{"full_name":"Vineis, Joseph H","first_name":"Joseph","last_name":"Vineis"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Jonathan Bollback"},{"first_name":"David","last_name":"Onyabe","full_name":"Onyabe, David Y"},{"first_name":"Richard","last_name":"Wilkerson","full_name":"Wilkerson, Richard C"},{"first_name":"Marinete","last_name":"Povoa","full_name":"Povoa, Marinete M"}],"volume":74,"date_updated":"2021-01-12T07:56:20Z","date_created":"2018-12-11T12:08:25Z","month":"05","day":"01","main_file_link":[{"url":"http://www.ajtmh.org/content/74/5/798.full","open_access":"0"}],"citation":{"short":"J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806.","mla":"Conn, Jan, et al. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5, American Society of Tropical Medicine and Hygiene, 2006, pp. 798–806.","chicago":"Conn, Jan, Joseph Vineis, Jonathan P Bollback, David Onyabe, Richard Wilkerson, and Marinete Povoa. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene, 2006.","ama":"Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 2006;74(5):798-806.","apa":"Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa, M. (2006). Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene.","ieee":"J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa, “Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil,” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene, pp. 798–806, 2006.","ista":"Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 2006. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 74(5), 798–806."},"publication":"The American Journal of Tropical Medicine and Hygiene","page":"798 - 806","quality_controlled":0,"date_published":"2006-05-01T00:00:00Z"},{"publist_id":"1109","abstract":[{"text":"BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Jonathan Bollback"}],"volume":7,"date_created":"2018-12-11T12:08:25Z","date_updated":"2021-01-12T07:56:20Z","year":"2006","_id":"4351","publisher":"BioMed Central","intvolume":" 7","publication_status":"published","title":"SIMMAP: stochastic character mapping of discrete traits on phylogenies","status":"public","day":"01","month":"01","date_published":"2006-01-01T00:00:00Z","doi":"10.1186/1471-2105-7-88","citation":{"short":"J.P. Bollback, BMC Bioinformatics 7 (2006).","mla":"Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.","chicago":"Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics. BioMed Central, 2006. https://doi.org/10.1186/1471-2105-7-88.","ama":"Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88","apa":"Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88","ieee":"J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.","ista":"Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 7."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"BMC Bioinformatics","quality_controlled":0},{"conference":{"name":"ECCV: European Conference on Computer Vision"},"date_published":"2006-05-03T00:00:00Z","doi":"10.1007/11744047_2","quality_controlled":0,"page":"16 - 29","citation":{"ista":"Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C. 2006. A comparative study of energy minimization methods for Markov random fields. ECCV: European Conference on Computer Vision vol. 3952, 16–29.","ieee":"R. Szeliski et al., “A comparative study of energy minimization methods for Markov random fields,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952, pp. 16–29.","apa":"Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala, A., … Rother, C. (2006). A comparative study of energy minimization methods for Markov random fields (Vol. 3952, pp. 16–29). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_2","ama":"Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization methods for Markov random fields. In: Vol 3952. Springer; 2006:16-29. doi:10.1007/11744047_2","chicago":"Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative Study of Energy Minimization Methods for Markov Random Fields,” 3952:16–29. Springer, 2006. https://doi.org/10.1007/11744047_2.","mla":"Szeliski, Richard, et al. A Comparative Study of Energy Minimization Methods for Markov Random Fields. Vol. 3952, Springer, 2006, pp. 16–29, doi:10.1007/11744047_2.","short":"R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala, M. Tappen, C. Rother, in:, Springer, 2006, pp. 16–29."},"main_file_link":[{"open_access":"0","url":"http://research-srv.microsoft.com/pubs/67896/szsvkatr-eccv06.pdf"}],"day":"03","month":"05","date_updated":"2021-01-12T07:41:37Z","date_created":"2018-12-11T12:01:51Z","volume":3952,"author":[{"last_name":"Szeliski","first_name":"Richard","full_name":"Szeliski, Richard S"},{"full_name":"Zabih, Ramin","last_name":"Zabih","first_name":"Ramin"},{"full_name":"Scharstein, Daniel","first_name":"Daniel","last_name":"Scharstein"},{"first_name":"Olga","last_name":"Veksler","full_name":"Veksler, Olga"},{"full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"first_name":"Aseem","last_name":"Agarwala","full_name":"Agarwala, Aseem"},{"full_name":"Tappen, Marshall F","first_name":"Marshall","last_name":"Tappen"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"title":"A comparative study of energy minimization methods for Markov random fields","status":"public","publication_status":"published","publisher":"Springer","intvolume":" 3952","year":"2006","_id":"3180","extern":1,"abstract":[{"lang":"eng","text":"One of the most exciting advances in early vision has been the development of efficient energy minimization algorithms. Many early vision tasks require labeling each pixel with some quantity such as depth or texture. While many such problems can be elegantly expressed in the language of Markov Random Fields (MRF's), the resulting energy minimization problems were widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. Unfortunately, most papers define their own energy function, which is minimized with a specific algorithm of their choice. As a result, the tradeoffs among different energy minimization algorithms are not well understood. In this paper we describe a set of energy minimization benchmarks, which we use to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods - graph cuts, LBP, and tree-reweighted message passing - as well as the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching and interactive segmentation. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods with minimal overhead. We expect that the availability of our benchmarks and interface will make it significantly easier for vision researchers to adopt the best method for their specific problems. Benchmarks, code, results and images are available at http://vision.middlebury.edu/MRF."}],"publist_id":"3499","type":"conference"},{"main_file_link":[{"url":"http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf","open_access":"0"}],"citation":{"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","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.","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","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.","short":"V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 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."},"quality_controlled":0,"page":"1 - 15","conference":{"name":"ECCV: European Conference on Computer Vision"},"date_published":"2006-05-03T00:00:00Z","doi":"10.1007/11744047_1","day":"03","month":"05","year":"2006","_id":"3184","title":"Comparison of energy minimization algorithms for highly connected graphs","publication_status":"published","status":"public","publisher":"Springer","author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"date_created":"2018-12-11T12:01:52Z","date_updated":"2021-01-12T07:41:39Z","volume":"3952 LNCS","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Algorithms for discrete energy minimization play a fundamental role for low-level vision. Known techniques include graph cuts, belief propagation (BP) and recently introduced tree-reweighted message passing (TRW). So far, the standard benchmark for their comparison has been a 4-connected grid-graph arising in pixel-labelling stereo. This minimization problem, however, has been largely solved: recent work shows that for many scenes TRW finds the global optimum. Furthermore, it is known that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions into account. We propose the problem of stereo with occlusions as a new test bed for minimization algorithms. This is a more challenging graph since it has much larger connectivity, and it also serves as a better stereo model. An attractive feature of this problem is that increased connectivity does not result in increased complexity of message passing algorithms. Indeed, one contribution of this paper is to show that sophisticated implementations of BP and TRW have the same time and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion of our experimental study is that for our problem graph cut outperforms both TRW and BP considerably. TRW achieves consistently a lower energy than BP. However, as connectivity increases the speed of convergence of TRW becomes slower. Unlike 4-connected grids, the difference between the energy of the best optimization method and the lower bound of TRW appears significant. This shows the hardness of the problem and motivates future research.","lang":"eng"}],"publist_id":"3498","extern":1},{"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf"}],"citation":{"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.","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.","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","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.","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492, 2006.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006). Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193"},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","page":"1480 - 1492","quality_controlled":0,"doi":"10.1109/TPAMI.2006.193","date_published":"2006-09-01T00:00:00Z","month":"09","day":"01","year":"2006","_id":"3185","intvolume":" 28","publisher":"IEEE","status":"public","publication_status":"published","title":"Probabilistic fusion of stereo with color and contrast for bilayer segmentation","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"full_name":"Criminisi, Antonio","last_name":"Criminisi","first_name":"Antonio"},{"full_name":"Blake, Andrew","first_name":"Andrew","last_name":"Blake"},{"full_name":"Cross, Geoffrey","first_name":"Geoffrey","last_name":"Cross"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"volume":28,"date_created":"2018-12-11T12:01:53Z","date_updated":"2021-01-12T07:41:39Z","type":"journal_article","issue":"9","publist_id":"3496","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."}],"extern":1},{"author":[{"full_name":"Boykov, Yuri","last_name":"Boykov","first_name":"Yuri"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"last_name":"Cremers","first_name":"Daniel","full_name":"Cremers, Daniel"},{"first_name":"Andrew","last_name":"Delong","full_name":"Delong, Andrew"}],"date_updated":"2021-01-12T07:41:39Z","date_created":"2018-12-11T12:01:53Z","volume":3953,"year":"2006","_id":"3186","title":"An integral solution to surface evolution PDEs via geo cuts","status":"public","publication_status":"published","publisher":"Springer","intvolume":" 3953","abstract":[{"text":"We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion.","lang":"eng"}],"publist_id":"3497","extern":1,"type":"conference","alternative_title":["LNCS"],"conference":{"name":"ECCV: European Conference on Computer Vision"},"date_published":"2006-04-28T00:00:00Z","doi":"10.1007/11744078_32","citation":{"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.","short":"Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp. 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.","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","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.","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"},"quality_controlled":0,"page":"409 - 422","month":"04","day":"28"},{"extern":1,"publist_id":"2998","alternative_title":["Manuals in Biomedical Research"],"type":"book_chapter","volume":2,"date_created":"2018-12-11T12:03:09Z","date_updated":"2021-01-12T07:43:15Z","author":[{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Harald Janovjak"},{"full_name":"Sawhney, Ravi K","last_name":"Sawhney","first_name":"Ravi"},{"full_name":"Stark, Martin","last_name":"Stark","first_name":"Martin"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"intvolume":" 2","publisher":"World Scientific Publishing","publication_status":"published","title":"Atomic force microscopy","status":"public","_id":"3404","year":"2006","month":"09","day":"28","date_published":"2006-09-28T00:00:00Z","page":"213 - 284","quality_controlled":0,"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.","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.","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.","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.","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.","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."},"publication":"Techniques in Microscopy for Biomedical Applications"},{"volume":357,"date_updated":"2021-01-12T07:43:18Z","date_created":"2018-12-11T12:03:12Z","author":[{"full_name":"Kessler, Max","last_name":"Kessler","first_name":"Max"},{"last_name":"Gottschalk","first_name":"Kay","full_name":"Gottschalk, Kay E"},{"full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"},{"first_name":"Hermann","last_name":"Gaub","full_name":"Gaub, Hermann"}],"intvolume":" 357","publisher":"Elsevier","publication_status":"published","title":"Bacteriorhodopsin folds into the membrane against an external force","status":"public","_id":"3413","year":"2006","extern":1,"publist_id":"2988","issue":"2","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.\n\nHere we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.\n\nWe discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state."}],"type":"journal_article","doi":"10.1016/j.jmb.2005.12.065","date_published":"2006-03-24T00:00:00Z","page":"644 - 654","quality_controlled":0,"citation":{"chicago":"Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065.","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.","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.","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","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.","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"},"publication":"Journal of Molecular Biology","month":"03","day":"24"},{"date_published":"2006-01-06T00:00:00Z","doi":"10.1016/j.jmb.2005.10.028","page":"2 - 8","quality_controlled":0,"citation":{"short":"A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 355 (2006) 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.","chicago":"Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt, and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.10.028.","ama":"Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028","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.","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","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."},"publication":"Journal of Molecular Biology","day":"06","month":"01","volume":355,"date_updated":"2021-01-12T07:43:19Z","date_created":"2018-12-11T12:03:12Z","author":[{"full_name":"Kedrov, Alexej","last_name":"Kedrov","first_name":"Alexej"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","full_name":"Harald Janovjak"},{"full_name":"Ziegler, Christine","last_name":"Ziegler","first_name":"Christine"},{"full_name":"Kühlbrandt, Werner","last_name":"Kühlbrandt","first_name":"Werner"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"publisher":"Elsevier","intvolume":" 355","status":"public","publication_status":"published","title":"Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli","_id":"3414","year":"2006","extern":1,"issue":"1","publist_id":"2987","abstract":[{"text":"Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter.","lang":"eng"}],"type":"journal_article"},{"author":[{"full_name":"Harald Janovjak","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"first_name":"David","last_name":"Cisneros","full_name":"Cisneros, David"},{"full_name":"Sapra, Tanuj K","first_name":"Tanuj","last_name":"Sapra"},{"full_name":"Struckmeier, Jens","last_name":"Struckmeier","first_name":"Jens"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"date_created":"2018-12-11T12:03:12Z","date_updated":"2019-04-26T07:22:27Z","volume":27,"_id":"3415","year":"2006","title":"Imaging and detecting molecular interactions of single membrane proteins","publication_status":"published","status":"public","intvolume":" 27","publisher":"Elsevier","publist_id":"2986","extern":1,"type":"review","date_published":"2006-01-01T00:00:00Z","doi":"10.1016/j.neurobiolaging.2005.03.031","publication":"Neurobiology of Aging","citation":{"chicago":"Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier, and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031.","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.","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.","ieee":"H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller, “Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology of Aging, vol. 27. Elsevier, pp. 546–561, 2006.","apa":"Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., & Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031","ama":"Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031"},"quality_controlled":0,"page":"546 - 561","month":"01","day":"01"},{"page":"618 - 623","quality_controlled":0,"citation":{"short":"A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development 16 (2006) 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.","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.","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","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."},"publication":"Current Opinion in Genetics & Development","date_published":"2006-12-01T00:00:00Z","doi":"10.1016/j.gde.2006.10.006","month":"12","day":"01","intvolume":" 16","publisher":"Elsevier","publication_status":"published","status":"public","title":"Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution","year":"2006","_id":"3437","volume":16,"date_updated":"2021-01-12T07:43:27Z","date_created":"2018-12-11T12:03:19Z","author":[{"full_name":"Betancourt, Andrea J","last_name":"Betancourt","first_name":"Andrea"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Jonathan Bollback"}],"type":"journal_article","extern":1,"publist_id":"2963","issue":"6","abstract":[{"text":"The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models.","lang":"eng"}]},{"page":"1 - 4","quality_controlled":0,"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.","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, .","short":"G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.","mla":"Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4.","chicago":"Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/q-bio/0611072"}],"oa":1,"publication":"ArXiv","date_published":"2006-11-22T00:00:00Z","month":"11","day":"22","publisher":"ArXiv","publication_status":"published","status":"public","title":"Ising models for networks of real neurons","year":"2006","_id":"3431","date_created":"2018-12-11T12:03:18Z","date_updated":"2021-01-12T07:43:25Z","author":[{"full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Schneidman, E.","last_name":"Schneidman","first_name":"E."},{"last_name":"Berry","first_name":"M.","full_name":"Berry, M. J."},{"full_name":"Bialek, William S","first_name":"William","last_name":"Bialek"}],"type":"preprint","extern":1,"publist_id":"2969","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."}]},{"extern":1,"publist_id":"2938","abstract":[{"text":"We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control.","lang":"eng"}],"type":"conference","date_updated":"2021-01-12T07:43:32Z","date_created":"2018-12-11T12:03:23Z","author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Jagadeesan, Rhada","last_name":"Jagadeesan","first_name":"Rhada"},{"last_name":"Pitcher","first_name":"Corin","full_name":"Pitcher, Corin"}],"publisher":"IEEE","status":"public","publication_status":"published","title":"Games for controls","_id":"3449","year":"2006","day":"31","month":"07","doi":"10.1109/CSFW.2006.14","date_published":"2006-07-31T00:00:00Z","conference":{"name":"CSF: Computer Security Foundations"},"page":"70 - 82","quality_controlled":0,"citation":{"ista":"Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer Security Foundations, 70–82.","apa":"Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls (pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14","ieee":"K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented at the CSF: Computer Security Foundations, 2006, pp. 70–82.","ama":"Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82. doi:10.1109/CSFW.2006.14","chicago":"Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14.","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."}},{"day":"01","month":"12","doi":"10.1007/s00424-006-0093-2","date_published":"2006-12-01T00:00:00Z","publication":"Pflugers Archiv : European Journal of Physiology","citation":{"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.","chicago":"Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology. Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.","ama":"Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2","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.","apa":"Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2","ieee":"J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review),” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–372, 2006."},"quality_controlled":0,"page":"361 - 372","abstract":[{"text":"It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network.","lang":"eng"}],"publist_id":"2924","issue":"3","extern":1,"type":"review","author":[{"last_name":"Bischofberger","first_name":"Joseph","full_name":"Bischofberger, Joseph"},{"last_name":"Engel","first_name":"Dominique","full_name":"Engel, Dominique"},{"full_name":"Frotscher, Michael","last_name":"Frotscher","first_name":"Michael"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Peter Jonas"}],"date_updated":"2019-04-26T07:22:28Z","date_created":"2018-12-11T12:03:28Z","volume":453,"_id":"3463","year":"2006","title":"Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review)","status":"public","publication_status":"published","intvolume":" 453","publisher":"Springer"},{"type":"conference","alternative_title":["LNCS "],"publist_id":"2888","abstract":[{"text":"We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. ","lang":"eng"}],"extern":1,"_id":"3499","year":"2006","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.","intvolume":" 4207","publisher":"Springer","status":"public","title":"Nash equilibrium for upward-closed objectives","publication_status":"published","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee"}],"volume":4207,"date_updated":"2021-01-12T07:43:52Z","date_created":"2018-12-11T12:03:39Z","month":"09","day":"28","citation":{"chicago":"Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,” 4207:271–86. Springer, 2006. https://doi.org/10.1007/11874683_18.","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.","ista":"Chatterjee K. 2006. Nash equilibrium for upward-closed objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 271–286.","ieee":"K. Chatterjee, “Nash equilibrium for upward-closed objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 271–286.","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","ama":"Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207. Springer; 2006:271-286. doi:10.1007/11874683_18"},"page":"271 - 286","quality_controlled":0,"date_published":"2006-09-28T00:00:00Z","doi":"10.1007/11874683_18","conference":{"name":"CSL: Computer Science Logic"}},{"publisher":"ACM","title":"Algorithms for Büchi Games","publication_status":"published","status":"public","_id":"3500","year":"2006","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.","date_created":"2018-12-11T12:03:39Z","date_updated":"2021-01-12T07:43:53Z","author":[{"full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger"},{"full_name":"Piterman, Nir","last_name":"Piterman","first_name":"Nir"}],"type":"conference","extern":1,"publist_id":"2887","abstract":[{"lang":"eng","text":"The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n)."}],"quality_controlled":0,"main_file_link":[{"open_access":"0","url":"http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf"}],"citation":{"ista":"Chatterjee K, Henzinger TA, Piterman N. 2006. Algorithms for Büchi Games. GDV: Games in Design and Verification.","apa":"Chatterjee, K., Henzinger, T. A., & Piterman, N. (2006). Algorithms for Büchi Games. Presented at the GDV: Games in Design and Verification, ACM.","ieee":"K. Chatterjee, T. A. Henzinger, and N. Piterman, “Algorithms for Büchi Games,” presented at the GDV: Games in Design and Verification, 2006.","ama":"Chatterjee K, Henzinger TA, Piterman N. Algorithms for Büchi Games. In: ACM; 2006.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms for Büchi Games.” ACM, 2006.","mla":"Chatterjee, Krishnendu, et al. Algorithms for Büchi Games. ACM, 2006.","short":"K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006."},"date_published":"2006-08-21T00:00:00Z","conference":{"name":"GDV: Games in Design and Verification"},"day":"21","month":"08"},{"oa_version":"Published Version","ipc":"G06F 7/60 ; G06F 17/10 ; G06F 101/00","date_updated":"2022-01-05T12:58:26Z","date_created":"2018-12-11T12:03:42Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Fu, Ping","last_name":"Fu","first_name":"Ping"},{"last_name":"Nekhayev","first_name":"Dmitry","full_name":"Nekhayev, Dmitry"},{"full_name":"Facello, Michael","last_name":"Facello","first_name":"Michael"},{"first_name":"Steven","last_name":"Williams","full_name":"Williams, Steven"}],"applicant":["Raindrop Geomagic, Inc."],"status":"public","title":"Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism","_id":"3510","year":"2006","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","publist_id":"2877","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."}],"type":"patent","date_published":"2006-02-07T00:00:00Z","oa":1,"publication_date":"2006-02-07","citation":{"short":"H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006).","mla":"Edelsbrunner, Herbert, et al. Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism. 2006.","chicago":"Edelsbrunner, Herbert, Ping Fu, Dmitry Nekhayev, Michael Facello, and Steven Williams. “Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism,” 2006.","ama":"Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. 2006.","apa":"Edelsbrunner, H., Fu, P., Nekhayev, D., Facello, M., & Williams, S. (2006). Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.","ieee":"H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, and S. Williams, “Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.” 2006.","ista":"Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. 2006. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism."},"main_file_link":[{"url":"https://patents.google.com/patent/US6996505","open_access":"1"}],"ipn":"US6996505B1","article_processing_charge":"No","month":"02","day":"07"},{"year":"2006","_id":"3511","acknowledgement":"sold to Siemens and Phonak","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Manufacturing methods and systems for rapid production of hearing-aid shells","status":"public","applicant":["Phonak AG"],"author":[{"first_name":"Ping","last_name":"Fu","full_name":"Fu, Ping"},{"last_name":"Nekhayev","first_name":"Dmitry","full_name":"Nekhayev, Dmitry"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"date_updated":"2022-01-05T13:03:56Z","date_created":"2018-12-11T12:03:43Z","ipc":"G06F 9/00","oa_version":"Published Version","type":"patent","abstract":[{"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. ","lang":"eng"}],"publist_id":"2876","extern":"1","ipn":"US7050876B1","citation":{"ieee":"P. Fu, D. Nekhayev, and H. Edelsbrunner, “Manufacturing methods and systems for rapid production of hearing-aid shells.” 2006.","apa":"Fu, P., Nekhayev, D., & Edelsbrunner, H. (2006). Manufacturing methods and systems for rapid production of hearing-aid shells.","ista":"Fu P, Nekhayev D, Edelsbrunner H. 2006. Manufacturing methods and systems for rapid production of hearing-aid shells.","ama":"Fu P, Nekhayev D, Edelsbrunner H. Manufacturing methods and systems for rapid production of hearing-aid shells. 2006.","chicago":"Fu, Ping, Dmitry Nekhayev, and Herbert Edelsbrunner. “Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells,” 2006.","short":"P. Fu, D. Nekhayev, H. Edelsbrunner, (2006).","mla":"Fu, Ping, et al. Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells. 2006."},"publication_date":"2006-05-23","main_file_link":[{"url":"https://patents.google.com/patent/US7050876B1","open_access":"1"}],"oa":1,"date_published":"2006-05-23T00:00:00Z","month":"05","day":"23","article_processing_charge":"No"},{"article_processing_charge":"No","month":"04","day":"04","citation":{"chicago":"Fletcher, Yates, Tobias Gloth, Herbert Edelsbrunner, and Ping Fu. “Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points,” 2006.","short":"Y. Fletcher, T. Gloth, H. Edelsbrunner, P. Fu, (2006).","mla":"Fletcher, Yates, et al. Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points. 2006.","ieee":"Y. Fletcher, T. Gloth, H. Edelsbrunner, and P. Fu, “Method, apparatus and computer products that reconstruct surfaces from data points.” 2006.","apa":"Fletcher, Y., Gloth, T., Edelsbrunner, H., & Fu, P. (2006). Method, apparatus and computer products that reconstruct surfaces from data points.","ista":"Fletcher Y, Gloth T, Edelsbrunner H, Fu P. 2006. Method, apparatus and computer products that reconstruct surfaces from data points.","ama":"Fletcher Y, Gloth T, Edelsbrunner H, Fu P. Method, apparatus and computer products that reconstruct surfaces from data points. 2006."},"ipn":"US7023432B2","oa":1,"main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/US7023432B2"}],"publication_date":"2006-04-04","date_published":"2006-04-04T00:00:00Z","type":"patent","extern":"1","publist_id":"2875","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."],"title":"Method, apparatus and computer products that reconstruct surfaces from data points","status":"public","_id":"3512","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2006","oa_version":"Published Version","ipc":" G06T17/20 ; B33Y50/00","date_created":"2018-12-11T12:03:43Z","date_updated":"2022-01-05T14:00:00Z","author":[{"last_name":"Fletcher","first_name":"Yates","full_name":"Fletcher, Yates"},{"last_name":"Gloth","first_name":"Tobias","full_name":"Gloth, Tobias"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"last_name":"Fu","first_name":"Ping","full_name":"Fu, Ping"}]},{"title":"Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo","publication_status":"published","status":"public","intvolume":" 26","publisher":"Society for Neuroscience","year":"2006","_id":"3545","date_created":"2018-12-11T12:03:53Z","date_updated":"2021-01-12T07:44:13Z","volume":26,"author":[{"first_name":"Peter","last_name":"Magill","full_name":"Magill,Peter J"},{"first_name":"Alek","last_name":"Pogosyan","full_name":"Pogosyan,Alek"},{"full_name":"Sharott,Andrew","first_name":"Andrew","last_name":"Sharott"},{"last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Jozsef Csicsvari"},{"full_name":"Bolam, John Paul","last_name":"Bolam","first_name":"John"},{"full_name":"Brown,Peter","first_name":"Peter","last_name":"Brown"}],"type":"journal_article","extern":1,"abstract":[{"text":"The functional organization of the basal ganglia ( BG) is often defined according to one of two opposing schemes. The first proposes multiple, essentially independent channels of information processing. The second posits convergence and lateral integration of striatal channels at the level of the globus pallidus ( GP). We tested the hypothesis that these proposed aspects of functional connectivity within the striatopallidal axis are dynamic and related to brain state. Local field potentials ( LFPs) were simultaneously recorded from multiple sites in striatum and GP in anesthetized rats during slow-wave activity( SWA) and during global activation evoked by sensory stimulation. Functional connectivity was inferred from comparative analyses of the internuclear and intranuclear coherence between bipolar derivations of LFPs. During prominent SWA, as shown in the electrocorticogram and local field potentials in the basal ganglia, intranuclear coherence, and, thus, lateral functional connectivity within striatum or globus pallidus was relatively weak. Furthermore, the temporal coupling of LFPs recorded across these two nuclei involved functional convergence at the level of GP. Global activation, indicated by a loss of SWA, was accompanied by a rapid functional reorganization of the striatopallidal axis. Prominent lateral functional connectivity developed within GP and, to a significantly more constrained spatial extent, striatum. Additionally, functional convergence on GP was no longer apparent, despite increased internuclear coherence. These data demonstrate that functional connectivity within the BG is highly dynamic and suggest that the relative expression of organizational principles, such as parallel, independent processing channels, striatopallidal convergence, and lateral integration within BG nuclei, is dependent on brain state.","lang":"eng"}],"issue":"23","publist_id":"2840","quality_controlled":0,"page":"6318 - 6329","publication":"Journal of Neuroscience","citation":{"short":"P. Magill, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, Journal of Neuroscience 26 (2006) 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.","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.","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","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."},"date_published":"2006-06-07T00:00:00Z","doi":"10.1523/JNEUROSCI.0620-06.2006","month":"06","day":"07"},{"day":"01","month":"06","page":"119 - 126","quality_controlled":0,"citation":{"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.","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","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.","ama":"Cohen Steiner D, Edelsbrunner H, Morozov D. Vines and vineyards by updating persistence in linear time. In: ACM; 2006:119-126. doi:10.1145/1137856.1137877","chicago":"Cohen Steiner, David, Herbert Edelsbrunner, and Dmitriy Morozov. “Vines and Vineyards by Updating Persistence in Linear Time,” 119–26. ACM, 2006. https://doi.org/10.1145/1137856.1137877.","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."},"date_published":"2006-06-01T00:00:00Z","doi":"10.1145/1137856.1137877","conference":{"name":"SCG: Symposium on Computational Geometry"},"type":"conference","extern":1,"publist_id":"2826","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."}],"publisher":"ACM","publication_status":"published","status":"public","title":"Vines and vineyards by updating persistence in linear time","_id":"3559","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.","year":"2006","date_updated":"2021-01-12T07:44:18Z","date_created":"2018-12-11T12:03:58Z","author":[{"full_name":"Cohen-Steiner, David","last_name":"Cohen Steiner","first_name":"David"},{"full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Morozov, Dmitriy","first_name":"Dmitriy","last_name":"Morozov"}]},{"month":"06","day":"01","conference":{"name":"SCG: Symposium on Computational Geometry"},"date_published":"2006-06-01T00:00:00Z","doi":"10.1145/1137856.1137878","quality_controlled":0,"page":"127 - 134","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.4465","open_access":"0"}],"citation":{"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.","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.","ista":"Edelsbrunner H, Morozov D, Pascucci V. 2006. Persistence-sensitive simplification of functions on 2-manifolds. SCG: Symposium on Computational Geometry, 127–134.","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.","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","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"},"extern":1,"abstract":[{"text":"We continue the study of topological persistence [5] by investigat- ing the problem of simplifying a function f in a way that removes topological noise as determined by its persistence diagram [2]. To state our results, we call a function g an ε-simplification of another function f if ∥f − g∥∞ ≤ ε, and the persistence diagrams of g are the same as those of f except all points within L1-distance at most ε from the diagonal have been removed. We prove that for func- tions f on a 2-manifold such ε-simplification exists, and we give an algorithm to construct them in the piecewise linear case.","lang":"eng"}],"publist_id":"2825","type":"conference","date_created":"2018-12-11T12:03:58Z","date_updated":"2021-01-12T07:44:19Z","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner"},{"first_name":"Dmitriy","last_name":"Morozov","full_name":"Morozov, Dmitriy"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"}],"publication_status":"published","status":"public","title":"Persistence-sensitive simplification of functions on 2-manifolds","publisher":"ACM","_id":"3560","acknowledgement":"Partially supported by NSF under grant CCR-00-86013, by DARPA under grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under grant B543154.","year":"2006"},{"author":[{"full_name":"Pemberton, Josephine M","last_name":"Pemberton","first_name":"Josephine"},{"full_name":"Swanson, Graeme M","last_name":"Swanson","first_name":"Graeme"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Nicholas Barton"},{"full_name":"Livingstone, Suzanne R","first_name":"Suzanne","last_name":"Livingstone"},{"last_name":"Senn","first_name":"Helen","full_name":"Senn, Helen V"}],"volume":13,"date_created":"2018-12-11T12:04:08Z","date_updated":"2019-04-26T07:22:31Z","year":"2006","_id":"3594","publisher":"BDS ","intvolume":" 13","publication_status":"published","status":"public","title":"Hybridisation between red and sika deer in Scotland","publist_id":"2789","issue":"9","extern":1,"type":"review","date_published":"2006-01-01T00:00:00Z","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.","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.","ieee":"J. Pemberton, G. Swanson, N. H. Barton, S. Livingstone, and H. Senn, “Hybridisation between red and sika deer in Scotland,” Deer, vol. 13, no. 9. BDS , pp. 22–26, 2006.","apa":"Pemberton, J., Swanson, G., Barton, N. H., Livingstone, S., & Senn, H. (2006). Hybridisation between red and sika deer in Scotland. Deer. BDS .","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.","chicago":"Pemberton, Josephine, Graeme Swanson, Nicholas H Barton, Suzanne Livingstone, and Helen Senn. “Hybridisation between Red and Sika Deer in Scotland.” Deer. BDS , 2006."},"publication":"Deer","page":"22 - 26","quality_controlled":0,"month":"01","day":"01"},{"extern":1,"issue":"3","publist_id":"2774","abstract":[{"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.","lang":"eng"}],"type":"journal_article","volume":60,"date_created":"2018-12-11T12:04:13Z","date_updated":"2021-01-12T07:44:38Z","author":[{"full_name":"Yanchukov, Alexey","first_name":"Alexey","last_name":"Yanchukov"},{"full_name":"Hofman, Sebastian","first_name":"Sebastian","last_name":"Hofman"},{"full_name":"Szymura, Jacek M","last_name":"Szymura","first_name":"Jacek"},{"first_name":"Sergey","last_name":"Mezhzherin","full_name":"Mezhzherin, Sergey V"},{"full_name":"Morozov-Leonov, Sviatoslav","last_name":"Morozov Leonov","first_name":"Sviatoslav"},{"full_name":"Nicholas Barton","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Nürnberger, Beate","last_name":"Nürnberger","first_name":"Beate"}],"publisher":"Wiley-Blackwell","intvolume":" 60","publication_status":"published","title":"Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time","status":"public","year":"2006","_id":"3609","month":"03","day":"01","doi":"10.1111/j.0014-3820.2006.tb01139.x","date_published":"2006-03-01T00:00:00Z","page":"583 - 600","quality_controlled":0,"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","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.","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.","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","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.","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."},"publication":"Evolution; International Journal of Organic Evolution"},{"doi":"10.1534/genetics.105.047985","date_published":"2006-05-01T00:00:00Z","citation":{"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.","short":"M. Kirkpatrick, N.H. Barton, Genetics 173 (2006) 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.","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","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.","ama":"Kirkpatrick M, Barton NH. Chromosome inversions, local adaptation, and speciation. Genetics. 2006;173(1):419-434. doi:10.1534/genetics.105.047985"},"publication":"Genetics","page":"419 - 434","quality_controlled":0,"day":"01","month":"05","author":[{"full_name":"Kirkpatrick, Mark","last_name":"Kirkpatrick","first_name":"Mark"},{"full_name":"Nicholas Barton","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":173,"date_created":"2018-12-11T12:04:13Z","date_updated":"2021-01-12T07:44:37Z","year":"2006","_id":"3608","intvolume":" 173","publisher":"Genetics Society of America","publication_status":"published","title":"Chromosome inversions, local adaptation, and speciation","status":"public","publist_id":"2775","issue":"1","abstract":[{"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. ","lang":"eng"}],"extern":1,"type":"journal_article"},{"extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2773","issue":"1","type":"journal_article","date_updated":"2021-01-12T07:44:39Z","date_created":"2018-12-11T12:04:14Z","volume":70,"author":[{"last_name":"Hill","first_name":"William","full_name":"Hill, William G"},{"full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"}],"title":"Prediction of effects of genetic drift on variance components under a general model of epistasis","publication_status":"published","status":"public","publisher":"Academic Press","intvolume":" 70","_id":"3610","year":"2006","day":"01","month":"08","doi":"10.1016/j.tpb.2005.10.001","date_published":"2006-08-01T00:00:00Z","quality_controlled":0,"page":"56 - 62","publication":"Theoretical Population Biology","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","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.","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","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.","short":"W. Hill, N.H. Barton, M. Turelli, Theoretical Population Biology 70 (2006) 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.","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."}},{"extern":1,"abstract":[{"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)".","lang":"eng"}],"publist_id":"2700","alternative_title":["LNCS"],"type":"conference","date_updated":"2021-01-12T07:45:05Z","date_created":"2018-12-11T12:04:35Z","volume":4225,"author":[{"last_name":"Ali","first_name":"Haider","full_name":"Ali,Haider"},{"full_name":"Christoph Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"last_name":"Breuel","first_name":"Thomas","full_name":"Breuel,Thomas M"}],"status":"public","title":"Satellite tracks removal in astronomical images","publication_status":"published","publisher":"Springer","intvolume":" 4225","year":"2006","_id":"3679","day":"31","month":"10","conference":{"name":"CIARP: Iberoamerican Congress in Pattern Recognition"},"doi":"10.1007/11892755_92","date_published":"2006-10-31T00:00:00Z","quality_controlled":0,"page":"892 - 901","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","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.","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","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.","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.","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."},"main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/~chl/papers/ali-ciarp2006.pdf"}]},{"author":[{"first_name":"Adrian","last_name":"Ulges","full_name":"Ulges, Adrian"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Christoph Lampert"},{"last_name":"Keysers","first_name":"Daniel","full_name":"Keysers,Daniel"}],"date_created":"2018-12-11T12:04:34Z","date_updated":"2021-01-12T07:45:04Z","_id":"3677","year":"2006","status":"public","publication_status":"published","title":"Spatiogram-based shot distances for video retrieval","publisher":"NIST (National Institute of Standards and Technology, US Department of Commerce)","abstract":[{"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.","lang":"eng"}],"publist_id":"2702","extern":1,"type":"conference","alternative_title":["TRECVID Notebook Papers and Slides"],"conference":{"name":"TRECVID Workshop"},"date_published":"2006-11-14T00:00:00Z","citation":{"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).","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.","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.","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.","short":"A. Ulges, C. Lampert, D. Keysers, in:, NIST (National Institute of Standards and Technology, US Department of Commerce), 2006, pp. 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."},"main_file_link":[{"url":"http://www-nlpir.nist.gov/projects/tvpubs/tv6.papers/dfki.pdf","open_access":"0"}],"quality_controlled":0,"page":"1 - 10","month":"11","day":"14"},{"type":"conference","publist_id":"2698","abstract":[{"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","lang":"eng"}],"extern":1,"_id":"3680","year":"2006","publisher":"IEEE","intvolume":" 1","status":"public","publication_status":"published","title":"Printing technique classification for document counterfeit detection","author":[{"full_name":"Christoph Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"last_name":"Mei","first_name":"Lin","full_name":"Mei,Lin"},{"first_name":"Thomas","last_name":"Breuel","full_name":"Breuel,Thomas M"}],"volume":1,"date_updated":"2021-01-12T07:45:06Z","date_created":"2018-12-11T12:04:35Z","month":"11","day":"03","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","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.","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","ista":"Lampert C, Mei L, Breuel T. 2006. Printing technique classification for document counterfeit detection. CIS: Computational Intelligence and Security vol. 1, 639–634.","short":"C. Lampert, L. Mei, T. Breuel, in:, IEEE, 2006, pp. 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.","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."},"main_file_link":[{"url":"http://pub.ist.ac.at/~chl/papers/lampert-cis2006.pdf","open_access":"0"}],"page":"639 - 634","quality_controlled":0,"date_published":"2006-11-03T00:00:00Z","doi":"10.1109/ICCIAS.2006.294214","conference":{"name":"CIS: Computational Intelligence and Security"}},{"month":"11","day":"01","publication":"IEEE Transactions on Image Processing (TIP)","oa":1,"citation":{"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.","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.","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 ","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 ","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 .","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."},"main_file_link":[{"url":"http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:386-kluedo-14003","open_access":"1"}],"quality_controlled":0,"page":"3501 - 3513","doi":" 10.1109/TIP.2006.877501 ","date_published":"2006-11-01T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"publist_id":"2669","issue":"11","extern":1,"_id":"3695","year":"2006","title":"An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter","publication_status":"published","status":"public","publisher":"IEEE","intvolume":" 15","author":[{"full_name":"Christoph Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"full_name":"Wirjadi,Oliver","first_name":"Oliver","last_name":"Wirjadi"}],"date_updated":"2021-01-12T07:49:01Z","date_created":"2018-12-11T12:04:40Z","volume":15},{"_id":"3693","year":"2006","publication_status":"published","title":"Anisotropic Gaussian filtering using fixed point arithmetic","status":"public","publisher":"IEEE","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Christoph Lampert"},{"first_name":"Oliver","last_name":"Wirjadi","full_name":"Wirjadi,Oliver"}],"date_updated":"2021-01-12T07:49:00Z","date_created":"2018-12-11T12:04:39Z","type":"conference","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."}],"publist_id":"2670","extern":1,"citation":{"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.","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.","ista":"Lampert C, Wirjadi O. 2006. Anisotropic Gaussian filtering using fixed point arithmetic. ICIP: IEEE International Conference on Image Processing, 1565–1568.","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","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.","ama":"Lampert C, Wirjadi O. Anisotropic Gaussian filtering using fixed point arithmetic. In: IEEE; 2006:1565-1568. doi:10.1109/ICIP.2006.312606"},"quality_controlled":0,"page":"1565 - 1568","conference":{"name":"ICIP: IEEE International Conference on Image Processing"},"doi":"10.1109/ICIP.2006.312606","date_published":"2006-10-08T00:00:00Z","month":"10","day":"08"},{"title":"Color image dequantization by constrained diffusion","status":"public","publication_status":"published","intvolume":" 6058","publisher":"SPIE","_id":"3692","year":"2006","date_updated":"2019-05-10T12:19:52Z","date_created":"2018-12-11T12:04:39Z","volume":6058,"author":[{"full_name":"Keysers,Daniel","first_name":"Daniel","last_name":"Keysers"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Christoph Lampert"},{"first_name":"Thomas","last_name":"Breuel","full_name":"Breuel,Thomas M"}],"type":"conference","extern":1,"publist_id":"2674","quality_controlled":0,"citation":{"ista":"Keysers D, Lampert C, Breuel T. 2006. Color image dequantization by constrained diffusion. SPIE Electronic Imaging vol. 6058.","ieee":"D. Keysers, C. Lampert, and T. Breuel, “Color image dequantization by constrained diffusion,” presented at the SPIE Electronic Imaging, 2006, vol. 6058.","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","ama":"Keysers D, Lampert C, Breuel T. Color image dequantization by constrained diffusion. In: Vol 6058. SPIE; 2006. doi: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.","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_published":"2006-01-15T00:00:00Z","doi":"10.1117/12.648713","month":"01","day":"15"},{"publication":"European Biophysics Journal","citation":{"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.","short":"C. Bippes, A. Humphris, M. Stark, D. Mueller, H.L. Janovjak, European Biophysics Journal 35 (2006) 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.","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.","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","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.","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"},"quality_controlled":0,"page":"287 - 292","date_published":"2006-02-01T00:00:00Z","doi":"10.1007/s00249-005-0023-9","day":"01","month":"02","year":"2006","_id":"3729","status":"public","publication_status":"published","title":"Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments","publisher":"Springer","intvolume":" 35","author":[{"first_name":"Christian","last_name":"Bippes","full_name":"Bippes, Christian A"},{"full_name":"Humphris, Andrew D","first_name":"Andrew","last_name":"Humphris"},{"first_name":"Martin","last_name":"Stark","full_name":"Stark, Martin"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel J"},{"full_name":"Harald Janovjak","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:51:46Z","date_created":"2018-12-11T12:04:51Z","volume":35,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3","publist_id":"2500","extern":1},{"month":"04","day":"01","page":"537 - 544","quality_controlled":0,"citation":{"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.","short":"M. Cieplak, S. Filipek, H.L. Janovjak, K. Krzysko, Biochimica et Biophysica Acta (BBA) - Biomembranes 1758 (2006) 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.","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","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.","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"},"publication":"Biochimica et Biophysica Acta (BBA) - Biomembranes","date_published":"2006-04-01T00:00:00Z","doi":"10.1016/j.bbamem.2006.03.028","type":"journal_article","extern":1,"issue":"4","publist_id":"2502","abstract":[{"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.","lang":"eng"}],"publisher":"Elsevier","intvolume":" 1758","publication_status":"published","title":"Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment","status":"public","_id":"3728","year":"2006","volume":1758,"date_created":"2018-12-11T12:04:50Z","date_updated":"2021-01-12T07:51:46Z","author":[{"last_name":"Cieplak","first_name":"Marek","full_name":"Cieplak, Marek"},{"full_name":"Filipek, Sławomir","first_name":"Sławomir","last_name":"Filipek"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"full_name":"Krzysko, Krystiana A","last_name":"Krzysko","first_name":"Krystiana"}]},{"_id":"3722","year":"2006","title":"Rastersondenmikroskopie","status":"public","publication_status":"published","publisher":"Spektrum Akademischer Verlag","author":[{"full_name":"Harald Janovjak","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"date_updated":"2021-01-12T07:51:44Z","date_created":"2018-12-11T12:04:48Z","type":"book_chapter","publist_id":"2508","extern":1,"publication":"Bioanalytik","citation":{"ama":"Janovjak HL, Mueller D. Rastersondenmikroskopie. In: Bioanalytik. Spektrum Akademischer Verlag; 2006.","ista":"Janovjak HL, Mueller D. 2006.Rastersondenmikroskopie. In: Bioanalytik. .","apa":"Janovjak, H. L., & Mueller, D. (2006). Rastersondenmikroskopie. In Bioanalytik. Spektrum Akademischer Verlag.","ieee":"H. L. Janovjak and D. Mueller, “Rastersondenmikroskopie,” in Bioanalytik, Spektrum Akademischer Verlag, 2006.","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.","chicago":"Janovjak, Harald L, and Daniel Mueller. “Rastersondenmikroskopie.” In Bioanalytik. Spektrum Akademischer Verlag, 2006."},"quality_controlled":0,"date_published":"2006-06-16T00:00:00Z","day":"16","month":"06"},{"page":"3315 - 3321","quality_controlled":0,"citation":{"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.","short":"T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90 (2006) 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.","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","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.","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"},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/","open_access":"1"}],"publication":"Biophysical Journal","date_published":"2006-01-01T00:00:00Z","doi":"10.1529/biophysj.105.073353","day":"01","month":"01","intvolume":" 90","publisher":"Biophysical Society","status":"public","title":"Dynamical determinants of drug-inducible gene expression in a single bacterium","publication_status":"published","_id":"3755","year":"2006","volume":90,"date_created":"2018-12-11T12:04:59Z","date_updated":"2021-01-12T07:51:58Z","author":[{"first_name":"Thuc","last_name":"Le","full_name":"Le,Thuc T."},{"full_name":"Emonet,Thierry","last_name":"Emonet","first_name":"Thierry"},{"full_name":"Harlepp, Sébastien","first_name":"Sébastien","last_name":"Harlepp"},{"full_name":"Calin Guet","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"last_name":"Cluzel","first_name":"Philippe","full_name":"Cluzel,Philippe"}],"type":"journal_article","extern":1,"publist_id":"2472","issue":"9","abstract":[{"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.","lang":"eng"}]},{"citation":{"ama":"Wojtan C, Mucha P, Turk G. Keyframe control of complex particle systems using the adjoint method. In: ACM; 2006:15-23.","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.","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.","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.","short":"C. Wojtan, P. Mucha, G. Turk, in:, ACM, 2006, pp. 15–23.","mla":"Wojtan, Chris, et al. Keyframe Control of Complex Particle Systems Using the Adjoint Method. ACM, 2006, pp. 15–23.","chicago":"Wojtan, Chris, Peter Mucha, and Greg Turk. “Keyframe Control of Complex Particle Systems Using the Adjoint Method,” 15–23. ACM, 2006."},"main_file_link":[{"url":"http://www.amath.unc.edu/Faculty/mucha/Reprints/SCAclothcontrolpreprint.pdf"}],"page":"15 - 23","date_published":"2006-09-01T00:00:00Z","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation"},"language":[{"iso":"eng"}],"article_processing_charge":"No","month":"09","day":"01","_id":"3758","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2006","publisher":"ACM","publication_status":"published","title":"Keyframe control of complex particle systems using the adjoint method","status":"public","author":[{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mucha, Peter","first_name":"Peter","last_name":"Mucha"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"}],"oa_version":"None","date_created":"2018-12-11T12:05:00Z","date_updated":"2023-02-23T11:41:22Z","type":"conference","publist_id":"2469","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."}],"extern":"1"},{"month":"01","day":"01","publication":"Nature Protocols","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 ","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.","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 ","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.","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.","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 ."},"quality_controlled":0,"page":"2075 - 81","doi":"10.1038/nprot.2006.312 ","date_published":"2006-01-01T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"4","publist_id":"2392","extern":1,"year":"2006","_id":"3818","title":"Patch-clamp recording from mossy fiber terminals in hippocampal slices","status":"public","publication_status":"published","publisher":"Nature Publishing Group","intvolume":" 1","author":[{"last_name":"Bischofberger","first_name":"Josef","full_name":"Bischofberger, Josef"},{"last_name":"Engel","first_name":"Dominique","full_name":"Engel, Dominique"},{"full_name":"Li, Liyi","first_name":"Liyi","last_name":"Li"},{"full_name":"Geiger, Jörg R","last_name":"Geiger","first_name":"Jörg"},{"full_name":"Peter Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"date_created":"2018-12-11T12:05:20Z","date_updated":"2021-01-12T07:52:25Z","volume":1},{"quality_controlled":0,"page":"678 - 687","citation":{"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.","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.","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","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative concurrent parity games. SODA: Symposium on Discrete Algorithms, 678–687.","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.","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"},"conference":{"name":"SODA: Symposium on Discrete Algorithms"},"date_published":"2006-01-01T00:00:00Z","doi":"10.1145/1109557.1109631","day":"01","month":"01","publication_status":"published","title":"The complexity of quantitative concurrent parity games","status":"public","publisher":"SIAM","_id":"3890","year":"2006","acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610.","date_updated":"2021-01-12T07:52:59Z","date_created":"2018-12-11T12:05:43Z","author":[{"full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"De Alfaro","first_name":"Luca","full_name":"de Alfaro, Luca"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger"}],"type":"conference","extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2273"},{"publist_id":"2276","abstract":[{"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.","lang":"eng"}],"extern":1,"type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean"}],"volume":4207,"date_updated":"2021-01-12T07:52:59Z","date_created":"2018-12-11T12:05:43Z","year":"2006","_id":"3889","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.","publisher":"Springer","intvolume":" 4207","status":"public","title":"Algorithms for omega-regular games with imperfect information","publication_status":"published","day":"13","month":"11","doi":"10.1007/11874683_19","date_published":"2006-11-13T00:00:00Z","conference":{"name":"CSL: Computer Science Logic"},"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","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.","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.","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","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.","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."},"page":"287 - 302","quality_controlled":0},{"day":"28","month":"09","citation":{"chicago":"Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives,” 4207:256–70. Springer, 2006. https://doi.org/10.1007/11874683_17.","short":"K. Chatterjee, in:, Springer, 2006, pp. 256–270.","mla":"Chatterjee, Krishnendu. Concurrent Games with Tail Objectives. Vol. 4207, Springer, 2006, pp. 256–70, 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","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.","ama":"Chatterjee K. Concurrent games with tail objectives. In: Vol 4207. Springer; 2006:256-270. doi:10.1007/11874683_17"},"page":"256 - 270","quality_controlled":0,"date_published":"2006-09-28T00:00:00Z","doi":"10.1007/11874683_17","conference":{"name":"CSL: Computer Science Logic"},"type":"conference","alternative_title":["LNCS "],"publist_id":"2272","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)."}],"extern":1,"_id":"3891","year":"2006","publisher":"Springer","intvolume":" 4207","title":"Concurrent games with tail objectives","publication_status":"published","status":"public","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Krishnendu Chatterjee"}],"volume":4207,"date_created":"2018-12-11T12:05:44Z","date_updated":"2021-01-12T07:53:00Z"},{"title":"Strategy improvement for stochastic Rabin and Streett games","status":"public","publication_status":"published","intvolume":" 4137","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"3888","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.","year":"2006","date_created":"2018-12-11T12:05:43Z","date_updated":"2021-01-12T07:52:58Z","volume":4137,"author":[{"full_name":"Krishnendu Chatterjee","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Thomas Henzinger"}],"alternative_title":["LNCS"],"type":"conference","extern":1,"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."}],"publist_id":"2278","quality_controlled":0,"page":"375 - 389","citation":{"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","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.","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","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.","short":"K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 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."},"conference":{"name":"CONCUR: Concurrency Theory"},"doi":"10.1007/11817949_25","date_published":"2006-08-10T00:00:00Z","month":"08","day":"10"},{"oa_version":"None","volume":62,"date_updated":"2021-01-12T07:53:07Z","date_created":"2018-12-11T12:05:49Z","author":[{"last_name":"Ustinova","first_name":"Jana","full_name":"Ustinova, Jana"},{"full_name":"Achmann, Roland","last_name":"Achmann","first_name":"Roland"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"},{"first_name":"Frieder","last_name":"Mayer","full_name":"Mayer, Frieder"}],"intvolume":" 62","publisher":"Springer","publication_status":"published","status":"public","title":"Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3908","year":"2006","extern":"1","issue":"2","publist_id":"2242","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00239-005-0022-6","date_published":"2006-02-01T00:00:00Z","page":"158 - 167","citation":{"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","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.","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","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.","short":"J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution 62 (2006) 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."},"publication":"Journal of Molecular Evolution","day":"01","month":"02"},{"doi":"10.1242/jcs.02840","date_published":"2006-04-01T00:00:00Z","page":"1396 - 1405","quality_controlled":0,"citation":{"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.","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.","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.","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","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.","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"},"publication":"Journal of Cell Science","month":"04","day":"01","volume":119,"date_created":"2018-12-11T12:05:58Z","date_updated":"2021-01-12T07:53:18Z","author":[{"full_name":"Drumea-Mirancea, Mihaela","first_name":"Mihaela","last_name":"Drumea Mirancea"},{"first_name":"Johannes","last_name":"Wessels","full_name":"Wessels, Johannes T"},{"last_name":"Müller","first_name":"Claudia","full_name":"Müller, Claudia A"},{"last_name":"Essl","first_name":"Mike","full_name":"Essl, Mike"},{"full_name":"Eble, Johannes A","first_name":"Johannes","last_name":"Eble"},{"first_name":"Eva","last_name":"Tolosa","full_name":"Tolosa, Eva"},{"first_name":"Manuel","last_name":"Koch","full_name":"Koch, Manuel"},{"last_name":"Reinhardt","first_name":"Dieter","full_name":"Reinhardt, Dieter P"},{"full_name":"Michael Sixt","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sorokin","first_name":"Lydia","full_name":"Sorokin, Lydia"},{"full_name":"Stierhof, York-Dieter","first_name":"York","last_name":"Stierhof"},{"full_name":"Schwarz, Heinz","first_name":"Heinz","last_name":"Schwarz"},{"first_name":"Gerd","last_name":"Klein","full_name":"Klein, Gerd"}],"intvolume":" 119","publisher":"Company of Biologists","publication_status":"published","title":"Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules","status":"public","year":"2006","_id":"3934","extern":1,"issue":"Pt 7","publist_id":"2192","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."}],"type":"journal_article"},{"date_updated":"2021-01-12T07:53:18Z","date_created":"2018-12-11T12:05:58Z","volume":26,"author":[{"first_name":"Haiyan","last_name":"Chu","full_name":"Chu, Haiyan"},{"last_name":"Thievessen","first_name":"Ingo","full_name":"Thievessen, Ingo"},{"full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Lämmermann, Tim","last_name":"Lämmermann","first_name":"Tim"},{"full_name":"Waisman, Ari","first_name":"Ari","last_name":"Waisman"},{"full_name":"Braun, Attila","last_name":"Braun","first_name":"Attila"},{"full_name":"Noegel, Angelika A","first_name":"Angelika","last_name":"Noegel"},{"full_name":"Fässler, Reinhard","first_name":"Reinhard","last_name":"Fässler"}],"status":"public","publication_status":"published","title":"γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response","intvolume":" 26","publisher":"American Society for Microbiology","_id":"3935","year":"2006","extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2193","issue":"5","type":"journal_article","date_published":"2006-03-01T00:00:00Z","doi":"10.1128/MCB.26.5.1817-1825.2006","quality_controlled":0,"page":"1817 - 1825","publication":"Molecular and Cellular Biology","citation":{"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.","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.","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","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.","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","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."},"day":"01","month":"03"},{"month":"10","day":"01","date_published":"2006-10-01T00:00:00Z","doi":"10.1016/j.ceb.2006.08.007","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","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.","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","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.","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.","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."},"publication":"Current Opinion in Cell Biology","page":"482 - 490","quality_controlled":0,"publist_id":"2191","issue":"5","abstract":[{"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.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Michael Sixt"},{"full_name":"Bauer, Martina","first_name":"Martina","last_name":"Bauer"},{"first_name":"Tim","last_name":"Lämmermann","full_name":"Lämmermann, Tim"},{"last_name":"Fässler","first_name":"Reinhard","full_name":"Fässler, Reinhard"}],"volume":18,"date_updated":"2021-01-12T07:53:19Z","date_created":"2018-12-11T12:05:59Z","year":"2006","_id":"3936","intvolume":" 18","publisher":"Elsevier","title":"β1 integrins: zip codes and signaling relay for blood cells","status":"public","publication_status":"published"},{"article_processing_charge":"No","day":"04","month":"12","doi":"10.1083/jcb.200606017","date_published":"2006-12-04T00:00:00Z","language":[{"iso":"eng"}],"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","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.","short":"S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg, Journal of Cell Biology 175 (2006) 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.","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."},"publication":"Journal of Cell Biology","page":"791 - 802","publist_id":"1980","issue":"5","abstract":[{"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.","lang":"eng"}],"extern":"1","type":"journal_article","author":[{"last_name":"Witzel","first_name":"Sabine","full_name":"Witzel, Sabine"},{"last_name":"Zimyanin","first_name":"Vitaly","full_name":"Zimyanin, Vitaly"},{"first_name":"Filipa","last_name":"Carreira Barbosa","full_name":"Carreira Barbosa, Filipa"},{"first_name":"Masazumi","last_name":"Tada","full_name":"Tada, Masazumi"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"volume":175,"oa_version":"None","date_updated":"2021-01-12T07:54:48Z","date_created":"2018-12-11T12:07:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4140","year":"2006","intvolume":" 175","publisher":"Rockefeller University Press","publication_status":"published","title":"Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane","status":"public"},{"oa_version":"None","volume":41,"date_created":"2018-12-11T12:07:12Z","date_updated":"2021-01-12T07:54:50Z","author":[{"first_name":"Davide","last_name":"Tonelli","full_name":"Tonelli, Davide"},{"full_name":"Calegari, Frederico","first_name":"Frederico","last_name":"Calegari"},{"last_name":"Fei","first_name":"Ji","full_name":"Fei, Ji"},{"first_name":"Tadashi","last_name":"Nomura","full_name":"Nomura, Tadashi"},{"full_name":"Osumi, Noriko","last_name":"Osumi","first_name":"Noriko"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Huttner","first_name":"Wieland","full_name":"Huttner, Wieland"}],"intvolume":" 41","publisher":"Informa Healthcare","title":"Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid","status":"public","publication_status":"published","year":"2006","_id":"4145","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"6","publist_id":"1974","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.2144/000112296","date_published":"2006-12-01T00:00:00Z","page":"727 - 732","citation":{"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.","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.","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.","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","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.","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"},"publication":"Biotechniques","article_processing_charge":"No","day":"01","month":"12"}]