[{"issue":"6","date_published":"2010-06-01T00:00:00Z","volume":22,"doi":"10.1105/tpc.110.074195","date_created":"2018-12-11T12:01:13Z","page":"1749 - 1761","day":"01","publication":"Plant Cell","year":"2010","publication_status":"published","month":"06","intvolume":" 22","quality_controlled":0,"publisher":"American Society of Plant Biologists","abstract":[{"lang":"eng","text":"Auxin is an essential phytohormone that regulates many aspects of plant development. To identify new genes that function in auxin signaling, we performed a genetic screen for Arabidopsis thaliana mutants with an alteration in the expression of the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One of the mutants recovered in this screen, called weak auxin response1 (wxr1), has a defect in auxin response and exhibits a variety of auxin-related growth defects in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels in the root apex. In addition, the levels of the PIN auxin transport proteins are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2), a member of the broadly conserved DUF647 domain protein family found in diverse eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport and to maintain the normal levels of PIN proteins in the root."}],"title":"Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport","publist_id":"3628","author":[{"first_name":"Lei","last_name":"Ge","full_name":"Ge, Lei"},{"first_name":"Wendy","full_name":"Peer, Wendy A","last_name":"Peer"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"last_name":"Ye","full_name":"Ye, Songqing","first_name":"Songqing"},{"last_name":"Prigge","full_name":"Prigge, Michael J","first_name":"Michael"},{"full_name":"Cohen, Jerry D","last_name":"Cohen","first_name":"Jerry"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Angus","full_name":"Murphy, Angus S","last_name":"Murphy"},{"full_name":"Tang, Ding","last_name":"Tang","first_name":"Ding"},{"first_name":"Mark","full_name":"Estelle, Mark A","last_name":"Estelle"}],"extern":1,"date_updated":"2021-01-12T07:40:52Z","citation":{"ista":"Ge L, Peer W, Robert S, Swarup R, Ye S, Prigge M, Cohen J, Friml J, Murphy A, Tang D, Estelle M. 2010. Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport. Plant Cell. 22(6), 1749–1761.","chicago":"Ge, Lei, Wendy Peer, Stéphanie Robert, Ranjan Swarup, Songqing Ye, Michael Prigge, Jerry Cohen, et al. “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 Is Required for Polar Auxin Transport.” Plant Cell. American Society of Plant Biologists, 2010. https://doi.org/10.1105/tpc.110.074195.","ieee":"L. Ge et al., “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport,” Plant Cell, vol. 22, no. 6. American Society of Plant Biologists, pp. 1749–1761, 2010.","short":"L. Ge, W. Peer, S. Robert, R. Swarup, S. Ye, M. Prigge, J. Cohen, J. Friml, A. Murphy, D. Tang, M. Estelle, Plant Cell 22 (2010) 1749–1761.","apa":"Ge, L., Peer, W., Robert, S., Swarup, R., Ye, S., Prigge, M., … Estelle, M. (2010). Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.110.074195","ama":"Ge L, Peer W, Robert S, et al. Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport. Plant Cell. 2010;22(6):1749-1761. doi:10.1105/tpc.110.074195","mla":"Ge, Lei, et al. “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 Is Required for Polar Auxin Transport.” Plant Cell, vol. 22, no. 6, American Society of Plant Biologists, 2010, pp. 1749–61, doi:10.1105/tpc.110.074195."},"status":"public","type":"journal_article","_id":"3074"},{"abstract":[{"text":"Auxin is a multifunctional hormone essential for plant development and pattern formation. A nuclear auxin-signaling system controlling auxin-induced gene expression is well established, but cytoplasmic auxin signaling, as in its coordination of cell polarization, is unexplored. We found a cytoplasmic auxin-signaling mechanism that modulates the interdigitated growth of Arabidopsis leaf epidermal pavement cells (PCs), which develop interdigitated lobes and indentations to form a puzzle-piece shape in a two-dimensional plane. PC interdigitation is compromised in leaves deficient in either auxin biosynthesis or its export mediated by PINFORMED 1 localized at the lobe tip. Auxin coordinately activates two Rho GTPases, ROP2 and ROP6, which promote the formation of complementary lobes and indentations, respectively. Activation of these ROPs by auxin occurs within 30 s and depends on AUXIN-BINDING PROTEIN 1. These findings reveal Rho GTPase-based auxin-signaling mechanisms, which modulate the spatial coordination of cell expansion across a field of cells.","lang":"eng"}],"publisher":"Cell Press","quality_controlled":0,"month":"10","intvolume":" 143","year":"2010","publication_status":"published","day":"01","publication":"Cell","page":"99 - 110","date_published":"2010-10-01T00:00:00Z","volume":143,"issue":"1","doi":"10.1016/j.cell.2010.09.003","date_created":"2018-12-11T12:01:14Z","_id":"3076","type":"journal_article","status":"public","date_updated":"2021-01-12T07:40:53Z","citation":{"mla":"Xu, Tongda, et al. “Cell Surface- and Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis.” Cell, vol. 143, no. 1, Cell Press, 2010, pp. 99–110, doi:10.1016/j.cell.2010.09.003.","ama":"Xu T, Wen M, Nagawa S, et al. Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. Cell. 2010;143(1):99-110. doi:10.1016/j.cell.2010.09.003","apa":"Xu, T., Wen, M., Nagawa, S., Fu, Y., Chen, J., Wu, M., … Yang, Z. (2010). Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2010.09.003","short":"T. Xu, M. Wen, S. Nagawa, Y. Fu, J. Chen, M. Wu, C. Perrot Rechenmann, J. Friml, A. Jones, Z. Yang, Cell 143 (2010) 99–110.","ieee":"T. Xu et al., “Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis,” Cell, vol. 143, no. 1. Cell Press, pp. 99–110, 2010.","chicago":"Xu, Tongda, Mingzhang Wen, Shingo Nagawa, Ying Fu, Jin Chen, Ming Wu, Catherine Perrot Rechenmann, Jiří Friml, Alan Jones, and Zhenbiao Yang. “Cell Surface- and Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis.” Cell. Cell Press, 2010. https://doi.org/10.1016/j.cell.2010.09.003.","ista":"Xu T, Wen M, Nagawa S, Fu Y, Chen J, Wu M, Perrot Rechenmann C, Friml J, Jones A, Yang Z. 2010. Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. Cell. 143(1), 99–110."},"extern":1,"author":[{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"first_name":"Mingzhang","last_name":"Wen","full_name":"Wen, Mingzhang"},{"first_name":"Shingo","full_name":"Nagawa, Shingo","last_name":"Nagawa"},{"full_name":"Fu, Ying","last_name":"Fu","first_name":"Ying"},{"full_name":"Chen, Jin-Gui","last_name":"Chen","first_name":"Jin"},{"last_name":"Wu","full_name":"Wu, Ming-Jing","first_name":"Ming"},{"first_name":"Catherine","last_name":"Perrot Rechenmann","full_name":"Perrot-Rechenmann, Catherine"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Jones","full_name":"Jones, Alan M","first_name":"Alan"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"}],"publist_id":"3625","title":"Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis"},{"pmid":1,"oa_version":"Published Version","publisher":"American Society of Plant Biologists","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/20921163","open_access":"1"}],"oa":1,"month":"10","intvolume":" 154","publication_status":"published","year":"2010","day":"01","language":[{"iso":"eng"}],"publication":"Plant Physiology","page":"458 - 462","volume":154,"date_published":"2010-10-01T00:00:00Z","issue":"2","doi":"10.1104/pp.110.161380","date_created":"2018-12-11T12:01:14Z","_id":"3077","type":"journal_article","status":"public","date_updated":"2021-01-12T07:40:53Z","citation":{"chicago":"Friml, Jiří, and Angharad Jones. “Endoplasmic Reticulum: The Rising Compartment in Auxin Biology.” Plant Physiology. American Society of Plant Biologists, 2010. https://doi.org/10.1104/pp.110.161380.","ista":"Friml J, Jones A. 2010. Endoplasmic reticulum: The rising compartment in auxin biology. Plant Physiology. 154(2), 458–462.","mla":"Friml, Jiří, and Angharad Jones. “Endoplasmic Reticulum: The Rising Compartment in Auxin Biology.” Plant Physiology, vol. 154, no. 2, American Society of Plant Biologists, 2010, pp. 458–62, doi:10.1104/pp.110.161380.","apa":"Friml, J., & Jones, A. (2010). Endoplasmic reticulum: The rising compartment in auxin biology. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.110.161380","ama":"Friml J, Jones A. Endoplasmic reticulum: The rising compartment in auxin biology. Plant Physiology. 2010;154(2):458-462. doi:10.1104/pp.110.161380","short":"J. Friml, A. Jones, Plant Physiology 154 (2010) 458–462.","ieee":"J. Friml and A. Jones, “Endoplasmic reticulum: The rising compartment in auxin biology,” Plant Physiology, vol. 154, no. 2. American Society of Plant Biologists, pp. 458–462, 2010."},"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3624","author":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Angharad","full_name":"Jones, Angharad","last_name":"Jones"}],"external_id":{"pmid":["20921163"]},"title":"Endoplasmic reticulum: The rising compartment in auxin biology"},{"type":"journal_article","status":"public","_id":"3146","publist_id":"3550","author":[{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Simon Hippenmeyer","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"first_name":"Yong","full_name":"Youn, Yong H","last_name":"Youn"},{"full_name":"Moon, Hyang M","last_name":"Moon","first_name":"Hyang"},{"full_name":"Miyamichi, Kazunari","last_name":"Miyamichi","first_name":"Kazunari"},{"first_name":"Hui","full_name":"Zong, Hui","last_name":"Zong"},{"first_name":"Anthony","full_name":"Wynshaw-Boris, Anthony","last_name":"Wynshaw Boris"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"}],"title":"Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration","date_updated":"2021-01-12T07:41:22Z","citation":{"chicago":"Hippenmeyer, Simon, Yong Youn, Hyang Moon, Kazunari Miyamichi, Hui Zong, Anthony Wynshaw Boris, and Liqun Luo. “Genetic Mosaic Dissection of Lis1 and Ndel1 in Neuronal Migration.” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.09.027.","ista":"Hippenmeyer S, Youn Y, Moon H, Miyamichi K, Zong H, Wynshaw Boris A, Luo L. 2010. Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. Neuron. 68(4), 695–709.","mla":"Hippenmeyer, Simon, et al. “Genetic Mosaic Dissection of Lis1 and Ndel1 in Neuronal Migration.” Neuron, vol. 68, no. 4, Elsevier, 2010, pp. 695–709, doi:10.1016/j.neuron.2010.09.027.","short":"S. Hippenmeyer, Y. Youn, H. Moon, K. Miyamichi, H. Zong, A. Wynshaw Boris, L. Luo, Neuron 68 (2010) 695–709.","ieee":"S. Hippenmeyer et al., “Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration,” Neuron, vol. 68, no. 4. Elsevier, pp. 695–709, 2010.","apa":"Hippenmeyer, S., Youn, Y., Moon, H., Miyamichi, K., Zong, H., Wynshaw Boris, A., & Luo, L. (2010). Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.09.027","ama":"Hippenmeyer S, Youn Y, Moon H, et al. Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. Neuron. 2010;68(4):695-709. doi:10.1016/j.neuron.2010.09.027"},"extern":1,"quality_controlled":0,"publisher":"Elsevier","intvolume":" 68","month":"11","abstract":[{"text":"Coordinated migration of newly born neurons to their prospective target laminae is a prerequisite for neural circuit assembly in the developing brain. The evolutionarily conserved LIS1/NDEL1 complex is essential for neuronal migration in the mammalian cerebral cortex. The cytoplasmic nature of LIS1 and NDEL1 proteins suggest that they regulate neuronal migration cell autonomously. Here, we extend mosaic analysis with double markers (MADM) to mouse chromosome 11 where Lis1, Ndel1, and 14-3-3e{open} (encoding a LIS1/NDEL1 signaling partner) are located. Analyses of sparse and uniquely labeled mutant cells in mosaic animals reveal distinct cell-autonomous functions for these three genes. Lis1 regulates neuronal migration efficiency in a dose-dependent manner, while Ndel1 is essential for a specific, previously uncharacterized, late step of neuronal migration: entry into the target lamina. Comparisons with previous genetic perturbations of Lis1 and Ndel1 also suggest a surprising degree of cell-nonautonomous function for these proteins in regulating neuronal migration.","lang":"eng"}],"page":"695 - 709","date_created":"2018-12-11T12:01:39Z","issue":"4","date_published":"2010-11-18T00:00:00Z","volume":68,"doi":"10.1016/j.neuron.2010.09.027","publication_status":"published","year":"2010","publication":"Neuron","day":"18"},{"title":"A faster algorithm for computing the principal sequence of partitions of a graph","publist_id":"3480","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"}],"extern":1,"citation":{"ista":"Kolmogorov V. 2010. A faster algorithm for computing the principal sequence of partitions of a graph. Algorithmica. 56(4), 394–412.","chicago":"Kolmogorov, Vladimir. “A Faster Algorithm for Computing the Principal Sequence of Partitions of a Graph.” Algorithmica. Springer, 2010. https://doi.org/10.1007/s00453-008-9177-z.","ieee":"V. Kolmogorov, “A faster algorithm for computing the principal sequence of partitions of a graph,” Algorithmica, vol. 56, no. 4. Springer, pp. 394–412, 2010.","short":"V. Kolmogorov, Algorithmica 56 (2010) 394–412.","apa":"Kolmogorov, V. (2010). A faster algorithm for computing the principal sequence of partitions of a graph. Algorithmica. Springer. https://doi.org/10.1007/s00453-008-9177-z","ama":"Kolmogorov V. A faster algorithm for computing the principal sequence of partitions of a graph. Algorithmica. 2010;56(4):394-412. doi:10.1007/s00453-008-9177-z","mla":"Kolmogorov, Vladimir. “A Faster Algorithm for Computing the Principal Sequence of Partitions of a Graph.” Algorithmica, vol. 56, no. 4, Springer, 2010, pp. 394–412, doi:10.1007/s00453-008-9177-z."},"date_updated":"2021-01-12T07:41:46Z","status":"public","type":"journal_article","_id":"3202","date_created":"2018-12-11T12:01:59Z","volume":56,"date_published":"2010-04-01T00:00:00Z","doi":"10.1007/s00453-008-9177-z","issue":"4","page":"394 - 412","publication":"Algorithmica","day":"01","year":"2010","publication_status":"published","intvolume":" 56","month":"04","quality_controlled":0,"publisher":"Springer","abstract":[{"lang":"eng","text":"We consider the following problem: given an undirected weighted graph G = (V,E,c) with nonnegative weights, minimize function c(δ(Π))- λ|Π| for all values of parameter λ. Here Π is a partition of the set of nodes, the first term is the cost of edges whose endpoints belong to different components of the partition, and |Π| is the number of components. The current best known algorithm for this problem has complexity O(|V| 2) maximum flow computations. We improve it to |V| parametric maximum flow computations. We observe that the complexity can be improved further for families of graphs which admit a good separator, e.g. for planar graphs."}]},{"month":"02","quality_controlled":"1","scopus_import":"1","publisher":"Society for Industrial and Applied Mathematics","acknowledgement":"Partially supported by the Austrian Science Fund under grantFSP-S9103-N04 and P20134-N13.","oa_version":"None","abstract":[{"text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field.","lang":"eng"}],"date_created":"2022-03-21T08:24:07Z","date_published":"2010-02-01T00:00:00Z","doi":"10.1137/1.9781611973075.129","related_material":{"record":[{"relation":"later_version","status":"public","id":"3267"}]},"page":"1594-1604","publication":"Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2010","publication_identifier":{"eisbn":["9781611973075"]},"status":"public","conference":{"end_date":"2010-01-19","location":"Austin, TX, United States","start_date":"2010-01-17","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","_id":"10909","title":"Hardness results for homology localization","department":[{"_id":"HeEd"}],"article_processing_charge":"No","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen","full_name":"Chen, Chao"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, 1594–1604. Society for Industrial and Applied Mathematics, 2010. https://doi.org/10.1137/1.9781611973075.129.","ista":"Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1594–1604.","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:10.1137/1.9781611973075.129.","ama":"Chen C, Freedman D. Hardness results for homology localization. In: Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2010:1594-1604. doi:10.1137/1.9781611973075.129","apa":"Chen, C., & Freedman, D. (2010). Hardness results for homology localization. In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973075.129","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” in Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Austin, TX, United States, 2010, pp. 1594–1604.","short":"C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–1604."},"date_updated":"2023-02-23T11:19:46Z"},{"intvolume":" 186","month":"12","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. ","lang":"eng"}],"ec_funded":1,"issue":"4","volume":186,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"3303","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:42:31Z","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","date_created":"2018-12-11T12:02:33Z","date_published":"2010-12-01T00:00:00Z","doi":"10.1534/genetics.110.123240","page":"1389 - 1410","publication":"Genetics","day":"01","year":"2010","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"title":"The rate of fitness-valley crossing in sexual populations","publist_id":"3337","author":[{"first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","full_name":"Weissman, Daniel"},{"last_name":"Feldman","full_name":"Feldman, Marcus","first_name":"Marcus"},{"full_name":"Fisher, Daniel","last_name":"Fisher","first_name":"Daniel"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:10.1534/genetics.110.123240.","apa":"Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.110.123240","ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240","ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010.","short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics. Genetics Society of America, 2010. https://doi.org/10.1534/genetics.110.123240.","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410."}},{"extern":1,"citation":{"apa":"Janovjak, H. L., Szobota, S., Wyart, C., Trauner, D., & Isacoff, E. (2010). A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2589","ama":"Janovjak HL, Szobota S, Wyart C, Trauner D, Isacoff E. A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing. Nature Neuroscience. 2010;13:1027-1032. doi:10.1038/nn.2589","short":"H.L. Janovjak, S. Szobota, C. Wyart, D. Trauner, E. Isacoff, Nature Neuroscience 13 (2010) 1027–1032.","ieee":"H. L. Janovjak, S. Szobota, C. Wyart, D. Trauner, and E. Isacoff, “A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing,” Nature Neuroscience, vol. 13. Nature Publishing Group, pp. 1027–1032, 2010.","mla":"Janovjak, Harald L., et al. “A Light-Gated, Potassium-Selective Glutamate Receptor for the Optical Inhibition of Neuronal Firing.” Nature Neuroscience, vol. 13, Nature Publishing Group, 2010, pp. 1027–32, doi:10.1038/nn.2589.","ista":"Janovjak HL, Szobota S, Wyart C, Trauner D, Isacoff E. 2010. A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing. Nature Neuroscience. 13, 1027–1032.","chicago":"Janovjak, Harald L, Stephanie Szobota, Claire Wyart, Dirk Trauner, and Ehud Isacoff. “A Light-Gated, Potassium-Selective Glutamate Receptor for the Optical Inhibition of Neuronal Firing.” Nature Neuroscience. Nature Publishing Group, 2010. https://doi.org/10.1038/nn.2589."},"date_updated":"2021-01-12T07:43:16Z","title":"A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing","author":[{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"first_name":"Stephanie","full_name":"Szobota, Stephanie","last_name":"Szobota"},{"full_name":"Wyart, Claire","last_name":"Wyart","first_name":"Claire"},{"first_name":"Dirk","last_name":"Trauner","full_name":"Trauner, Dirk"},{"first_name":"Ehud","last_name":"Isacoff","full_name":"Isacoff, Ehud Y"}],"publist_id":"2995","_id":"3407","status":"public","type":"journal_article","day":"27","publication":"Nature Neuroscience","publication_status":"published","year":"2010","date_published":"2010-06-27T00:00:00Z","volume":13,"doi":"10.1038/nn.2589","date_created":"2018-12-11T12:03:10Z","page":"1027 - 1032","abstract":[{"text":"Genetically targeted light-activated ion channels and pumps make it possible to determine the role of specific neurons in neuronal circuits, information processing and behavior. We developed a K+-selective ionotropic glutamate receptor that reversibly inhibits neuronal activity in response to light in dissociated neurons and brain slice and also reversibly suppresses behavior in zebrafish. The receptor is a chimera of the pore region of a K+-selective bacterial glutamate receptor and the ligand-binding domain of a light-gated mammalian kainate receptor. This hyperpolarizing light-gated channel, HyLighter, is turned on by a brief light pulse at one wavelength and turned off by a pulse at a second wavelength. The control is obtained at moderate intensity. After optical activation, the photocurrent and optical silencing of activity persists in the dark for extended periods. The low light requirement and bi-stability of HyLighter represent advantages for the dissection of neural circuitry.","lang":"eng"}],"month":"06","intvolume":" 13","quality_controlled":0,"publisher":"Nature Publishing Group"},{"_id":"3406","type":"review","status":"public","citation":{"ista":"Stawski P, Janovjak HL, Trauner D. 2010. Pharmacology of ionotropic glutamate receptors: a structural perspective. Bioorganic and Medicinal Chemistry. 18(22), 7759–7772.","chicago":"Stawski, Philipp, Harald L Janovjak, and Dirk Trauner. “Pharmacology of Ionotropic Glutamate Receptors: A Structural Perspective.” Bioorganic and Medicinal Chemistry. Elsevier, 2010. https://doi.org/10.1016/j.bmc.2010.09.012.","ama":"Stawski P, Janovjak HL, Trauner D. Pharmacology of ionotropic glutamate receptors: a structural perspective. Bioorganic and Medicinal Chemistry. 2010;18(22):7759-7772. doi:10.1016/j.bmc.2010.09.012","apa":"Stawski, P., Janovjak, H. L., & Trauner, D. (2010). Pharmacology of ionotropic glutamate receptors: a structural perspective. Bioorganic and Medicinal Chemistry. Elsevier. https://doi.org/10.1016/j.bmc.2010.09.012","short":"P. Stawski, H.L. Janovjak, D. Trauner, Bioorganic and Medicinal Chemistry 18 (2010) 7759–7772.","ieee":"P. Stawski, H. L. Janovjak, and D. Trauner, “Pharmacology of ionotropic glutamate receptors: a structural perspective,” Bioorganic and Medicinal Chemistry, vol. 18, no. 22. Elsevier, pp. 7759–7772, 2010.","mla":"Stawski, Philipp, et al. “Pharmacology of Ionotropic Glutamate Receptors: A Structural Perspective.” Bioorganic and Medicinal Chemistry, vol. 18, no. 22, Elsevier, 2010, pp. 7759–72, doi:10.1016/j.bmc.2010.09.012."},"date_updated":"2019-04-26T07:22:27Z","extern":1,"publist_id":"2996","author":[{"first_name":"Philipp","last_name":"Stawski","full_name":"Stawski, Philipp"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"first_name":"Dirk","full_name":"Trauner, Dirk","last_name":"Trauner"}],"title":"Pharmacology of ionotropic glutamate receptors: a structural perspective","abstract":[{"text":"The impact of structural biology on the design of ligands (agonists, antagonists and modulators) for ionotropic glutamate receptors is reviewed.","lang":"eng"}],"publisher":"Elsevier","quality_controlled":0,"month":"11","intvolume":" 18","year":"2010","publication_status":"published","day":"15","publication":"Bioorganic and Medicinal Chemistry","page":"7759 - 7772","volume":18,"date_published":"2010-11-15T00:00:00Z","doi":"10.1016/j.bmc.2010.09.012","issue":"22","date_created":"2018-12-11T12:03:10Z"},{"extern":1,"date_updated":"2021-01-12T07:43:29Z","citation":{"chicago":"Dupret, David, Joseph O’Neill, Barty Pleydell Bouverie, and Jozsef L Csicsvari. “The Reorganization and Reactivation of Hippocampal Maps Predict Spatial Memory Performance.” Nature Neuroscience. Nature Publishing Group, 2010. https://doi.org/10.1038/nn.2599.","ista":"Dupret D, O’Neill J, Pleydell Bouverie B, Csicsvari JL. 2010. The reorganization and reactivation of hippocampal maps predict spatial memory performance. Nature Neuroscience. 13(8), 995–1002.","mla":"Dupret, David, et al. “The Reorganization and Reactivation of Hippocampal Maps Predict Spatial Memory Performance.” Nature Neuroscience, vol. 13, no. 8, Nature Publishing Group, 2010, pp. 995–1002, doi:10.1038/nn.2599.","short":"D. Dupret, J. O’Neill, B. Pleydell Bouverie, J.L. Csicsvari, Nature Neuroscience 13 (2010) 995–1002.","ieee":"D. Dupret, J. O’Neill, B. Pleydell Bouverie, and J. L. Csicsvari, “The reorganization and reactivation of hippocampal maps predict spatial memory performance,” Nature Neuroscience, vol. 13, no. 8. Nature Publishing Group, pp. 995–1002, 2010.","ama":"Dupret D, O’Neill J, Pleydell Bouverie B, Csicsvari JL. The reorganization and reactivation of hippocampal maps predict spatial memory performance. Nature Neuroscience. 2010;13(8):995-1002. doi:10.1038/nn.2599","apa":"Dupret, D., O’Neill, J., Pleydell Bouverie, B., & Csicsvari, J. L. (2010). The reorganization and reactivation of hippocampal maps predict spatial memory performance. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2599"},"title":"The reorganization and reactivation of hippocampal maps predict spatial memory performance","publist_id":"2946","author":[{"full_name":"Dupret, David","last_name":"Dupret","first_name":"David"},{"first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","full_name":"Joseph O'Neill"},{"first_name":"Barty","last_name":"Pleydell Bouverie","full_name":"Pleydell-Bouverie, Barty"},{"last_name":"Csicsvari","full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"}],"_id":"3441","status":"public","type":"journal_article","day":"01","publication":"Nature Neuroscience","publication_status":"published","year":"2010","doi":"10.1038/nn.2599","volume":13,"date_published":"2010-08-01T00:00:00Z","issue":"8","date_created":"2018-12-11T12:03:21Z","page":"995 - 1002","acknowledgement":"Discussed in the News and Views section of the journal by Jeffery and Cacucci\n","abstract":[{"lang":"eng","text":"The hippocampus is an important brain circuit for spatial memory and the spatially selective spiking of hippocampal neuronal assemblies is thought to provide a mnemonic representation of space. We found that remembering newly learnt goal locations required NMDA receptorĝ€"dependent stabilization and enhanced reactivation of goal-related hippocampal assemblies. During spatial learning, place-related firing patterns in the CA1, but not CA3, region of the rat hippocampus were reorganized to represent new goal locations. Such reorganization did not occur when goals were marked by visual cues. The stabilization and successful retrieval of these newly acquired CA1 representations of behaviorally relevant places was NMDAR dependent and necessary for subsequent memory retention performance. Goal-related assembly patterns associated with sharp wave/ripple network oscillations, during both learning and subsequent rest periods, predicted memory performance. Together, these results suggest that the reorganization and reactivation of assembly firing patterns in the hippocampus represent the formation and expression of new spatial memory traces. © 2010 Nature America, Inc. All rights reserved."}],"month":"08","intvolume":" 13","quality_controlled":0,"publisher":"Nature Publishing Group"},{"month":"05","intvolume":" 33","quality_controlled":0,"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Episodic and spatial memories each involve the encoding of complex associations in hippocampal neuronal circuits. Such memory traces could be stabilised from short- to long-term forms by consolidation processes involving the 'reactivation' of the original network firing patterns during sleep and rest. Waking experience can be replayed in many different brain areas, but an important role for the hippocampus lies in the organisation of the 'reactivation' process. Emerging evidence suggests that sharp wave/ripple (SWR) events in the hippocampus could coordinate the reactivation of memory traces and direct their reinstatement in cortical circuits. Although the mechanisms remain uncertain, there is a growing consensus that such SWR-directed reactivation of brain-wide memory traces could underlie memory consolidation. © 2010 Elsevier Ltd."}],"doi":"10.1016/j.tins.2010.01.006","volume":33,"issue":"5","date_published":"2010-05-01T00:00:00Z","date_created":"2018-12-11T12:03:21Z","page":"220 - 229","day":"01","publication":"Trends in Neurosciences","year":"2010","publication_status":"published","status":"public","type":"journal_article","_id":"3442","title":"Play it again: reactivation of waking experience and memory","author":[{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","full_name":"Joseph O'Neill","last_name":"O'Neill"},{"first_name":"Barty","full_name":"Pleydell-Bouverie, Barty","last_name":"Pleydell Bouverie"},{"first_name":"David","full_name":"Dupret, David","last_name":"Dupret"},{"last_name":"Csicsvari","full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2945","extern":1,"date_updated":"2021-01-12T07:43:29Z","citation":{"ista":"O’Neill J, Pleydell Bouverie B, Dupret D, Csicsvari JL. 2010. Play it again: reactivation of waking experience and memory. Trends in Neurosciences. 33(5), 220–229.","chicago":"O’Neill, Joseph, Barty Pleydell Bouverie, David Dupret, and Jozsef L Csicsvari. “Play It Again: Reactivation of Waking Experience and Memory.” Trends in Neurosciences. Elsevier, 2010. https://doi.org/10.1016/j.tins.2010.01.006.","ieee":"J. O’Neill, B. Pleydell Bouverie, D. Dupret, and J. L. Csicsvari, “Play it again: reactivation of waking experience and memory,” Trends in Neurosciences, vol. 33, no. 5. Elsevier, pp. 220–229, 2010.","short":"J. O’Neill, B. Pleydell Bouverie, D. Dupret, J.L. Csicsvari, Trends in Neurosciences 33 (2010) 220–229.","ama":"O’Neill J, Pleydell Bouverie B, Dupret D, Csicsvari JL. Play it again: reactivation of waking experience and memory. Trends in Neurosciences. 2010;33(5):220-229. doi:10.1016/j.tins.2010.01.006","apa":"O’Neill, J., Pleydell Bouverie, B., Dupret, D., & Csicsvari, J. L. (2010). Play it again: reactivation of waking experience and memory. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2010.01.006","mla":"O’Neill, Joseph, et al. “Play It Again: Reactivation of Waking Experience and Memory.” Trends in Neurosciences, vol. 33, no. 5, Elsevier, 2010, pp. 220–29, doi:10.1016/j.tins.2010.01.006."}},{"editor":[{"last_name":"Schmidt","full_name":"Schmidt, R. F.","first_name":"R."},{"full_name":"Heckmann, M.","last_name":"Heckmann","first_name":"M."},{"last_name":"Lang","full_name":"Lang, Florian","first_name":"Florian"}],"title":"Grundlagen zellulärer Erregbarkeit","author":[{"last_name":"Fakler","full_name":"Fakler, Bernd","first_name":"Bernd"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"publist_id":"2928","extern":1,"date_updated":"2021-01-12T07:43:35Z","citation":{"ista":"Fakler B, Jonas PM. 2010.Grundlagen zellulärer Erregbarkeit. In: Physiologie Des Menschen. .","chicago":"Fakler, Bernd, and Peter M Jonas. “Grundlagen Zellulärer Erregbarkeit.” In Physiologie Des Menschen, edited by R. Schmidt, M. Heckmann, and Florian Lang. Springer, 2010.","short":"B. Fakler, P.M. Jonas, in:, R. Schmidt, M. Heckmann, F. Lang (Eds.), Physiologie Des Menschen, Springer, 2010.","ieee":"B. Fakler and P. M. Jonas, “Grundlagen zellulärer Erregbarkeit,” in Physiologie Des Menschen, R. Schmidt, M. Heckmann, and F. Lang, Eds. Springer, 2010.","ama":"Fakler B, Jonas PM. Grundlagen zellulärer Erregbarkeit. In: Schmidt R, Heckmann M, Lang F, eds. Physiologie Des Menschen. Springer; 2010.","apa":"Fakler, B., & Jonas, P. M. (2010). Grundlagen zellulärer Erregbarkeit. In R. Schmidt, M. Heckmann, & F. Lang (Eds.), Physiologie Des Menschen. Springer.","mla":"Fakler, Bernd, and Peter M. Jonas. “Grundlagen Zellulärer Erregbarkeit.” Physiologie Des Menschen, edited by R. Schmidt et al., Springer, 2010."},"status":"public","type":"book_chapter","_id":"3459","date_created":"2018-12-11T12:03:26Z","date_published":"2010-01-01T00:00:00Z","publication":"Physiologie Des Menschen","day":"01","year":"2010","publication_status":"published","month":"01","publisher":"Springer","quality_controlled":0},{"type":"journal_article","status":"public","_id":"3538","publist_id":"2848","author":[{"first_name":"Premysl","full_name":"Jiruska, Premysl","last_name":"Jiruska"},{"last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"},{"first_name":"Andrew","full_name":"Powell, Andrew","last_name":"Powell"},{"last_name":"Fox","full_name":"Fox, John","first_name":"John"},{"last_name":"Chang","full_name":"Chang, Wei","first_name":"Wei"},{"full_name":"Vreugdenhil, Martin","last_name":"Vreugdenhil","first_name":"Martin"},{"first_name":"Xiaoli","last_name":"Li","full_name":"Li, Xiaoli"},{"first_name":"Milan","last_name":"Palus","full_name":"Palus, Milan"},{"first_name":"Alejandro","last_name":"Bujan","full_name":"Bujan, Alejandro"},{"full_name":"Dearden, Richard","last_name":"Dearden","first_name":"Richard"},{"last_name":"Jefferys","full_name":"Jefferys, John","first_name":"John"}],"title":"High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro","date_updated":"2021-01-12T07:44:10Z","citation":{"mla":"Jiruska, Premysl, et al. “High-Frequency Network Activity, Global Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.” Journal of Neuroscience, vol. 30, no. 16, Society for Neuroscience, 2010, pp. 5690–701, doi:10.1523/JNEUROSCI.0535-10.2010.","ama":"Jiruska P, Csicsvari JL, Powell A, et al. High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. Journal of Neuroscience. 2010;30(16):5690-5701. doi:10.1523/JNEUROSCI.0535-10.2010","apa":"Jiruska, P., Csicsvari, J. L., Powell, A., Fox, J., Chang, W., Vreugdenhil, M., … Jefferys, J. (2010). High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0535-10.2010","short":"P. Jiruska, J.L. Csicsvari, A. Powell, J. Fox, W. Chang, M. Vreugdenhil, X. Li, M. Palus, A. Bujan, R. Dearden, J. Jefferys, Journal of Neuroscience 30 (2010) 5690–5701.","ieee":"P. Jiruska et al., “High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro,” Journal of Neuroscience, vol. 30, no. 16. Society for Neuroscience, pp. 5690–5701, 2010.","chicago":"Jiruska, Premysl, Jozsef L Csicsvari, Andrew Powell, John Fox, Wei Chang, Martin Vreugdenhil, Xiaoli Li, et al. “High-Frequency Network Activity, Global Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.” Journal of Neuroscience. Society for Neuroscience, 2010. https://doi.org/10.1523/JNEUROSCI.0535-10.2010.","ista":"Jiruska P, Csicsvari JL, Powell A, Fox J, Chang W, Vreugdenhil M, Li X, Palus M, Bujan A, Dearden R, Jefferys J. 2010. High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. Journal of Neuroscience. 30(16), 5690–5701."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","main_file_link":[{"open_access":"1","url":"http://www.jneurosci.org/content/30/16/5690"}],"oa":1,"quality_controlled":"1","publisher":"Society for Neuroscience","intvolume":" 30","month":"04","abstract":[{"text":"How seizures start is a major question in epilepsy research. Preictal EEG changes occur in both human patients and animal models, but their underlying mechanisms and relationship with seizure initiation remain unknown. Here we demonstrate the existence, in the hippocampal CA1 region, of a preictal state characterized by the progressive and global increase in neuronal activity associated with a widespread buildup of low-amplitude high-frequency activity (HFA) (> 100 Hz) and reduction in system complexity. HFA is generated by the firing of neurons, mainly pyramidal cells, at much lower frequencies. Individual cycles of HFA are generated by the near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization; the presence of very similar HFA in the high-potassium model shows that it does not depend on an absence of synaptic transmission. Immediately before seizure onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing perturbations can trigger seizures. Transition to seizure is characterized by a rapid expansion and fusion of the neuronal populations responsible for HFA, associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous cluster generating the high-amplitude low-frequency activity of the seizure.","lang":"eng"}],"oa_version":"None","page":"5690 - 5701","date_created":"2018-12-11T12:03:51Z","doi":"10.1523/JNEUROSCI.0535-10.2010","date_published":"2010-04-21T00:00:00Z","issue":"16","volume":30,"year":"2010","publication_status":"published","language":[{"iso":"eng"}],"publication":"Journal of Neuroscience","day":"21"},{"quality_controlled":"1","scopus_import":1,"publisher":"Wiley-Blackwell","month":"03","intvolume":" 19","abstract":[{"text":"We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales.","lang":"eng"}],"oa_version":"None","page":"910 - 924","issue":"5","volume":19,"doi":"10.1111/j.1365-294X.2009.04497.x","date_published":"2010-03-01T00:00:00Z","date_created":"2018-12-11T12:04:12Z","year":"2010","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Molecular Ecology","type":"journal_article","status":"public","_id":"3604","publist_id":"2779","author":[{"first_name":"Helen","full_name":"Senn, Helen","last_name":"Senn"},{"first_name":"Simon","full_name":"Goodman, Simon","last_name":"Goodman"},{"first_name":"Graeme","last_name":"Swanson","full_name":"Swanson, Graeme"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josephine","full_name":"Pemberton, Josephine","last_name":"Pemberton"}],"department":[{"_id":"NiBa"}],"title":"Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland","citation":{"chicago":"Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-294X.2009.04497.x.","ista":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 19(5), 910–924.","mla":"Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x.","short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924.","ieee":"H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,” Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.","ama":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x","apa":"Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010). Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x"},"date_updated":"2021-01-12T07:44:36Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"month":"09","intvolume":" 64","quality_controlled":0,"publisher":"Wiley-Blackwell","abstract":[{"lang":"eng","text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci."}],"doi":"10.1111/j.1558-5646.2010.01019.x","issue":"9","volume":64,"date_published":"2010-09-01T00:00:00Z","date_created":"2018-12-11T12:04:11Z","page":"2701 - 2715","day":"01","publication":"Evolution; International Journal of Organic Evolution","publication_status":"published","year":"2010","status":"public","type":"journal_article","_id":"3603","title":"A new model for large-scale population dynamics: quantifying phylogeography ","publist_id":"2780","author":[{"full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison M"}],"extern":1,"date_updated":"2021-01-12T07:44:36Z","citation":{"short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution; International Journal of Organic Evolution 64 (2010) 2701–2715.","ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for large-scale population dynamics: quantifying phylogeography ,” Evolution; International Journal of Organic Evolution, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","ama":"Barton NH, Kelleher J, Etheridge A. A new model for large-scale population dynamics: quantifying phylogeography . Evolution; International Journal of Organic Evolution. 2010;64(9):2701-2715. doi:10.1111/j.1558-5646.2010.01019.x","apa":"Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for large-scale population dynamics: quantifying phylogeography . Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x","mla":"Barton, Nicholas H., et al. “A New Model for Large-Scale Population Dynamics: Quantifying Phylogeography .” Evolution; International Journal of Organic Evolution, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.","ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for large-scale population dynamics: quantifying phylogeography . Evolution; International Journal of Organic Evolution. 64(9), 2701–2715.","chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Large-Scale Population Dynamics: Quantifying Phylogeography .” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x."}},{"date_updated":"2021-01-12T07:48:57Z","citation":{"ieee":"S. Nowozin and C. Lampert, “Global interactions in random field models: A potential function ensuring connectedness,” SIAM Journal on Imaging Sciences, vol. 3, no. 4 (Special Section on Optimization in Imaging Sciences). Society for Industrial and Applied Mathematics , pp. 1048–1074, 2010.","short":"S. Nowozin, C. Lampert, SIAM Journal on Imaging Sciences 3 (2010) 1048–1074.","apa":"Nowozin, S., & Lampert, C. (2010). Global interactions in random field models: A potential function ensuring connectedness. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/090752614","ama":"Nowozin S, Lampert C. Global interactions in random field models: A potential function ensuring connectedness. SIAM Journal on Imaging Sciences. 2010;3(4 (Special Section on Optimization in Imaging Sciences)):1048-1074. doi:10.1137/090752614","mla":"Nowozin, Sebastian, and Christoph Lampert. “Global Interactions in Random Field Models: A Potential Function Ensuring Connectedness.” SIAM Journal on Imaging Sciences, vol. 3, no. 4 (Special Section on Optimization in Imaging Sciences), Society for Industrial and Applied Mathematics , 2010, pp. 1048–74, doi:10.1137/090752614.","ista":"Nowozin S, Lampert C. 2010. Global interactions in random field models: A potential function ensuring connectedness. SIAM Journal on Imaging Sciences. 3(4 (Special Section on Optimization in Imaging Sciences)), 1048–1074.","chicago":"Nowozin, Sebastian, and Christoph Lampert. “Global Interactions in Random Field Models: A Potential Function Ensuring Connectedness.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics , 2010. https://doi.org/10.1137/090752614."},"extern":1,"author":[{"first_name":"Sebastian","last_name":"Nowozin","full_name":"Nowozin, Sebastian"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"publist_id":"2684","title":"Global interactions in random field models: A potential function ensuring connectedness","_id":"3686","type":"journal_article","status":"public","year":"2010","publication_status":"published","publication":"SIAM Journal on Imaging Sciences","day":"21","page":"1048 - 1074","date_created":"2018-12-11T12:04:37Z","doi":"10.1137/090752614","volume":3,"issue":"4 (Special Section on Optimization in Imaging Sciences)","date_published":"2010-12-21T00:00:00Z","abstract":[{"lang":"eng","text":"Markov random field (MRF) models, including conditional random field models, are popular in computer vision. However, in order to be computationally tractable, they are limited to incorporating only local interactions and cannot model global properties such as connectedness, which is a potentially useful high-level prior for object segmentation. In this work, we overcome this limitation by deriving a potential function that forces the output labeling to be connected and that can naturally be used in the framework of recent maximum a posteriori (MAP)-MRF linear program (LP) relaxations. Using techniques from polyhedral combinatorics, we show that a provably strong approximation to the MAP solution of the resulting MRF can still be found efficiently by solving a sequence of max-flow problems. The efficiency of the inference procedure also allows us to learn the parameters of an MRF with global connectivity potentials by means of a cutting plane algorithm. We experimentally evaluate our algorithm on both synthetic data and on the challenging image segmentation task of the PASCAL Visual Object Classes 2008 data set. We show that in both cases the addition of a connectedness prior significantly reduces the segmentation error.\n\n\n"}],"acknowledgement":"This work was funded in part by the EU CLASS project, IST 027978. This work was also supported in part by the IST Programme of the European Community under the PASCAL Network of Excellence, IST-2002-506778.","quality_controlled":0,"publisher":"Society for Industrial and Applied Mathematics ","intvolume":" 3","month":"12"},{"abstract":[{"text":"For object category recognition to scale beyond a small number of classes, it is important that algorithms be able to learn from a small amount of labeled data per additional class. One-shot recognition aims to apply the knowledge gained from a set of categories with plentiful data to categories for which only a single exemplar is available for each. As with earlier efforts motivated by transfer learning, we seek an internal representation for the domain that generalizes across classes. However, in contrast to existing work, we formulate the problem in a fundamentally new manner by optimizing the internal representation for the one-shot task using the notion of micro-sets. A micro-set is a sample of data that contains only a single instance of each category, sampled from the pool of available data, which serves as a mechanism to force the learned representation to explicitly address the variability and noise inherent in the one-shot recognition task. We optimize our learned domain features so that they minimize an expected loss over micro-sets drawn from the training set and show that these features generalize effectively to previously unseen categories. We detail a discriminative approach for optimizing one-shot recognition using micro-sets and present experiments on the Animals with Attributes and Caltech-101 datasets that demonstrate the benefits of our formulation.","lang":"eng"}],"month":"06","publisher":"IEEE","quality_controlled":0,"day":"18","year":"2010","publication_status":"published","date_created":"2018-12-11T12:04:36Z","doi":"10.1109/CVPR.2010.5540053","date_published":"2010-06-18T00:00:00Z","page":"3027 - 3034","_id":"3682","status":"public","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","extern":1,"date_updated":"2021-01-12T07:45:06Z","citation":{"mla":"Tang, Kevin, et al. Optimizing One-Shot Recognition with Micro-Set Learning. IEEE, 2010, pp. 3027–34, doi:10.1109/CVPR.2010.5540053.","short":"K. Tang, M. Tappen, R. Sukthankar, C. Lampert, in:, IEEE, 2010, pp. 3027–3034.","ieee":"K. Tang, M. Tappen, R. Sukthankar, and C. Lampert, “Optimizing one-shot recognition with micro-set learning,” presented at the CVPR: Computer Vision and Pattern Recognition, 2010, pp. 3027–3034.","apa":"Tang, K., Tappen, M., Sukthankar, R., & Lampert, C. (2010). Optimizing one-shot recognition with micro-set learning (pp. 3027–3034). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2010.5540053","ama":"Tang K, Tappen M, Sukthankar R, Lampert C. Optimizing one-shot recognition with micro-set learning. In: IEEE; 2010:3027-3034. doi:10.1109/CVPR.2010.5540053","chicago":"Tang, Kevin, Marshall Tappen, Rahul Sukthankar, and Christoph Lampert. “Optimizing One-Shot Recognition with Micro-Set Learning,” 3027–34. IEEE, 2010. https://doi.org/10.1109/CVPR.2010.5540053.","ista":"Tang K, Tappen M, Sukthankar R, Lampert C. 2010. Optimizing one-shot recognition with micro-set learning. CVPR: Computer Vision and Pattern Recognition, 3027–3034."},"title":"Optimizing one-shot recognition with micro-set learning","publist_id":"2696","author":[{"last_name":"Tang","full_name":"Tang, Kevin D","first_name":"Kevin"},{"last_name":"Tappen","full_name":"Tappen, Marshall F","first_name":"Marshall"},{"first_name":"Rahul","last_name":"Sukthankar","full_name":"Sukthankar,Rahul"},{"last_name":"Lampert","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}]},{"citation":{"ista":"Kober J, Mülling K, Krömer O, Lampert C, Schölkopf B, Peters J. 2010. Movement templates for learning of hitting and batting. ICRA: International Conference on Robotics and Automation, 853–858.","chicago":"Kober, Jens, Katharina Mülling, Oliver Krömer, Christoph Lampert, Bernhard Schölkopf, and Jan Peters. “Movement Templates for Learning of Hitting and Batting,” 853–58. IEEE, 2010. https://doi.org/10.1109/ROBOT.2010.5509672.","ieee":"J. Kober, K. Mülling, O. Krömer, C. Lampert, B. Schölkopf, and J. Peters, “Movement templates for learning of hitting and batting,” presented at the ICRA: International Conference on Robotics and Automation, 2010, pp. 853–858.","short":"J. Kober, K. Mülling, O. Krömer, C. Lampert, B. Schölkopf, J. Peters, in:, IEEE, 2010, pp. 853–858.","apa":"Kober, J., Mülling, K., Krömer, O., Lampert, C., Schölkopf, B., & Peters, J. (2010). Movement templates for learning of hitting and batting (pp. 853–858). Presented at the ICRA: International Conference on Robotics and Automation, IEEE. https://doi.org/10.1109/ROBOT.2010.5509672","ama":"Kober J, Mülling K, Krömer O, Lampert C, Schölkopf B, Peters J. Movement templates for learning of hitting and batting. In: IEEE; 2010:853-858. doi:10.1109/ROBOT.2010.5509672","mla":"Kober, Jens, et al. Movement Templates for Learning of Hitting and Batting. IEEE, 2010, pp. 853–58, doi:10.1109/ROBOT.2010.5509672."},"date_updated":"2021-01-12T07:51:35Z","extern":1,"publist_id":"2654","author":[{"last_name":"Kober","full_name":"Kober,Jens","first_name":"Jens"},{"first_name":"Katharina","full_name":"Mülling,Katharina","last_name":"Mülling"},{"first_name":"Oliver","full_name":"Krömer,Oliver","last_name":"Krömer"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887"},{"last_name":"Schölkopf","full_name":"Schölkopf,Bernhard","first_name":"Bernhard"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"title":"Movement templates for learning of hitting and batting","_id":"3702","conference":{"name":"ICRA: International Conference on Robotics and Automation"},"type":"conference","status":"public","publication_status":"published","year":"2010","day":"07","page":"853 - 858","date_created":"2018-12-11T12:04:42Z","doi":"10.1109/ROBOT.2010.5509672","date_published":"2010-05-07T00:00:00Z","abstract":[{"lang":"eng","text":"Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al. [1]) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation. We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements. All experiments were carried out on a Barrett WAM using a four camera vision system."}],"main_file_link":[{"open_access":"0","url":"http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/ICRA2010-Kober_6231%5b1%5d.pdf"}],"publisher":"IEEE","quality_controlled":0,"month":"05"},{"title":"Lumpability abstractions of rule-based systems","publist_id":"2511","author":[{"last_name":"Feret","full_name":"Feret, Jérôme","first_name":"Jérôme"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana"}],"external_id":{"arxiv":["1011.0496"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.","ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process Calculi, EPTCS, vol. 40, 142–161.","mla":"Feret, Jérôme, et al. Lumpability Abstractions of Rule-Based Systems. Vol. 40, Open Publishing Association, 2010, pp. 142–61.","ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2010). Lumpability abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open Publishing Association.","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161."},"date_published":"2010-10-30T00:00:00Z","date_created":"2018-12-11T12:04:47Z","page":"142-161","day":"30","has_accepted_license":"1","year":"2010","quality_controlled":"1","publisher":"Open Publishing Association","oa":1,"acknowledgement":"Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support from SystemsX.ch, the Swiss Initiative in Systems Biology.","file_date_updated":"2020-07-14T12:46:14Z","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"ddc":["570"],"date_updated":"2023-02-23T11:15:19Z","status":"public","type":"conference","conference":{"name":"MECBIC: Membrane Computing and Biologically Inspired Process Calculi","start_date":"2010-08-23","end_date":"2010-08-23","location":"Jena, Germany"},"_id":"3719","related_material":{"record":[{"relation":"later_version","status":"public","id":"3168"}]},"volume":40,"file":[{"file_size":907155,"date_updated":"2020-07-14T12:46:14Z","creator":"kschuh","file_name":"Lumpability_abstractions_of_rule-based_systems.pdf","date_created":"2019-01-31T12:09:09Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"eaaba991a86fff37606b0eb5196878e8","file_id":"5904"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 40","alternative_title":["EPTCS"],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.","lang":"eng"}]},{"page":"406 - 415","date_created":"2018-12-11T12:04:47Z","issue":"6","volume":59,"date_published":"2010-11-01T00:00:00Z","doi":"10.1016/j.neuropharm.2010.05.013","year":"2010","publication_status":"published","language":[{"iso":"eng"}],"publication":"Neuropharmacology","day":"01","scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","intvolume":" 59","month":"11","abstract":[{"lang":"eng","text":"Long-term depression (LTD) is a form of synaptic plasticity that may contribute to information storage in the central nervous system. Here we report that LTD can be elicited in layer 5 pyramidal neurons of the rat prefrontal cortex by pairing low frequency stimulation with a modest postsynaptic depolarization. The induction of LTD required the activation of both metabotropic glutamate receptors of the mGlu1 subtype and voltage-sensitive Ca(2+) channels (VSCCs) of the T/R, P/Q and N types, leading to the stimulation of intracellular inositol trisphosphate (IP3) receptors by IP3 and Ca(2+). The subsequent release of Ca(2+) from intracellular stores activated the protein phosphatase cascade involving calcineurin and protein phosphatase 1. The activation of purinergic P2Y(1) receptors blocked LTD. This effect was prevented by P2Y(1) receptor antagonists and was absent in mice lacking P2Y(1) but not P2Y(2) receptors. We also found that activation of P2Y(1) receptors inhibits Ca(2+) transients via VSCCs in the apical dendrites and spines of pyramidal neurons. In addition, we show that the release of ATP under hypoxia is able to inhibit LTD by acting on postsynaptic P2Y(1) receptors. In conclusion, these data suggest that the reduction of Ca(2+) influx via VSCCs caused by the activation of P2Y(1) receptors by ATP is the possible mechanism for the inhibition of LTD in prefrontal cortex."}],"acknowledgement":" The financial support of the Deutsche Forschungsgemeinschaft (IL 20/12-1, KI 677/2-4) is gratefully acknowledged.\r\nWe thank B. H. Koller (Department of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, NC, USA) for the generous supply of P2Y1−/− and P2Y2−/− mice. We are grateful to Dr. A. Schulz for reanalysing the genotype of the P2Y1−/− mice. The authors thank P. Jonas and U. Heinemann for many helpful comments and A-K. Krause, L Feige and M. Eberts for their excellent technical support.","oa_version":"None","publist_id":"2512","author":[{"first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","full_name":"Guzmán, José"},{"full_name":"Schmidt, Hartmut","last_name":"Schmidt","first_name":"Hartmut"},{"full_name":"Franke, Heike","last_name":"Franke","first_name":"Heike"},{"last_name":"Krügel","full_name":"Krügel, Ute","first_name":"Ute"},{"full_name":"Eilers, Jens","last_name":"Eilers","first_name":"Jens"},{"last_name":"Illes","full_name":"Illes, Peter","first_name":"Peter"},{"first_name":"Zoltan","full_name":"Gerevich, Zoltan","last_name":"Gerevich"}],"department":[{"_id":"PeJo"}],"title":"P2Y1 receptors inhibit long-term depression in the prefrontal cortex.","date_updated":"2021-01-12T07:51:42Z","citation":{"chicago":"Guzmán, José, Hartmut Schmidt, Heike Franke, Ute Krügel, Jens Eilers, Peter Illes, and Zoltan Gerevich. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” Neuropharmacology. Elsevier, 2010. https://doi.org/10.1016/j.neuropharm.2010.05.013.","ista":"Guzmán J, Schmidt H, Franke H, Krügel U, Eilers J, Illes P, Gerevich Z. 2010. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. 59(6), 406–415.","mla":"Guzmán, José, et al. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” Neuropharmacology, vol. 59, no. 6, Elsevier, 2010, pp. 406–15, doi:10.1016/j.neuropharm.2010.05.013.","short":"J. Guzmán, H. Schmidt, H. Franke, U. Krügel, J. Eilers, P. Illes, Z. Gerevich, Neuropharmacology 59 (2010) 406–415.","ieee":"J. Guzmán et al., “P2Y1 receptors inhibit long-term depression in the prefrontal cortex.,” Neuropharmacology, vol. 59, no. 6. Elsevier, pp. 406–415, 2010.","ama":"Guzmán J, Schmidt H, Franke H, et al. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. 2010;59(6):406-415. doi:10.1016/j.neuropharm.2010.05.013","apa":"Guzmán, J., Schmidt, H., Franke, H., Krügel, U., Eilers, J., Illes, P., & Gerevich, Z. (2010). P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. Elsevier. https://doi.org/10.1016/j.neuropharm.2010.05.013"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"3718"},{"citation":{"ista":"Tkačik G, Prentice J, Victor J, Balasubramanian V. 2010. Local statistics in natural scenes predict the saliency of synthetic textures. PNAS. 107(42), 18149–18154.","chicago":"Tkačik, Gašper, Jason Prentice, Jonathan Victor, and Vijay Balasubramanian. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.0914916107.","apa":"Tkačik, G., Prentice, J., Victor, J., & Balasubramanian, V. (2010). Local statistics in natural scenes predict the saliency of synthetic textures. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0914916107","ama":"Tkačik G, Prentice J, Victor J, Balasubramanian V. Local statistics in natural scenes predict the saliency of synthetic textures. PNAS. 2010;107(42):18149-18154. doi:10.1073/pnas.0914916107","ieee":"G. Tkačik, J. Prentice, J. Victor, and V. Balasubramanian, “Local statistics in natural scenes predict the saliency of synthetic textures,” PNAS, vol. 107, no. 42. National Academy of Sciences, pp. 18149–18154, 2010.","short":"G. Tkačik, J. Prentice, J. Victor, V. Balasubramanian, PNAS 107 (2010) 18149–18154.","mla":"Tkačik, Gašper, et al. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS, vol. 107, no. 42, National Academy of Sciences, 2010, pp. 18149–54, doi:10.1073/pnas.0914916107."},"date_updated":"2021-01-12T07:51:49Z","extern":1,"author":[{"last_name":"Tkacik","full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason S"},{"last_name":"Victor","full_name":"Victor,Jonathan D","first_name":"Jonathan"},{"last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay","first_name":"Vijay"}],"publist_id":"2491","title":"Local statistics in natural scenes predict the saliency of synthetic textures","_id":"3735","type":"journal_article","status":"public","publication_status":"published","year":"2010","publication":"PNAS","day":"19","page":"18149 - 18154","date_created":"2018-12-11T12:04:53Z","date_published":"2010-10-19T00:00:00Z","doi":"10.1073/pnas.0914916107","issue":"42","volume":107,"abstract":[{"lang":"eng","text":"The visual system is challenged with extracting and representing behaviorally relevant information contained in natural inputs of great complexity and detail. This task begins in the sensory periphery: retinal receptive fields and circuits are matched to the first and second-order statistical structure of natural inputs. This matching enables the retina to remove stimulus components that are predictable (and therefore uninformative), and primarily transmit what is unpredictable (and therefore informative). Here we show that this design principle applies to more complex aspects of natural scenes, and to central visual processing. We do this by classifying high-order statistics of natural scenes according to whether they are uninformative vs. informative. We find that the uninformative ones are perceptually nonsalient, while the informative ones are highly salient, and correspond to previously identified perceptual mechanisms whose neural basis is likely central. Our results suggest that the principle of efficient coding not only accounts for filtering operations in the sensory periphery, but also shapes subsequent stages of sensory processing that are sensitive to high-order image statistics."}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964243/","open_access":"0"}],"quality_controlled":0,"publisher":"National Academy of Sciences","intvolume":" 107","month":"10"},{"type":"journal_article","status":"public","_id":"3736","publist_id":"2492","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik"},{"full_name":"Prentice, Jason S","last_name":"Prentice","first_name":"Jason"},{"first_name":"Vijay","full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"}],"title":"Optimal population coding by noisy spiking neurons","citation":{"ista":"Tkačik G, Prentice J, Balasubramanian V, Schneidman E. 2010. Optimal population coding by noisy spiking neurons. PNAS. 107(32), 14419–14424.","chicago":"Tkačik, Gašper, Jason Prentice, Vijay Balasubramanian, and Elad Schneidman. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1004906107.","ama":"Tkačik G, Prentice J, Balasubramanian V, Schneidman E. Optimal population coding by noisy spiking neurons. PNAS. 2010;107(32):14419-14424. doi:10.1073/pnas.1004906107","apa":"Tkačik, G., Prentice, J., Balasubramanian, V., & Schneidman, E. (2010). Optimal population coding by noisy spiking neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1004906107","ieee":"G. Tkačik, J. Prentice, V. Balasubramanian, and E. Schneidman, “Optimal population coding by noisy spiking neurons,” PNAS, vol. 107, no. 32. National Academy of Sciences, pp. 14419–14424, 2010.","short":"G. Tkačik, J. Prentice, V. Balasubramanian, E. Schneidman, PNAS 107 (2010) 14419–14424.","mla":"Tkačik, Gašper, et al. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24, doi:10.1073/pnas.1004906107."},"date_updated":"2021-01-12T07:51:50Z","extern":1,"main_file_link":[{"open_access":"0","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922524/"}],"publisher":"National Academy of Sciences","quality_controlled":0,"intvolume":" 107","month":"08","abstract":[{"lang":"eng","text":"In retina and in cortical slice the collective response of spiking neural populations is well described by "maximum-entropy" models in which only pairs of neurons interact. We asked, how should such interactions be organized to maximize the amount of information represented in population responses? To this end, we extended the linear-nonlinear-Poisson model of single neural response to include pairwise interactions, yielding a stimulus-dependent, pairwise maximum-entropy model. We found that as we varied the noise level in single neurons and the distribution of network inputs, the optimal pairwise interactions smoothly interpolated to achieve network functions that are usually regarded as discrete–stimulus decorrelation, error correction, and independent encoding. These functions reflected a trade-off between efficient consumption of finite neural bandwidth and the use of redundancy to mitigate noise. Spontaneous activity in the optimal network reflected stimulus-induced activity patterns, and single-neuron response variability overestimated network noise. Our analysis suggests that rather than having a single coding principle hardwired in their architecture, networks in the brain should adapt their function to changing noise and stimulus correlations."}],"acknowledgement":"R01 EY08124/EY/NEI NIH HHS/United States; T32-07035/PHS HHS/United States","page":"14419 - 14424","date_created":"2018-12-11T12:04:53Z","issue":"32","volume":107,"date_published":"2010-08-10T00:00:00Z","doi":"10.1073/pnas.1004906107","publication_status":"published","year":"2010","publication":"PNAS","day":"10"},{"status":"public","type":"journal_article","_id":"3738","title":"Optimizing information flow in small genetic networks. II. Feed-forward interactions","publist_id":"2494","author":[{"first_name":"Aleksandra","last_name":"Walczak","full_name":"Walczak, Aleksandra M"},{"last_name":"Tkacik","full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"full_name":"Bialek, William S","last_name":"Bialek","first_name":"William"}],"extern":1,"date_updated":"2021-01-12T07:51:50Z","citation":{"ieee":"A. Walczak, G. Tkačik, and W. Bialek, “Optimizing information flow in small genetic networks. II. Feed-forward interactions,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4. American Institute of Physics, 2010.","short":"A. Walczak, G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 81 (2010).","ama":"Walczak A, Tkačik G, Bialek W. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2010;81(4). doi:10.1103/PhysRevE.81.041905","apa":"Walczak, A., Tkačik, G., & Bialek, W. (2010). Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.81.041905","mla":"Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, American Institute of Physics, 2010, doi:10.1103/PhysRevE.81.041905.","ista":"Walczak A, Tkačik G, Bialek W. 2010. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics. 81(4).","chicago":"Walczak, Aleksandra, Gašper Tkačik, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2010. https://doi.org/10.1103/PhysRevE.81.041905."},"intvolume":" 81","month":"04","main_file_link":[{"open_access":"0","url":"http://arxiv.org/abs/0912.5500"}],"publisher":"American Institute of Physics","quality_controlled":0,"abstract":[{"text":"Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes. As the concentration of the transcription factor varies, the target genes thus undergo correlated changes, and this redundancy limits the ability of the cell to transmit information about input signals. We explore how interactions among the target genes can reduce this redundancy and optimize information transmission. Our discussion builds on recent work [Tkacik, Phys. Rev. E 80, 031920 (2009)], and there are connections to much earlier work on the role of lateral inhibition in enhancing the efficiency of information transmission in neural circuits; for simplicity we consider here the case where the interactions have a feed forward structure, with no loops. Even with this limitation, the networks that optimize information transmission have a structure reminiscent of the networks found in real biological systems.","lang":"eng"}],"date_created":"2018-12-11T12:04:54Z","issue":"4","volume":81,"date_published":"2010-04-06T00:00:00Z","doi":"10.1103/PhysRevE.81.041905","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"06","publication_status":"published","year":"2010"},{"type":"journal_article","status":"public","_id":"3748","author":[{"last_name":"Park","full_name":"Park, Heungwon","first_name":"Heungwon"},{"last_name":"Pontius","full_name":"Pontius, William","first_name":"William"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Calin Guet","last_name":"Guet"},{"first_name":"John","full_name":"Marko, John F","last_name":"Marko"},{"first_name":"Thierry","last_name":"Emonet","full_name":"Emonet,Thierry"},{"last_name":"Cluzel","full_name":"Cluzel,Philippe","first_name":"Philippe"}],"publist_id":"2480","title":"Interdependence of behavioural variability and response to small stimuli in bacteria","citation":{"ama":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. 2010;468:819-823. doi:10.1038/nature09551","apa":"Park, H., Pontius, W., Guet, C. C., Marko, J., Emonet, T., & Cluzel, P. (2010). Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09551","short":"H. Park, W. Pontius, C.C. Guet, J. Marko, T. Emonet, P. Cluzel, Nature 468 (2010) 819–823.","ieee":"H. Park, W. Pontius, C. C. Guet, J. Marko, T. Emonet, and P. Cluzel, “Interdependence of behavioural variability and response to small stimuli in bacteria,” Nature, vol. 468. Nature Publishing Group, pp. 819–823, 2010.","mla":"Park, Heungwon, et al. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” Nature, vol. 468, Nature Publishing Group, 2010, pp. 819–23, doi:10.1038/nature09551.","ista":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. 2010. Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. 468, 819–823.","chicago":"Park, Heungwon, William Pontius, Calin C Guet, John Marko, Thierry Emonet, and Philippe Cluzel. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature09551."},"date_updated":"2021-01-12T07:51:55Z","extern":1,"quality_controlled":0,"publisher":"Nature Publishing Group","oa":1,"main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3230254"}],"month":"12","intvolume":" 468","abstract":[{"lang":"eng","text":"The chemotaxis signalling network in Escherichia coli that controls the locomotion of bacteria is a classic model system for signal transduction1, 2. This pathway modulates the behaviour of flagellar motors to propel bacteria towards sources of chemical attractants. Although this system relaxes to a steady state in response to environmental changes, the signalling events within the chemotaxis network are noisy and cause large temporal variations of the motor behaviour even in the absence of stimulus3. That the same signalling network governs both behavioural variability and cellular response raises the question of whether these two traits are independent. Here, we experimentally establish a fluctuation–response relationship in the chemotaxis system of living bacteria. Using this relationship, we demonstrate the possibility of inferring the cellular response from the behavioural variability measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour of individual bacterial motors, we found that variability scales linearly with the response time for different functioning states of the cell. This study highlights that the fundamental relationship between fluctuation and response is not constrained to physical systems at thermodynamic equilibrium4 but is extensible to living cells5. Such a relationship not only implies that behavioural variability and cellular response can be coupled traits, but it also provides a general framework within which we can examine how the selection of a network design shapes this interdependence"}],"page":"819 - 823","volume":468,"date_published":"2010-12-09T00:00:00Z","doi":"10.1038/nature09551","date_created":"2018-12-11T12:04:57Z","year":"2010","publication_status":"published","day":"09","publication":"Nature"},{"publication_status":"published","year":"2010","publication":"Current Microbiology","day":"23","page":"764 - 769","date_created":"2018-12-11T12:04:57Z","date_published":"2010-10-23T00:00:00Z","issue":"3","volume":62,"doi":"10.1007/s00284-010-9778-z","abstract":[{"text":"In E. coli, chemotactic behavior exhibits perfect adaptation that is robust to changes in the intracellular concentration of the chemotactic proteins, such as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly imply a robust chemotactic response. Previous studies on the robustness of the chemotactic response relied on swarming assays, which can be confounded by processes besides chemotaxis, such as cellular growth and depletion of nutrients. Here, using a high-throughput capillary assay that eliminates the effects of growth, we experimentally studied how the chemotactic response depends on the relative concentration of the chemotactic proteins. We simultaneously measured both the chemotactic response of E. coli cells to L: -aspartate and the concentrations of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable to the chemotactic response of wild-type behavior. In contrast to adaptation in chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB] ratio.","lang":"eng"}],"acknowledgement":"P50 GM081892-04/GM/NIGMS NIH HHS/United States\nR01 AI059195-01A1/AI/NIAID NIH HHS/United States\nR01 AI059195-02/AI/NIAID NIH HHS/United States\nR01 AI059195-03/AI/NIAID NIH HHS/United States\nR01AI059195-03/AI/NIAID NIH HHS/United States\n\n\nPMCID: PMC3230253 ","main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3230253"}],"oa":1,"quality_controlled":0,"publisher":"Springer","intvolume":" 62","month":"10","date_updated":"2021-01-12T07:51:55Z","citation":{"ista":"Park H, Guet CC, Emonet T, Cluzel P. 2010. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. Current Microbiology. 62(3), 764–769.","chicago":"Park, Heungwon, Calin C Guet, Thierry Emonet, and Philippe Cluzel. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” Current Microbiology. Springer, 2010. https://doi.org/10.1007/s00284-010-9778-z.","apa":"Park, H., Guet, C. C., Emonet, T., & Cluzel, P. (2010). Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. Current Microbiology. Springer. https://doi.org/10.1007/s00284-010-9778-z","ama":"Park H, Guet CC, Emonet T, Cluzel P. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. Current Microbiology. 2010;62(3):764-769. doi:10.1007/s00284-010-9778-z","short":"H. Park, C.C. Guet, T. Emonet, P. Cluzel, Current Microbiology 62 (2010) 764–769.","ieee":"H. Park, C. C. Guet, T. Emonet, and P. Cluzel, “Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay,” Current Microbiology, vol. 62, no. 3. Springer, pp. 764–769, 2010.","mla":"Park, Heungwon, et al. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” Current Microbiology, vol. 62, no. 3, Springer, 2010, pp. 764–69, doi:10.1007/s00284-010-9778-z."},"extern":1,"author":[{"first_name":"Heungwon","full_name":"Park, Heungwon","last_name":"Park"},{"full_name":"Calin Guet","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thierry","last_name":"Emonet","full_name":"Emonet,Thierry"},{"full_name":"Cluzel,Philippe","last_name":"Cluzel","first_name":"Philippe"}],"publist_id":"2479","title":"Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay","_id":"3749","type":"journal_article","status":"public"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T11:41:44Z","citation":{"mla":"Thürey, Nils, et al. “A Multiscale Approach to Mesh-Based Surface Tension Flows.” ACM Transactions on Graphics, vol. 29, no. 4, ACM, 2010, doi:10.1145/1778765.1778785.","apa":"Thürey, N., Wojtan, C., Gross, M., & Turk, G. (2010). A multiscale approach to mesh-based surface tension flows. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1778765.1778785","ama":"Thürey N, Wojtan C, Gross M, Turk G. A multiscale approach to mesh-based surface tension flows. ACM Transactions on Graphics. 2010;29(4). doi:10.1145/1778765.1778785","short":"N. Thürey, C. Wojtan, M. Gross, G. Turk, ACM Transactions on Graphics 29 (2010).","ieee":"N. Thürey, C. Wojtan, M. Gross, and G. Turk, “A multiscale approach to mesh-based surface tension flows,” ACM Transactions on Graphics, vol. 29, no. 4. ACM, 2010.","chicago":"Thürey, Nils, Chris Wojtan, Markus Gross, and Greg Turk. “A Multiscale Approach to Mesh-Based Surface Tension Flows.” ACM Transactions on Graphics. ACM, 2010. https://doi.org/10.1145/1778765.1778785.","ista":"Thürey N, Wojtan C, Gross M, Turk G. 2010. A multiscale approach to mesh-based surface tension flows. ACM Transactions on Graphics. 29(4)."},"title":"A multiscale approach to mesh-based surface tension flows","author":[{"first_name":"Nils","full_name":"Thürey, Nils","last_name":"Thürey"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"},{"full_name":"Gross, Markus","last_name":"Gross","first_name":"Markus"},{"first_name":"Greg","full_name":"Turk, Greg","last_name":"Turk"}],"publist_id":"2463","article_processing_charge":"No","_id":"3766","status":"public","type":"journal_article","day":"01","publication":"ACM Transactions on Graphics","language":[{"iso":"eng"}],"publication_status":"published","year":"2010","issue":"4","date_published":"2010-07-01T00:00:00Z","volume":29,"doi":"10.1145/1778765.1778785","date_created":"2018-12-11T12:05:03Z","oa_version":"None","abstract":[{"lang":"eng","text":"We present an approach to simulate flows driven by surface tension based on triangle meshes. Our method consists of two simulation layers: the first layer is an Eulerian method for simulating surface tension forces that is free from typical strict time step constraints. The second simulation layer is a Lagrangian finite element method that simulates sub-grid scale wave details on the fluid surface. The surface wave simulation employs an unconditionally stable, symplectic time integration method that allows for a high propagation speed due to strong surface tension. Our approach can naturally separate the grid-and sub-grid scales based on a volumepreserving mean curvature flow. As our model for the sub-grid dynamics enforces a local conservation of mass, it leads to realistic pinch off and merging effects. In addition to this method for simulating dynamic surface tension effects, we also present an efficient non-oscillatory approximation for capturing damped surface tension behavior. These approaches allow us to efficiently simulate complex phenomena associated with strong surface tension, such as Rayleigh-Plateau instabilities and crown splashes, in a short amount of time."}],"month":"07","intvolume":" 29","publisher":"ACM"},{"_id":"3783","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:52:10Z","citation":{"short":"F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 247–249.","ieee":"F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no. 2. Oxford University Press, pp. 247–249, 2010.","ama":"Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111","apa":"Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/esq111","mla":"Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press, 2010, pp. 247–49, doi:10.1093/jhered/esq111.","ista":"Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.","chicago":"Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford University Press, 2010. https://doi.org/10.1093/jhered/esq111."},"department":[{"_id":"NiBa"}],"title":"Microsatelight – Pipeline to expedite microsatellite analysis","author":[{"first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","full_name":"Palero, Ferran","orcid":"0000-0002-0343-8329"},{"first_name":"Fernando","full_name":"González Candelas, Fernando","last_name":"González Candelas"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"}],"publist_id":"2444","acknowledgement":"Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635). M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya. F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous referees for their valuable comments. These comments certainly helped to improve the manuscript.","oa_version":"None","abstract":[{"text":"MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/.","lang":"eng"}],"intvolume":" 102","month":"12","quality_controlled":"1","scopus_import":1,"publisher":"Oxford University Press","language":[{"iso":"eng"}],"publication":"Journal of Heredity","day":"02","year":"2010","publication_status":"published","date_created":"2018-12-11T12:05:09Z","date_published":"2010-12-02T00:00:00Z","volume":102,"issue":"2","doi":"10.1093/jhered/esq111","page":"247 - 249"},{"month":"12","intvolume":" 6533","publisher":"Springer","scopus_import":1,"quality_controlled":"1","alternative_title":["LNCS"],"oa_version":"None","acknowledgement":"Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers for helpful comments.","abstract":[{"lang":"eng","text":"In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically."}],"doi":"10.1007/978-3-642-18421-5_4","volume":6533,"date_published":"2010-12-31T00:00:00Z","date_created":"2018-12-11T12:05:08Z","page":"31 - 42","day":"31","publication":" Conference proceedings MCV 2010","language":[{"iso":"eng"}],"year":"2010","publication_status":"published","status":"public","type":"conference","conference":{"start_date":"2010-09-20","end_date":"2010-09-20","location":"Beijing, China","name":"MCV: Medical Computer Vision"},"_id":"3782","title":"Topology noise removal for curve and surface evolution","department":[{"_id":"HeEd"}],"publist_id":"2445","author":[{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface Evolution.” In Conference Proceedings MCV 2010, 6533:31–42. Springer, 2010. https://doi.org/10.1007/978-3-642-18421-5_4.","ista":"Chen C, Freedman D. 2010. Topology noise removal for curve and surface evolution. Conference proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.","mla":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface Evolution.” Conference Proceedings MCV 2010, vol. 6533, Springer, 2010, pp. 31–42, doi:10.1007/978-3-642-18421-5_4.","ieee":"C. Chen and D. Freedman, “Topology noise removal for curve and surface evolution,” in Conference proceedings MCV 2010, Beijing, China, 2010, vol. 6533, pp. 31–42.","short":"C. Chen, D. Freedman, in:, Conference Proceedings MCV 2010, Springer, 2010, pp. 31–42.","apa":"Chen, C., & Freedman, D. (2010). Topology noise removal for curve and surface evolution. In Conference proceedings MCV 2010 (Vol. 6533, pp. 31–42). Beijing, China: Springer. https://doi.org/10.1007/978-3-642-18421-5_4","ama":"Chen C, Freedman D. Topology noise removal for curve and surface evolution. In: Conference Proceedings MCV 2010. Vol 6533. Springer; 2010:31-42. doi:10.1007/978-3-642-18421-5_4"},"date_updated":"2021-01-12T07:52:10Z"},{"publist_id":"2428","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Morozov, Dmitriy","last_name":"Morozov","first_name":"Dmitriy"},{"last_name":"Patel","full_name":"Patel, Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","first_name":"Amit"}],"title":"The stability of the apparent contour of an orientable 2-manifold","citation":{"mla":"Edelsbrunner, Herbert, et al. “The Stability of the Apparent Contour of an Orientable 2-Manifold.” Topological Data Analysis and Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42, doi:10.1007/978-3-642-15014-2_3.","short":"H. Edelsbrunner, D. Morozov, A. Patel, in:, Topological Data Analysis and Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.","ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “The stability of the apparent contour of an orientable 2-manifold,” in Topological Data Analysis and Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.","apa":"Edelsbrunner, H., Morozov, D., & Patel, A. (2010). The stability of the apparent contour of an orientable 2-manifold. In Topological Data Analysis and Visualization: Theory, Algorithms and Applications (pp. 27–42). Springer. https://doi.org/10.1007/978-3-642-15014-2_3","ama":"Edelsbrunner H, Morozov D, Patel A. The stability of the apparent contour of an orientable 2-manifold. In: Topological Data Analysis and Visualization: Theory, Algorithms and Applications. Springer; 2010:27-42. doi:10.1007/978-3-642-15014-2_3","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “The Stability of the Apparent Contour of an Orientable 2-Manifold.” In Topological Data Analysis and Visualization: Theory, Algorithms and Applications, 27–42. Springer, 2010. https://doi.org/10.1007/978-3-642-15014-2_3.","ista":"Edelsbrunner H, Morozov D, Patel A. 2010.The stability of the apparent contour of an orientable 2-manifold. In: Topological Data Analysis and Visualization: Theory, Algorithms and Applications. Mathematics and Visualization, , 27–42."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","page":"27 - 42","date_published":"2010-12-22T00:00:00Z","doi":"10.1007/978-3-642-15014-2_3","date_created":"2018-12-11T12:05:13Z","has_accepted_license":"1","year":"2010","day":"22","publication":"Topological Data Analysis and Visualization: Theory, Algorithms and Applications","type":"book_chapter","status":"public","pubrep_id":"538","_id":"3795","file_date_updated":"2020-07-14T12:46:16Z","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:52:15Z","ddc":["000"],"scopus_import":1,"alternative_title":["Mathematics and Visualization"],"month":"12","abstract":[{"text":"The (apparent) contour of a smooth mapping from a 2-manifold to the plane, f: M → R2 , is the set of critical values, that is, the image of the points at which the gradients of the two component functions are linearly dependent. Assuming M is compact and orientable and measuring difference with the erosion distance, we prove that the contour is stable.","lang":"eng"}],"oa_version":"Submitted Version","publication_status":"published","file":[{"file_size":210710,"date_updated":"2020-07-14T12:46:16Z","creator":"system","file_name":"IST-2016-538-v1+1_2011-B-02-ApparentContour.pdf","date_created":"2018-12-12T10:11:40Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4896","checksum":"f03a44c3d1c3e2d4fedb3b94404f3fd5"}],"language":[{"iso":"eng"}]},{"type":"conference","conference":{"name":"ECCV: European Conference on Computer Vision","end_date":"2010-09-11","location":"Heraklion, Crete, Greece","start_date":"2010-09-05"},"status":"public","_id":"3794","author":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krömer, Oliver","last_name":"Krömer","first_name":"Oliver"}],"publist_id":"2433","title":"Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning","department":[{"_id":"ChLa"}],"citation":{"ama":"Lampert C, Krömer O. Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning. In: Vol 6312. Springer; 2010:566-579. doi:10.1007/978-3-642-15552-9_41","apa":"Lampert, C., & Krömer, O. (2010). Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning (Vol. 6312, pp. 566–579). Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece: Springer. https://doi.org/10.1007/978-3-642-15552-9_41","short":"C. Lampert, O. Krömer, in:, Springer, 2010, pp. 566–579.","ieee":"C. Lampert and O. Krömer, “Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning,” presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6312, pp. 566–579.","mla":"Lampert, Christoph, and Oliver Krömer. Weakly-Paired Maximum Covariance Analysis for Multimodal Dimensionality Reduction and Transfer Learning. Vol. 6312, Springer, 2010, pp. 566–79, doi:10.1007/978-3-642-15552-9_41.","ista":"Lampert C, Krömer O. 2010. Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning. ECCV: European Conference on Computer Vision, LNCS, vol. 6312, 566–579.","chicago":"Lampert, Christoph, and Oliver Krömer. “Weakly-Paired Maximum Covariance Analysis for Multimodal Dimensionality Reduction and Transfer Learning,” 6312:566–79. Springer, 2010. https://doi.org/10.1007/978-3-642-15552-9_41."},"date_updated":"2021-01-12T07:52:14Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","scopus_import":1,"quality_controlled":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"http://www.ics.forth.gr/eccv2010/intro.php"}],"month":"11","intvolume":" 6312","abstract":[{"lang":"eng","text":"We study the problem of multimodal dimensionality reduction assuming that data samples can be missing at training time, and not all data modalities may be present at application time. Maximum covariance analysis, as a generalization of PCA, has many desirable properties, but its application to practical problems is limited by its need for perfectly paired data. We overcome this limitation by a latent variable approach that allows working with weakly paired data and is still able to efficiently process large datasets using standard numerical routines. The resulting weakly paired maximum covariance analysis often finds better representations than alternative methods, as we show in two exemplary tasks: texture discrimination and transfer learning."}],"oa_version":"None","page":"566 - 579","doi":"10.1007/978-3-642-15552-9_41","volume":6312,"date_published":"2010-11-10T00:00:00Z","date_created":"2018-12-11T12:05:12Z","publication_status":"published","year":"2010","day":"10","language":[{"iso":"eng"}]},{"extern":1,"citation":{"mla":"Norenberg, Anja, et al. “Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation of Fast-Spiking GABAergic Interneurons.” PNAS, vol. 107, no. 2, National Academy of Sciences, 2010, pp. 894–99, doi:10.1073/pnas.0910716107.","ama":"Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. PNAS. 2010;107(2):894-899. doi:10.1073/pnas.0910716107","apa":"Norenberg, A., Hu, H., Vida, I., Bartos, M., & Jonas, P. M. (2010). Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0910716107","short":"A. Norenberg, H. Hu, I. Vida, M. Bartos, P.M. Jonas, PNAS 107 (2010) 894–9.","ieee":"A. Norenberg, H. Hu, I. Vida, M. Bartos, and P. M. Jonas, “Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons,” PNAS, vol. 107, no. 2. National Academy of Sciences, pp. 894–9, 2010.","chicago":"Norenberg, Anja, Hua Hu, Imre Vida, Marlene Bartos, and Peter M Jonas. “Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation of Fast-Spiking GABAergic Interneurons.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.0910716107.","ista":"Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. 2010. Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. PNAS. 107(2), 894–9."},"date_updated":"2021-01-12T07:52:31Z","title":"Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons","author":[{"first_name":"Anja","full_name":"Norenberg, Anja","last_name":"Norenberg"},{"id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua","full_name":"Hua Hu","last_name":"Hu"},{"first_name":"Imre","full_name":"Vida, Imre","last_name":"Vida"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"publist_id":"2379","_id":"3831","status":"public","type":"journal_article","publication":"PNAS","day":"01","publication_status":"published","year":"2010","date_created":"2018-12-11T12:05:24Z","issue":"2","date_published":"2010-01-01T00:00:00Z","doi":"10.1073/pnas.0910716107","volume":107,"page":"894 - 9","abstract":[{"text":"Fast-spiking, parvalbumin-expressing basket cells (BCs) play a key role in feedforward and feedback inhibition in the hippocampus. However, the dendritic mechanisms underlying rapid interneuron recruitment have remained unclear. To quantitatively address this question, we developed detailed passive cable models of BCs in the dentate gyrus based on dual somatic or somatodendritic recordings and complete morphologic reconstructions. Both specific membrane capacitance and axial resistivity were comparable to those of pyramidal neurons, but the average somatodendritic specific membrane resistance (R(m)) was substantially lower in BCs. Furthermore, R(m) was markedly nonuniform, being lowest in soma and proximal dendrites, intermediate in distal dendrites, and highest in the axon. Thus, the somatodendritic gradient of R(m) was the reverse of that in pyramidal neurons. Further computational analysis revealed that these unique cable properties accelerate the time course of synaptic potentials at the soma in response to fast inputs, while boosting the efficacy of slow distal inputs. These properties will facilitate both rapid phasic and efficient tonic activation of BCs in hippocampal microcircuits.","lang":"eng"}],"intvolume":" 107","month":"01","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818894/#!po=4.16667"}],"oa":1,"quality_controlled":0,"publisher":"National Academy of Sciences"},{"department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T07:52:31Z","status":"public","type":"journal_article","_id":"3832","volume":66,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 66","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/20399724","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"A recent paper by von Engelhardt et al. identifies a novel auxiliary subunit of native AMPARs, termedCKAMP44. Unlike other auxiliary subunits, CKAMP44 accelerates desensitization and prolongs recovery from desensitization. CKAMP44 is highly expressed in hippocampal dentate gyrus granule cells and decreases the paired-pulse ratio at perforant path input synapses. Thus, both principal and auxiliary AMPAR subunits control the time course of signaling at glutamatergic synapses.","lang":"eng"}],"title":"Beyond TARPs: The growing list of auxiliary AMPAR subunits","author":[{"full_name":"Guzmán, José","last_name":"Guzmán","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"publist_id":"2377","article_processing_charge":"No","external_id":{"pmid":["20399724"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Guzmán, José, and Peter M Jonas. “Beyond TARPs: The Growing List of Auxiliary AMPAR Subunits.” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.04.003.","ista":"Guzmán J, Jonas PM. 2010. Beyond TARPs: The growing list of auxiliary AMPAR subunits. Neuron. 66(1), 8–10.","mla":"Guzmán, José, and Peter M. Jonas. “Beyond TARPs: The Growing List of Auxiliary AMPAR Subunits.” Neuron, vol. 66, no. 1, Elsevier, 2010, pp. 8–10, doi:10.1016/j.neuron.2010.04.003.","short":"J. Guzmán, P.M. Jonas, Neuron 66 (2010) 8–10.","ieee":"J. Guzmán and P. M. Jonas, “Beyond TARPs: The growing list of auxiliary AMPAR subunits,” Neuron, vol. 66, no. 1. Elsevier, pp. 8–10, 2010.","apa":"Guzmán, J., & Jonas, P. M. (2010). Beyond TARPs: The growing list of auxiliary AMPAR subunits. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.04.003","ama":"Guzmán J, Jonas PM. Beyond TARPs: The growing list of auxiliary AMPAR subunits. Neuron. 2010;66(1):8-10. doi:10.1016/j.neuron.2010.04.003"},"date_published":"2010-04-15T00:00:00Z","doi":"10.1016/j.neuron.2010.04.003","date_created":"2018-12-11T12:05:25Z","page":"8 - 10","day":"15","publication":"Neuron","year":"2010","publisher":"Elsevier","quality_controlled":"1","oa":1},{"status":"public","type":"journal_article","_id":"3830","title":"Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons","author":[{"full_name":"Hua Hu","last_name":"Hu","first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martina","full_name":"Martina, Marco","first_name":"Marco"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2381","extern":1,"citation":{"short":"H. Hu, M. Martina, P.M. Jonas, Science 327 (2010) 52–8.","ieee":"H. Hu, M. Martina, and P. M. Jonas, “Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons,” Science, vol. 327, no. 5961. American Association for the Advancement of Science, pp. 52–8, 2010.","apa":"Hu, H., Martina, M., & Jonas, P. M. (2010). Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1177876","ama":"Hu H, Martina M, Jonas PM. Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons. Science. 2010;327(5961):52-58. doi:10.1126/science.1177876","mla":"Hu, Hua, et al. “Dendritic Mechanisms Underlying Rapid Synaptic Activation of Fast-Spiking Hippocampal Interneurons.” Science, vol. 327, no. 5961, American Association for the Advancement of Science, 2010, pp. 52–58, doi:10.1126/science.1177876.","ista":"Hu H, Martina M, Jonas PM. 2010. Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons. Science. 327(5961), 52–8.","chicago":"Hu, Hua, Marco Martina, and Peter M Jonas. “Dendritic Mechanisms Underlying Rapid Synaptic Activation of Fast-Spiking Hippocampal Interneurons.” Science. American Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1177876."},"date_updated":"2021-01-12T07:52:30Z","intvolume":" 327","month":"01","publisher":"American Association for the Advancement of Science","quality_controlled":0,"abstract":[{"text":"Fast-spiking, parvalbumin-expressing basket cells (BCs) are important for feedforward and feedback inhibition. During network activity, BCs respond with short latency and high temporal precision. It is thought that the specific properties of input synapses are responsible for rapid recruitment. However, a potential contribution of active dendritic conductances has not been addressed. We combined confocal imaging and patch-clamp techniques to obtain simultaneous somatodendritic recordings from BCs. Action potentials were initiated in the BC axon and backpropagated into the dendrites with reduced amplitude and little activity dependence. These properties were explained by a high K+ to Na+ conductance ratio in BC dendrites. Computational analysis indicated that dendritic K+ channels convey unique integration properties to BCs, leading to the rapid and temporally precise activation by excitatory inputs.","lang":"eng"}],"date_created":"2018-12-11T12:05:24Z","volume":327,"date_published":"2010-01-01T00:00:00Z","doi":"10.1126/science.1177876","issue":"5961","page":"52 - 8","publication":"Science","day":"01","year":"2010","publication_status":"published"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jonas, Peter M., and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons: Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali & Todorova).” The European Journal of Neuroscience, vol. 31, no. 7, Wiley-Blackwell, 2010, pp. 1194–95, doi:10.1111/j.1460-9568.2010.07189.x.","ama":"Jonas PM, Hefft S. GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova). The European Journal of Neuroscience. 2010;31(7):1194-1195. doi:10.1111/j.1460-9568.2010.07189.x","apa":"Jonas, P. M., & Hefft, S. (2010). GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova). The European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2010.07189.x","short":"P.M. Jonas, S. Hefft, The European Journal of Neuroscience 31 (2010) 1194–1195.","ieee":"P. M. Jonas and S. Hefft, “GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova),” The European Journal of Neuroscience, vol. 31, no. 7. Wiley-Blackwell, pp. 1194–1195, 2010.","chicago":"Jonas, Peter M, and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons: Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali & Todorova).” The European Journal of Neuroscience. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1460-9568.2010.07189.x.","ista":"Jonas PM, Hefft S. 2010. GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova). The European Journal of Neuroscience. 31(7), 1194–1195."},"date_updated":"2021-01-12T07:52:31Z","department":[{"_id":"PeJo"}],"title":"GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova)","publist_id":"2378","author":[{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","full_name":"Hefft, Stefan","last_name":"Hefft"}],"article_processing_charge":"No","_id":"3833","status":"public","type":"journal_article","day":"19","language":[{"iso":"eng"}],"publication":"The European Journal of Neuroscience","publication_status":"published","year":"2010","volume":31,"doi":"10.1111/j.1460-9568.2010.07189.x","issue":"7","date_published":"2010-03-19T00:00:00Z","date_created":"2018-12-11T12:05:25Z","page":"1194 - 1195","oa_version":"None","month":"03","intvolume":" 31","scopus_import":1,"quality_controlled":"1","publisher":"Wiley-Blackwell"},{"month":"01","intvolume":" 13","quality_controlled":0,"publisher":"Nature Publishing Group","abstract":[{"text":"To determine the number of open Ca(2+) channels necessary for transmitter release at the inhibitory basket cell-granule cell synapse in rat hippocampus, we combined presynaptic Ca(2+) imaging, recording of postsynaptic currents and modeling. We found that that the opening of three or fewer Ca(2+) channels triggered transmitter release. Furthermore, a small number of Ca(2+) channels were able to evoke release with high temporal precision, despite stochastic Ca(2+) channel opening.","lang":"eng"}],"date_published":"2010-01-01T00:00:00Z","volume":13,"doi":"10.1038/nn.2461 ","issue":"1","date_created":"2018-12-11T12:05:24Z","page":"19 - 21","day":"01","publication":"Nature Neuroscience","publication_status":"published","year":"2010","status":"public","type":"journal_article","_id":"3829","title":"A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse","publist_id":"2380","author":[{"first_name":"Iancu","full_name":"Bucurenciu, Iancu","last_name":"Bucurenciu"},{"first_name":"Josef","last_name":"Bischofberger","full_name":"Bischofberger, Josef"},{"full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"extern":1,"date_updated":"2021-01-12T07:52:29Z","citation":{"ista":"Bucurenciu I, Bischofberger J, Jonas PM. 2010. A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse. Nature Neuroscience. 13(1), 19–21.","chicago":"Bucurenciu, Iancu, Josef Bischofberger, and Peter M Jonas. “A Small Number of Open Ca(2+) Channels Trigger Transmitter Release at a Central GABAergic Synapse.” Nature Neuroscience. Nature Publishing Group, 2010. https://doi.org/10.1038/nn.2461 .","short":"I. Bucurenciu, J. Bischofberger, P.M. Jonas, Nature Neuroscience 13 (2010) 19–21.","ieee":"I. Bucurenciu, J. Bischofberger, and P. M. Jonas, “A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse,” Nature Neuroscience, vol. 13, no. 1. Nature Publishing Group, pp. 19–21, 2010.","apa":"Bucurenciu, I., Bischofberger, J., & Jonas, P. M. (2010). A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2461 ","ama":"Bucurenciu I, Bischofberger J, Jonas PM. A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse. Nature Neuroscience. 2010;13(1):19-21. doi:10.1038/nn.2461 ","mla":"Bucurenciu, Iancu, et al. “A Small Number of Open Ca(2+) Channels Trigger Transmitter Release at a Central GABAergic Synapse.” Nature Neuroscience, vol. 13, no. 1, Nature Publishing Group, 2010, pp. 19–21, doi:10.1038/nn.2461 ."}},{"file":[{"file_name":"IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf","date_created":"2018-12-12T10:09:03Z","file_size":433824,"date_updated":"2020-07-14T12:46:17Z","creator":"system","checksum":"38707b149d2174f01be406e794ffa849","file_id":"4726","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these reactions can be modeled as transitions of a Markov chain. SABRE accepts as input the formalism of guarded commands, which it interprets either as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic analysis by directly computing a mean-field approximation of the system under study. We illustrate the different functionalities of SABRE by means of biological case studies."}],"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:17Z","ddc":["004"],"date_updated":"2021-01-12T07:52:37Z","status":"public","pubrep_id":"63","type":"conference","conference":{"name":"QEST: Quantitative Evaluation of Systems","location":"Williamsburg, USA","end_date":"2010-09-18","start_date":"2010-09-15"},"_id":"3847","date_published":"2010-10-14T00:00:00Z","doi":"10.1109/QEST.2010.33","date_created":"2018-12-11T12:05:29Z","page":"193 - 194","day":"14","has_accepted_license":"1","year":"2010","publisher":"IEEE","quality_controlled":"1","oa":1,"title":"SABRE: A tool for the stochastic analysis of biochemical reaction networks","author":[{"last_name":"Didier","full_name":"Didier, Frédéric","first_name":"Frédéric"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria"},{"first_name":"Verena","last_name":"Wolf","full_name":"Wolf, Verena"}],"publist_id":"2339","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). SABRE: A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194). Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA: IEEE. https://doi.org/10.1109/QEST.2010.33","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. SABRE: A tool for the stochastic analysis of biochemical reaction networks. In: IEEE; 2010:193-194. doi:10.1109/QEST.2010.33","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for the stochastic analysis of biochemical reaction networks,” presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.","mla":"Didier, Frédéric, et al. SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks. IEEE, 2010, pp. 193–94, doi:10.1109/QEST.2010.33.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems, 193–194.","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,” 193–94. IEEE, 2010. https://doi.org/10.1109/QEST.2010.33."}},{"publist_id":"2342","author":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thibaud","last_name":"Hottelier","full_name":"Hottelier, Thibaud"},{"first_name":"Laura","last_name":"Kovács","full_name":"Kovács, Laura"},{"last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey","first_name":"Andrey"}],"title":"Aligators for arrays","citation":{"chicago":"Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrey Rybalchenko. “Aligators for Arrays,” 6397:348–56. Springer, 2010. https://doi.org/10.1007/978-3-642-16242-8_25.","ista":"Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. 2010. Aligators for arrays. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 6397, 348–356.","mla":"Henzinger, Thomas A., et al. Aligators for Arrays. Vol. 6397, Springer, 2010, pp. 348–56, doi:10.1007/978-3-642-16242-8_25.","ieee":"T. A. Henzinger, T. Hottelier, L. Kovács, and A. Rybalchenko, “Aligators for arrays,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Yogyakarta, Indonesia, 2010, vol. 6397, pp. 348–356.","short":"T.A. Henzinger, T. Hottelier, L. Kovács, A. Rybalchenko, in:, Springer, 2010, pp. 348–356.","apa":"Henzinger, T. A., Hottelier, T., Kovács, L., & Rybalchenko, A. (2010). Aligators for arrays (Vol. 6397, pp. 348–356). 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Springer; 2010:348-356. doi:10.1007/978-3-642-16242-8_25"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"348 - 356","date_created":"2018-12-11T12:05:29Z","date_published":"2010-10-01T00:00:00Z","doi":"10.1007/978-3-642-16242-8_25","year":"2010","has_accepted_license":"1","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer","file_date_updated":"2020-07-14T12:46:17Z","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:52:37Z","ddc":["005"],"conference":{"location":"Yogyakarta, Indonesia","end_date":"2010-10-15","start_date":"2010-10-10","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning"},"type":"conference","pubrep_id":"64","status":"public","_id":"3845","volume":6397,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"913af269da6710f2174f470b48ab7a82","file_id":"4790","file_size":186143,"date_updated":"2020-07-14T12:46:17Z","creator":"system","file_name":"IST-2012-64-v1+1_Aligators_for_arrays.pdf","date_created":"2018-12-12T10:10:05Z"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 6397","month":"10","abstract":[{"lang":"eng","text":"This paper presents Aligators, a tool for the generation of universally quantified array invariants. Aligators leverages recurrence solving and algebraic techniques to carry out inductive reasoning over array content. The Aligators’ loop extraction module allows treatment of multi-path loops by exploiting their commutativity and serializability properties. Our experience in applying Aligators on a collection of loops from open source software projects indicates the applicability of recurrence and algebraic solving techniques for reasoning about arrays."}],"oa_version":"Submitted Version"},{"author":[{"full_name":"Didier, Frédéric","last_name":"Didier","first_name":"Frédéric"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Mateescu, Maria","last_name":"Mateescu","first_name":"Maria"},{"last_name":"Wolf","full_name":"Wolf, Verena","first_name":"Verena"}],"publist_id":"2349","title":"Fast adaptive uniformization of the chemical master equation","citation":{"ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization of the chemical master equation. 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An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). The uniformization technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this paper we present an on-the-fly variant of uniformization, where we improve the original algorithm at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks."}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"earlier_version","id":"3843","status":"public"}]},"issue":"6","volume":4,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2012-66-v1+1_Fast_adaptive_uniformization_of_the_chemical_master_equation.pdf","date_created":"2018-12-12T10:17:02Z","creator":"system","file_size":222890,"date_updated":"2020-07-14T12:46:16Z","checksum":"9a3bde48f43203991a0b3c6a277c2f5b","file_id":"5254","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}]},{"quality_controlled":"1","publisher":"Springer","alternative_title":["LNCS"],"scopus_import":1,"month":"09","intvolume":" 6346","abstract":[{"lang":"eng","text":"We define the robustness of a level set homology class of a function f:XR as the magnitude of a perturbation necessary to kill the class. Casting this notion into a group theoretic framework, we compute the robustness for each class, using a connection to extended persistent homology. The special case X=R3 has ramifications in medical imaging and scientific visualization."}],"oa_version":"None","page":"1 - 10","doi":"10.1007/978-3-642-15775-2_1","date_published":"2010-09-01T00:00:00Z","volume":6346,"date_created":"2018-12-11T12:05:30Z","year":"2010","publication_status":"published","day":"01","language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2010-09-08","location":"Liverpool, UK","start_date":"2010-09-06","name":"ESA: European Symposium on Algorithms"},"status":"public","_id":"3848","publist_id":"2336","author":[{"first_name":"Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich","full_name":"Bendich, Paul"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Dmitriy","last_name":"Morozov","full_name":"Morozov, Dmitriy"},{"first_name":"Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","full_name":"Patel, Amit","last_name":"Patel"}],"department":[{"_id":"HeEd"}],"title":"The robustness of level sets","citation":{"chicago":"Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “The Robustness of Level Sets,” 6346:1–10. 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Patel, in:, Springer, 2010, pp. 1–10."},"date_updated":"2021-01-12T07:52:38Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"_id":"3858","type":"conference","conference":{"start_date":"2010-10-10","end_date":"2010-10-15","location":"Yogyakarta, Indonesia","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning"},"status":"public","date_updated":"2021-01-12T07:52:43Z","ddc":["000"],"file_date_updated":"2020-07-14T12:46:18Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"We consider two-player zero-sum games on graphs. On the basis of the information available to the players these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have com- plete view of the game). We survey the complexity results for the problem of de- ciding the winner in various classes of partial-observation games with ω-regular winning conditions specified as parity objectives. We present a reduction from the class of parity objectives that depend on sequence of states of the game to the sub-class of parity objectives that only depend on the sequence of observations. We also establish that partial-observation acyclic games are PSPACE-complete."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"month":"12","intvolume":" 6397","publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"770e86e5d78c56fddb4786a8da7ef126","file_id":"7872","creator":"dernst","date_updated":"2020-07-14T12:46:18Z","file_size":142836,"date_created":"2020-05-19T16:29:04Z","file_name":"2010_LPAR_Chatterjee.pdf"}],"language":[{"iso":"eng"}],"volume":6397,"citation":{"ista":"Chatterjee K, Doyen L. 2010. The complexity of partial-observation parity games. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 6397, 1–14.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “The Complexity of Partial-Observation Parity Games,” 6397:1–14. Springer, 2010. https://doi.org/10.1007/978-3-642-16242-8_1.","apa":"Chatterjee, K., & Doyen, L. (2010). 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Vol. 6397, Springer, 2010, pp. 1–14, doi:10.1007/978-3-642-16242-8_1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2323","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"article_processing_charge":"No","title":"The complexity of partial-observation parity games","quality_controlled":"1","publisher":"Springer","oa":1,"has_accepted_license":"1","year":"2010","day":"09","page":"1 - 14","doi":"10.1007/978-3-642-16242-8_1","date_published":"2010-12-09T00:00:00Z","date_created":"2018-12-11T12:05:33Z"},{"project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Gimbert","full_name":"Gimbert, Hugo","first_name":"Hugo"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"publist_id":"2325","title":"Randomness for free","citation":{"mla":"Chatterjee, Krishnendu, et al. Randomness for Free. Vol. 6281, Springer, 2010, pp. 246–57, doi:10.1007/978-3-642-15155-2_23.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., & Henzinger, T. A. (2010). Randomness for free (Vol. 6281, pp. 246–257). Presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-15155-2_23","ama":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. Randomness for free. In: Vol 6281. Springer; 2010:246-257. doi:10.1007/978-3-642-15155-2_23","short":"K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, in:, Springer, 2010, pp. 246–257.","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and T. A. Henzinger, “Randomness for free,” presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic, 2010, vol. 6281, pp. 246–257.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Thomas A Henzinger. “Randomness for Free,” 6281:246–57. Springer, 2010. https://doi.org/10.1007/978-3-642-15155-2_23.","ista":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2010. Randomness for free. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6281, 246–257."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"This research was supported by the European Union project COMBEST and the European Network of Excellence ArtistDesign.","page":"246 - 257","date_created":"2018-12-11T12:05:32Z","doi":"10.1007/978-3-642-15155-2_23","date_published":"2010-09-06T00:00:00Z","year":"2010","day":"06","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2010-08-23","end_date":"2010-08-27","location":"Brno, Czech Republic"},"type":"conference","pubrep_id":"60","status":"public","_id":"3856","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-02-23T10:12:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1006.0673v1"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 6281","month":"09","abstract":[{"text":"We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (players interact simultaneously); and (b) turn-based (players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. We present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function (probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. ","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"status":"public","id":"1731","relation":"later_version"}]},"volume":6281,"publication_status":"published","language":[{"iso":"eng"}]},{"oa_version":"None","abstract":[{"lang":"eng","text":"This book constitutes the proceedings of the 8th International Conference on Formal Modeling and Analysis of Timed Systems, FORMATS 2010, held in Klosterneuburg, Austria in September 2010. The 14 papers presented were carefully reviewed and selected from 31 submissions. In addition, the volume contains 3 invited talks and 2 invited tutorials.The aim of FORMATS is to promote the study of fundamental and practical aspects of timed systems, and to bring together researchers from different disciplines that share an interest in the modeling and analysis of timed systems. Typical topics include foundations and semantics, methods and tools, and applications."}],"month":"09","intvolume":" 6246","quality_controlled":"1","publisher":"Springer","alternative_title":["LNCS"],"day":"20","language":[{"iso":"eng"}],"publication_status":"published","year":"2010","related_material":{"link":[{"relation":"other","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=12721","description":"eBook available via IST BookList"}]},"date_published":"2010-09-20T00:00:00Z","volume":6246,"doi":"10.1007/978-3-642-15297-9","date_created":"2018-12-11T12:05:33Z","_id":"3859","status":"public","type":"conference_editor","conference":{"end_date":"2010-09-10","location":"Klosterneuburg, Austria","start_date":"2010-09-08","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2019-11-14T08:42:42Z","citation":{"ista":"Chatterjee K, Henzinger TA eds. 2010. Formal modeling and analysis of timed systems, Springer,p.","chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger, eds. Formal Modeling and Analysis of Timed Systems. Vol. 6246. Springer, 2010. https://doi.org/10.1007/978-3-642-15297-9.","ieee":"K. Chatterjee and T. A. Henzinger, Eds., Formal modeling and analysis of timed systems, vol. 6246. Springer, 2010.","short":"K. Chatterjee, T.A. Henzinger, eds., Formal Modeling and Analysis of Timed Systems, Springer, 2010.","apa":"Chatterjee, K., & Henzinger, T. A. (Eds.). (2010). Formal modeling and analysis of timed systems (Vol. 6246). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-15297-9","ama":"Chatterjee K, Henzinger TA, eds. Formal Modeling and Analysis of Timed Systems. Vol 6246. Springer; 2010. doi:10.1007/978-3-642-15297-9","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger, editors. Formal Modeling and Analysis of Timed Systems. Vol. 6246, Springer, 2010, doi:10.1007/978-3-642-15297-9."},"editor":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Formal modeling and analysis of timed systems","publist_id":"2322"},{"date_updated":"2021-01-12T07:52:47Z","ddc":["004"],"file_date_updated":"2020-07-14T12:46:19Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"3866","type":"conference","conference":{"name":"CAV: Computer Aided Verification","start_date":"2010-07-15","end_date":"2010-07-19","location":"Edinburgh, UK"},"status":"public","pubrep_id":"54","publication_status":"published","file":[{"file_id":"5243","checksum":"9d204611c8d7855bed8134f8708a0010","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:52Z","file_name":"IST-2012-54-v1+1_Robustness_in_the_presence_of_liveness.pdf","creator":"system","date_updated":"2020-07-14T12:46:19Z","file_size":213083}],"language":[{"iso":"eng"}],"volume":6174,"ec_funded":1,"abstract":[{"text":"Systems ought to behave reasonably even in circumstances that are not anticipated in their specifications. We propose a definition of robustness for liveness specifications which prescribes, for any number of environment assumptions that are violated, a minimal number of system guarantees that must still be fulfilled. This notion of robustness can be formulated and realized using a Generalized Reactivity formula. We present an algorithm for synthesizing robust systems from such formulas. For the important special case of Generalized Reactivity formulas of rank 1, our algorithm improves the complexity of [PPS06] for large specifications with a small number of assumptions and guarantees.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"month":"07","intvolume":" 6174","citation":{"short":"R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, T. Touili, B. Cook, P. Jackson (Eds.), Springer, 2010, pp. 410–424.","ieee":"R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Robustness in the presence of liveness,” presented at the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 410–424.","ama":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Robustness in the presence of liveness. In: Touili T, Cook B, Jackson P, eds. Vol 6174. Springer; 2010:410-424. doi:10.1007/978-3-642-14295-6_36","apa":"Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann, B. (2010). Robustness in the presence of liveness. In T. Touili, B. Cook, & P. Jackson (Eds.) (Vol. 6174, pp. 410–424). Presented at the CAV: Computer Aided Verification, Edinburgh, UK: Springer. https://doi.org/10.1007/978-3-642-14295-6_36","mla":"Bloem, Roderick, et al. Robustness in the Presence of Liveness. Edited by Tayssir Touili et al., vol. 6174, Springer, 2010, pp. 410–24, doi:10.1007/978-3-642-14295-6_36.","ista":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2010. Robustness in the presence of liveness. CAV: Computer Aided Verification, LNCS, vol. 6174, 410–424.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Robustness in the Presence of Liveness.” edited by Tayssir Touili, Byron Cook, and Paul Jackson, 6174:410–24. Springer, 2010. https://doi.org/10.1007/978-3-642-14295-6_36."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"2310","author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Karin","full_name":"Greimel, Karin","last_name":"Greimel"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"title":"Robustness in the presence of liveness","editor":[{"first_name":"Tayssir","last_name":"Touili","full_name":"Touili, Tayssir"},{"last_name":"Cook","full_name":"Cook, Byron","first_name":"Byron"},{"first_name":"Paul","last_name":"Jackson","full_name":"Jackson, Paul"}],"project":[{"name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","grant_number":"214373"}],"has_accepted_license":"1","year":"2010","day":"01","page":"410 - 424","date_published":"2010-07-01T00:00:00Z","doi":"10.1007/978-3-642-14295-6_36","date_created":"2018-12-11T12:05:36Z","publisher":"Springer","quality_controlled":"1","oa":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath Raman. “Algorithms for Game Metrics.” Logical Methods in Computer Science. International Federation of Computational Logic, 2010. https://doi.org/10.2168/LMCS-6(3:13)2010.","ista":"Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2010. Algorithms for game metrics. Logical Methods in Computer Science. 6(3), 1–27.","mla":"Chatterjee, Krishnendu, et al. “Algorithms for Game Metrics.” Logical Methods in Computer Science, vol. 6, no. 3, International Federation of Computational Logic, 2010, pp. 1–27, doi:10.2168/LMCS-6(3:13)2010.","short":"K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, Logical Methods in Computer Science 6 (2010) 1–27.","ieee":"K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game metrics,” Logical Methods in Computer Science, vol. 6, no. 3. International Federation of Computational Logic, pp. 1–27, 2010.","apa":"Chatterjee, K., De Alfaro, L., Majumdar, R., & Raman, V. (2010). Algorithms for game metrics. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-6(3:13)2010","ama":"Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics. Logical Methods in Computer Science. 2010;6(3):1-27. doi:10.2168/LMCS-6(3:13)2010"},"title":"Algorithms for game metrics","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Luca","full_name":"De Alfaro, Luca","last_name":"De Alfaro"},{"last_name":"Majumdar","full_name":"Majumdar, Ritankar","first_name":"Ritankar"},{"first_name":"Vishwanath","full_name":"Raman, Vishwanath","last_name":"Raman"}],"publist_id":"2312","quality_controlled":"1","publisher":"International Federation of Computational Logic","oa":1,"day":"01","publication":"Logical Methods in Computer Science","has_accepted_license":"1","year":"2010","date_published":"2010-09-01T00:00:00Z","doi":"10.2168/LMCS-6(3:13)2010","date_created":"2018-12-11T12:05:36Z","page":"1 - 27","_id":"3868","status":"public","pubrep_id":"370","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"ddc":["000"],"date_updated":"2023-02-23T11:30:18Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:19Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Simulation and bisimulation metrics for stochastic systems provide a quantitative generalization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative mu-calculus and related probabilistic logics. We first show that the metrics provide a bound for the difference in long-run average and discounted average behavior across states, indicating that the metrics can be used both in system verification, and in performance evaluation. For turn-based games and MDPs, we provide a polynomial-time algorithm for the computation of the one-step metric distance between states. The algorithm is based on linear programming; it improves on the previous known exponential-time algorithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known algorithms for Markov chains. For the bisimulation kernel of the metric our algorithm works in time O(n(4)) for both turn-based games and MDPs; improving the previously best known O(n(9).log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance be tween states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be done via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(vertical bar G vertical bar(O(vertical bar G vertical bar 5))) time complexity, improving the previously known reduction, which yielded O(vertical bar G vertical bar(O(vertical bar G vertical bar 7))) time complexity. These algorithms can be iterated to approximate the metrics using binary search"}],"month":"09","intvolume":" 6","scopus_import":1,"file":[{"date_created":"2018-12-12T10:08:11Z","file_name":"IST-2015-370-v1+1_0809.4326.pdf","creator":"system","date_updated":"2020-07-14T12:46:19Z","file_size":346527,"checksum":"a18988135fef3016c93808ecb15b55f5","file_id":"4671","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"3504","relation":"earlier_version"}]},"volume":6,"issue":"3","license":"https://creativecommons.org/licenses/by-nd/4.0/"},{"abstract":[{"text":"Combining concepts from topology and algorithms, this book delivers what its title promises: an introduction to the field of computational topology. Starting with motivating problems in both mathematics and computer science and building up from classic topics in geometric and algebraic topology, the third part of the text advances to persistent homology. This point of view is critically important in turning a mostly theoretical field of mathematics into one that is relevant to a multitude of disciplines in the sciences and engineering. The main approach is the discovery of topology through algorithms. The book is ideal for teaching a graduate or advanced undergraduate course in computational topology, as it develops all the background of both the mathematical and algorithmic aspects of the subject from first principles. Thus the text could serve equally well in a course taught in a mathematics department or computer science department.","lang":"eng"}],"oa_version":"None","main_file_link":[{"url":"https://www.ams.org/books/mbk/069/"}],"publisher":"American Mathematical Society","quality_controlled":"1","intvolume":" 69","month":"01","publication_status":"published","year":"2010","publication_identifier":{"isbn":["978-0-8218-4925-5"],"eisbn":["978-1-4704-1208-1"]},"language":[{"iso":"eng"}],"day":"15","page":"XII, 241","date_created":"2018-12-11T12:05:46Z","doi":"10.1090/mbk/069","related_material":{"link":[{"url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=3289","relation":"other","description":"available via catalog IST BookList"}]},"volume":69,"date_published":"2010-01-15T00:00:00Z","_id":"3899","type":"book","status":"public","date_updated":"2021-12-21T12:26:50Z","citation":{"mla":"Edelsbrunner, Herbert, and John Harer. Computational Topology: An Introduction. Vol. 69, American Mathematical Society, 2010, doi:10.1090/mbk/069.","short":"H. Edelsbrunner, J. Harer, Computational Topology: An Introduction, American Mathematical Society, 2010.","ieee":"H. Edelsbrunner and J. Harer, Computational Topology: An Introduction, vol. 69. American Mathematical Society, 2010.","ama":"Edelsbrunner H, Harer J. Computational Topology: An Introduction. Vol 69. American Mathematical Society; 2010. doi:10.1090/mbk/069","apa":"Edelsbrunner, H., & Harer, J. (2010). Computational Topology: An Introduction (Vol. 69). American Mathematical Society. https://doi.org/10.1090/mbk/069","chicago":"Edelsbrunner, Herbert, and John Harer. Computational Topology: An Introduction. Vol. 69. American Mathematical Society, 2010. https://doi.org/10.1090/mbk/069.","ista":"Edelsbrunner H, Harer J. 2010. Computational Topology: An Introduction, American Mathematical Society, XII, 241p."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","article_processing_charge":"No","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Harer","full_name":"Harer, John","first_name":"John"}],"publist_id":"2258","title":"Computational Topology: An Introduction"},{"intvolume":" 4","month":"01","publisher":"Springer","oa_version":"None","abstract":[{"text":"Almost all species of the orchid genus Ophrys are pollinated by sexual deception. The orchids mimic the sex pheromone of receptive female insects, mainly hymenopterans, in order to attract males seeking to copulate. Most Ophrys species have achromatic flowers, but some exhibit a coloured perianth and a bright, conspicuous labellum pattern. We recently showed that the pink perianth of Ophrys heldreichii flowers increases detectability by its pollinator, males of the long-horned bee Eucera berlandi. Here we tested the hypothesis that the bright, complex labellum pattern mimics the female of the pollinator to increase attractiveness toward males. In a dual-choice test we offered E. berlandi males an O. heldreichii flower and a flower from O. dictynnae, which also exhibits a pinkish perianth but no conspicuous labellum pattern. Both flowers were housed in UV-transmitting acrylic glass boxes to exclude olfactory signals. Males significantly preferred O. heldreichii to O. dictynnae flowers. In a second experiment, we replaced the perianth of both flowers with identical artificial perianths made from pink card, so that only the labellum differed between the two flower stimuli. Males then chose between both stimuli at random, suggesting that the presence of a labellum pattern does not affect their choice. Spectral measurements revealed higher colour contrast with the background of the perianth of O. heldreichii compared to O. dictynnae, but no difference in green receptor-specific contrast or brightness. Our results show that male choice is guided by the chromatic contrast of the perianth during the initial flower approach but is not affected by the presence of a labellum pattern. Instead, we hypothesise that the labellum pattern is involved in aversive learning during post-copulatory behaviour and used by the orchid as a strategy to increase outcrossing.","lang":"eng"}],"date_created":"2018-12-11T12:06:08Z","volume":4,"doi":"10.1007/s11829-010-9093-4","issue":"3","date_published":"2010-01-01T00:00:00Z","page":"141 - 148","publication":"Arthropod-Plant Interactions","language":[{"iso":"eng"}],"day":"01","year":"2010","publication_status":"published","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","_id":"3963","title":"Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator","article_processing_charge":"No","author":[{"full_name":"Streinzer, M.","last_name":"Streinzer","first_name":"M."},{"orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Paulus","full_name":"Paulus, H.","first_name":"H."},{"full_name":"Spaethe, J.","last_name":"Spaethe","first_name":"J."}],"publist_id":"2164","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T07:53:30Z","citation":{"chicago":"Streinzer, M., Thomas Ellis, H. Paulus, and J. Spaethe. “Visual Discrimination between Two Sexually Deceptive Ophrys Species by a Bee Pollinator.” Arthropod-Plant Interactions. Springer, 2010. https://doi.org/10.1007/s11829-010-9093-4.","ista":"Streinzer M, Ellis T, Paulus H, Spaethe J. 2010. Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions. 4(3), 141–148.","mla":"Streinzer, M., et al. “Visual Discrimination between Two Sexually Deceptive Ophrys Species by a Bee Pollinator.” Arthropod-Plant Interactions, vol. 4, no. 3, Springer, 2010, pp. 141–48, doi:10.1007/s11829-010-9093-4.","ieee":"M. Streinzer, T. Ellis, H. Paulus, and J. Spaethe, “Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator,” Arthropod-Plant Interactions, vol. 4, no. 3. Springer, pp. 141–148, 2010.","short":"M. Streinzer, T. Ellis, H. Paulus, J. Spaethe, Arthropod-Plant Interactions 4 (2010) 141–148.","apa":"Streinzer, M., Ellis, T., Paulus, H., & Spaethe, J. (2010). Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions. Springer. https://doi.org/10.1007/s11829-010-9093-4","ama":"Streinzer M, Ellis T, Paulus H, Spaethe J. Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions. 2010;4(3):141-148. doi:10.1007/s11829-010-9093-4"}},{"publisher":"Cell Press","intvolume":" 32","month":"05","abstract":[{"lang":"eng","text":"Chemokines orchestrate immune cell trafficking by eliciting either directed or random migration and by activating integrins in order to induce cell adhesion. Analyzing dendritic cell (DC) migration, we showed that these distinct cellular responses depended on the mode of chemokine presentation within tissues. The surface-immobilized form of the chemokine CCL21, the heparan sulfate-anchoring ligand of the CC-chemokine receptor 7 (CCR7), caused random movement of DCs that was confined to the chemokine-presenting surface because it triggered integrin-mediated adhesion. Upon direct contact with CCL21, DCs truncated the anchoring residues of CCL21, thereby releasing it from the solid phase. Soluble CCL21 functionally resembles the second CCR7 ligand, CCL19, which lacks anchoring residues and forms soluble gradients. Both soluble CCR7 ligands triggered chemotactic movement, but not surface adhesion. Adhesive random migration and directional steering cooperate to produce dynamic but spatially restricted locomotion patterns closely resembling the cellular dynamics observed in secondary lymphoid organs."}],"oa_version":"None","page":"703 - 713","date_created":"2018-12-11T12:06:07Z","issue":"5","date_published":"2010-05-28T00:00:00Z","doi":"10.1016/j.immuni.2010.04.017","volume":32,"year":"2010","publication_status":"published","language":[{"iso":"eng"}],"publication":"Immunity","day":"28","type":"journal_article","status":"public","_id":"3959","publist_id":"2168","author":[{"full_name":"Schumann, Kathrin","last_name":"Schumann","first_name":"Kathrin","id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F"},{"last_name":"Lämmermann","full_name":"Lämmermann, Tim","first_name":"Tim"},{"last_name":"Bruckner","full_name":"Bruckner, Markus","first_name":"Markus"},{"last_name":"Legler","full_name":"Legler, Daniel","first_name":"Daniel"},{"first_name":"Julien","full_name":"Polleux, Julien","last_name":"Polleux"},{"full_name":"Spatz, Joachim","last_name":"Spatz","first_name":"Joachim"},{"full_name":"Schuler, Gerold","last_name":"Schuler","first_name":"Gerold"},{"last_name":"Förster","full_name":"Förster, Reinhold","first_name":"Reinhold"},{"full_name":"Lutz, Manfred","last_name":"Lutz","first_name":"Manfred"},{"first_name":"Lydia","full_name":"Sorokin, Lydia","last_name":"Sorokin"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells","citation":{"mla":"Schumann, Kathrin, et al. “Immobilized Chemokine Fields and Soluble Chemokine Gradients Cooperatively Shape Migration Patterns of Dendritic Cells.” Immunity, vol. 32, no. 5, Cell Press, 2010, pp. 703–13, doi:10.1016/j.immuni.2010.04.017.","ieee":"K. Schumann et al., “Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells,” Immunity, vol. 32, no. 5. Cell Press, pp. 703–713, 2010.","short":"K. Schumann, T. Lämmermann, M. Bruckner, D. Legler, J. Polleux, J. Spatz, G. Schuler, R. Förster, M. Lutz, L. Sorokin, M.K. Sixt, Immunity 32 (2010) 703–713.","apa":"Schumann, K., Lämmermann, T., Bruckner, M., Legler, D., Polleux, J., Spatz, J., … Sixt, M. K. (2010). Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2010.04.017","ama":"Schumann K, Lämmermann T, Bruckner M, et al. Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells. Immunity. 2010;32(5):703-713. doi:10.1016/j.immuni.2010.04.017","chicago":"Schumann, Kathrin, Tim Lämmermann, Markus Bruckner, Daniel Legler, Julien Polleux, Joachim Spatz, Gerold Schuler, et al. “Immobilized Chemokine Fields and Soluble Chemokine Gradients Cooperatively Shape Migration Patterns of Dendritic Cells.” Immunity. Cell Press, 2010. https://doi.org/10.1016/j.immuni.2010.04.017.","ista":"Schumann K, Lämmermann T, Bruckner M, Legler D, Polleux J, Spatz J, Schuler G, Förster R, Lutz M, Sorokin L, Sixt MK. 2010. Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells. Immunity. 32(5), 703–713."},"date_updated":"2021-01-12T07:53:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"year":"2010","publication_status":"published","day":"01","publication":"Brain Pathology","page":"966 - 975","issue":"5","date_published":"2010-09-01T00:00:00Z","doi":"10.1111/j.1750-3639.2010.00399.x","volume":20,"date_created":"2018-12-11T12:06:07Z","abstract":[{"lang":"eng","text":"Extracellular matrix (ECM) proteins can modify immune reactions, e.g. by sequestering or displaying growth factors and by interacting with immune and glial cells. Here we quantified by quantitative polymerase chain reaction (qPCR) expression of 50 ECM components and 34 ECM degrading enzymes in multiple sclerosis (MS) active and inactive white matter lesions. COL1A1, COL3A1, COL5A1 and COL5A2 chains were induced strongly in active lesions and even more in inactive lesions. These chains interact to form collagen types I, III and V, which are fibrillar collagens. Biglycan and decorin, which can decorate fibrillar collagens, were also induced strongly. The fibrillar collagens, biglycan and decorin were largely found between the endothelium and astrocytic glia limitans in the perivascular space where they formed a meshwork which was closely associated with infiltrating immune cells. In active lesions collagen V was also seen in the heavily infiltrated parenchyma. Fibrillar collagens I and III inhibited in vitro human monocyte production of CCL2 (MCP-1), an inflammatory chemokine involved in recruitment of immune cells. Together, ECM changes in lesions with different activities were quantified and proteins forming a perivascular fibrosis were identified. Induced fibrillar collagens may contribute to limiting enlargement of MS lesions by inhibiting the production of CCL2 by monocytes."}],"quality_controlled":0,"publisher":"Wiley-Blackwell","month":"09","intvolume":" 20","date_updated":"2021-01-12T07:53:28Z","citation":{"ista":"Mohan H, Krumbholz M, Sharma R, Eisele S, Junker A, Sixt MK, Newcombe J, Wekerle H, Hohlfeld R, Lassmann H, Meinl E. 2010. Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells. Brain Pathology. 20(5), 966–975.","chicago":"Mohan, Hema, Markus Krumbholz, Rakhi Sharma, Sylvia Eisele, Andreas Junker, Michael K Sixt, Jia Newcombe, et al. “Extracellular Matrix in Multiple Sclerosis Lesions: Fibrillar Collagens, Biglycan and Decorin Are Upregulated and Associated with Infiltrating Immune Cells.” Brain Pathology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1750-3639.2010.00399.x.","apa":"Mohan, H., Krumbholz, M., Sharma, R., Eisele, S., Junker, A., Sixt, M. K., … Meinl, E. (2010). Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells. Brain Pathology. Wiley-Blackwell. https://doi.org/10.1111/j.1750-3639.2010.00399.x","ama":"Mohan H, Krumbholz M, Sharma R, et al. Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells. Brain Pathology. 2010;20(5):966-975. doi:10.1111/j.1750-3639.2010.00399.x","short":"H. Mohan, M. Krumbholz, R. Sharma, S. Eisele, A. Junker, M.K. Sixt, J. Newcombe, H. Wekerle, R. Hohlfeld, H. Lassmann, E. Meinl, Brain Pathology 20 (2010) 966–975.","ieee":"H. Mohan et al., “Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells,” Brain Pathology, vol. 20, no. 5. Wiley-Blackwell, pp. 966–975, 2010.","mla":"Mohan, Hema, et al. “Extracellular Matrix in Multiple Sclerosis Lesions: Fibrillar Collagens, Biglycan and Decorin Are Upregulated and Associated with Infiltrating Immune Cells.” Brain Pathology, vol. 20, no. 5, Wiley-Blackwell, 2010, pp. 966–75, doi:10.1111/j.1750-3639.2010.00399.x."},"extern":1,"author":[{"first_name":"Hema","full_name":"Mohan, Hema","last_name":"Mohan"},{"first_name":"Markus","last_name":"Krumbholz","full_name":"Krumbholz, Markus"},{"first_name":"Rakhi","full_name":"Sharma, Rakhi","last_name":"Sharma"},{"full_name":"Eisele, Sylvia","last_name":"Eisele","first_name":"Sylvia"},{"full_name":"Junker, Andreas","last_name":"Junker","first_name":"Andreas"},{"full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"last_name":"Newcombe","full_name":"Newcombe, Jia","first_name":"Jia"},{"first_name":"Hartmut","last_name":"Wekerle","full_name":"Wekerle, Hartmut"},{"first_name":"Reinhard","full_name":"Hohlfeld, Reinhard","last_name":"Hohlfeld"},{"last_name":"Lassmann","full_name":"Lassmann, Hans","first_name":"Hans"},{"last_name":"Meinl","full_name":"Meinl, Edgar","first_name":"Edgar"}],"publist_id":"2169","title":"Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells","_id":"3958","type":"journal_article","status":"public"},{"title":"Mechanisms of force generation and force transmission during interstitial leukocyte migration","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","orcid":"0000-0003-2856-3369","full_name":"Jörg Renkawitz","last_name":"Renkawitz"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Michael Sixt","last_name":"Sixt"}],"publist_id":"2166","extern":1,"date_updated":"2021-01-12T07:53:30Z","citation":{"short":"J. Renkawitz, M.K. Sixt, EMBO Reports 11 (2010) 744–750.","ieee":"J. Renkawitz and M. K. Sixt, “Mechanisms of force generation and force transmission during interstitial leukocyte migration,” EMBO Reports, vol. 11, no. 10. Wiley-Blackwell, pp. 744–750, 2010.","apa":"Renkawitz, J., & Sixt, M. K. (2010). Mechanisms of force generation and force transmission during interstitial leukocyte migration. EMBO Reports. Wiley-Blackwell. https://doi.org/10.1038/embor.2010.147","ama":"Renkawitz J, Sixt MK. Mechanisms of force generation and force transmission during interstitial leukocyte migration. EMBO Reports. 2010;11(10):744-750. doi:10.1038/embor.2010.147","mla":"Renkawitz, Jörg, and Michael K. Sixt. “Mechanisms of Force Generation and Force Transmission during Interstitial Leukocyte Migration.” EMBO Reports, vol. 11, no. 10, Wiley-Blackwell, 2010, pp. 744–50, doi:10.1038/embor.2010.147.","ista":"Renkawitz J, Sixt MK. 2010. Mechanisms of force generation and force transmission during interstitial leukocyte migration. EMBO Reports. 11(10), 744–750.","chicago":"Renkawitz, Jörg, and Michael K Sixt. “Mechanisms of Force Generation and Force Transmission during Interstitial Leukocyte Migration.” EMBO Reports. Wiley-Blackwell, 2010. https://doi.org/10.1038/embor.2010.147."},"status":"public","type":"journal_article","_id":"3961","issue":"10","doi":"10.1038/embor.2010.147","volume":11,"date_published":"2010-09-24T00:00:00Z","date_created":"2018-12-11T12:06:08Z","page":"744 - 750","day":"24","publication":"EMBO Reports","year":"2010","publication_status":"published","month":"09","intvolume":" 11","quality_controlled":0,"publisher":"Wiley-Blackwell","acknowledgement":"We are grateful to Michele Weber for critical comments on the manuscript. Work in the laboratory of M.S. is supported by the German Research Foundation, the Peter Hans Hofschneider Foundation for Experimental Biomedicine and the Max Planck Society. J.R. is supported by a PhD fellowship of the Böhringer Ingelheim Fond. We thank Reinhard Fässler and Stefan Jentsch for their continuous support.","abstract":[{"text":"For innate and adaptive immune responses it is essential that inflammatory cells use quick and flexible locomotion strategies. Accordingly, most leukocytes can efficiently infiltrate and traverse almost every physiological or artificial environment. Here, we review how leukocytes might achieve this task mechanistically, and summarize recent findings on the principles of cytoskeletal force generation and transduction at the leading edge of leukocytes. We propose a model in which the cells switch between adhesion-receptor-mediated force transmission and locomotion modes that are based on cellular deformations, but independent of adhesion receptors. This plasticity in migration strategies allows leukocytes to adapt to the geometry and molecular composition of their environment.","lang":"eng"}]},{"citation":{"chicago":"Weber, Michele, and Michael K Sixt. “MEK Signalling Tunes Actin Treadmilling for Interstitial Lymphocyte Migration.” EMBO Journal. Wiley-Blackwell, 2010. https://doi.org/10.1038/emboj.2010.183.","ista":"Weber M, Sixt MK. 2010. MEK signalling tunes actin treadmilling for interstitial lymphocyte migration. EMBO Journal. 29(17), 2861–2863.","mla":"Weber, Michele, and Michael K. Sixt. “MEK Signalling Tunes Actin Treadmilling for Interstitial Lymphocyte Migration.” EMBO Journal, vol. 29, no. 17, Wiley-Blackwell, 2010, pp. 2861–63, doi:10.1038/emboj.2010.183.","ieee":"M. Weber and M. K. Sixt, “MEK signalling tunes actin treadmilling for interstitial lymphocyte migration,” EMBO Journal, vol. 29, no. 17. Wiley-Blackwell, pp. 2861–2863, 2010.","short":"M. Weber, M.K. Sixt, EMBO Journal 29 (2010) 2861–2863.","apa":"Weber, M., & Sixt, M. K. (2010). MEK signalling tunes actin treadmilling for interstitial lymphocyte migration. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2010.183","ama":"Weber M, Sixt MK. MEK signalling tunes actin treadmilling for interstitial lymphocyte migration. EMBO Journal. 2010;29(17):2861-2863. doi:10.1038/emboj.2010.183"},"date_updated":"2021-01-12T07:53:29Z","extern":1,"author":[{"last_name":"Weber","full_name":"Michele Weber","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"last_name":"Sixt","full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2167","title":"MEK signalling tunes actin treadmilling for interstitial lymphocyte migration","_id":"3960","type":"journal_article","status":"public","year":"2010","publication_status":"published","day":"01","publication":"EMBO Journal","page":"2861 - 2863","doi":"10.1038/emboj.2010.183","date_published":"2010-09-01T00:00:00Z","volume":29,"issue":"17","date_created":"2018-12-11T12:06:07Z","abstract":[{"text":"When lymphocytes follow chemotactic cues, they can adopt different migratory modes depending on the geometry and molecular composition of their extracellular environment. In this issue of The EMBO Journal, Klemke et al (2010) describe a novel Ras-dependent chemokine receptor signalling pathway that leads to activation of cofilin, which in turn amplifies actin turnover. This signalling module is exclusively required for lymphocyte migration in three-dimensional (3D) environments, but not for locomotion on two-dimensional (2D) surfaces.","lang":"eng"}],"quality_controlled":0,"publisher":"Wiley-Blackwell","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/issues/190105/"}],"month":"09","intvolume":" 29"}]