--- _id: '2922' author: - first_name: Sara full_name: Vicente, Sara last_name: Vicente - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Vicente S, Kolmogorov V, Rother C. Graph-cut Based Image Segmentation with Connectivity Priors. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Vicente, S., Kolmogorov, V., & Rother, C. (2011). Graph-cut Based Image Segmentation with Connectivity Priors. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph-Cut Based Image Segmentation with Connectivity Priors.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: S. Vicente, V. Kolmogorov, and C. Rother, “Graph-cut Based Image Segmentation with Connectivity Priors,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Vicente S, Kolmogorov V, Rother C. 2011.Graph-cut Based Image Segmentation with Connectivity Priors. In: Markov Random Fields for Vision and Image Processing. .' mla: Vicente, Sara, et al. “Graph-Cut Based Image Segmentation with Connectivity Priors.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: S. Vicente, V. Kolmogorov, C. Rother, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:21Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:43Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3815' quality_controlled: 0 status: public title: Graph-cut Based Image Segmentation with Connectivity Priors type: book_chapter year: '2011' ... --- _id: '2923' author: - first_name: M Pawan full_name: Kumar, M Pawan last_name: Kumar - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Philip full_name: Torr, Philip H last_name: Torr citation: ama: 'Kumar MP, Kolmogorov V, Torr P. Analyzing Convex Relaxations for MAP Estimation. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2011). Analyzing Convex Relaxations for MAP Estimation. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “Analyzing Convex Relaxations for MAP Estimation.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “Analyzing Convex Relaxations for MAP Estimation,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Kumar MP, Kolmogorov V, Torr P. 2011.Analyzing Convex Relaxations for MAP Estimation. In: Markov Random Fields for Vision and Image Processing. .' mla: Kumar, M. Pawan, et al. “Analyzing Convex Relaxations for MAP Estimation.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: M.P. Kumar, V. Kolmogorov, P. Torr, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:21Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:43Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3814' quality_controlled: 0 status: public title: Analyzing Convex Relaxations for MAP Estimation type: book_chapter year: '2011' ... --- _id: '2924' author: - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer Segmentation of Video. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2011). Bilayer Segmentation of Video. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov. “Bilayer Segmentation of Video.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer Segmentation of Video,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2011.Bilayer Segmentation of Video. In: Markov Random Fields for Vision and Image Processing. .' mla: Criminisi, Antonio, et al. “Bilayer Segmentation of Video.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:22Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:43Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3813' quality_controlled: 0 status: public title: Bilayer Segmentation of Video type: book_chapter year: '2011' ... --- _id: '2925' author: - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Andrew full_name: Blake, Andrew last_name: Blake citation: ama: 'Rother C, Kolmogorov V, Boykov Y, Blake A. Interactive Foreground Extraction using graph cut. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Rother, C., Kolmogorov, V., Boykov, Y., & Blake, A. (2011). Interactive Foreground Extraction using graph cut. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Rother, Carsten, Vladimir Kolmogorov, Yuri Boykov, and Andrew Blake. “Interactive Foreground Extraction Using Graph Cut.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: C. Rother, V. Kolmogorov, Y. Boykov, and A. Blake, “Interactive Foreground Extraction using graph cut,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Rother C, Kolmogorov V, Boykov Y, Blake A. 2011.Interactive Foreground Extraction using graph cut. In: Markov Random Fields for Vision and Image Processing. .' mla: Rother, Carsten, et al. “Interactive Foreground Extraction Using Graph Cut.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: C. Rother, V. Kolmogorov, Y. Boykov, A. Blake, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:22Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:44Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3812' quality_controlled: 0 status: public title: Interactive Foreground Extraction using graph cut type: book_chapter year: '2011' ... --- _id: '2935' author: - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Boykov Y, Kolmogorov V. Basic graph cut algorithms. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011:31-50.' apa: Boykov, Y., & Kolmogorov, V. (2011). Basic graph cut algorithms. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing (pp. 31–50). Massachusetts Institute of Technology Press. chicago: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother, 31–50. Massachusetts Institute of Technology Press, 2011. ieee: Y. Boykov and V. Kolmogorov, “Basic graph cut algorithms,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011, pp. 31–50. ista: 'Boykov Y, Kolmogorov V. 2011.Basic graph cut algorithms. In: Markov Random Fields for Vision and Image Processing. , 31–50.' mla: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011, pp. 31–50. short: Y. Boykov, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011, pp. 31–50. date_created: 2018-12-11T12:00:26Z date_published: 2011-07-22T00:00:00Z date_updated: 2021-01-12T07:39:53Z day: '22' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '07' page: 31 - 50 publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3801' quality_controlled: 0 status: public title: Basic graph cut algorithms type: book_chapter year: '2011' ... --- _id: '2961' abstract: - lang: eng text: |- Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs). acknowledgement: Anna-Sapfo Malaspinas is supported by a Janggen-Poehn Fellowship. Caroline Uhler is supported by an International Fulbright Science and Technology Fellowship. author: - first_name: Anna full_name: 'Malaspinas, Anna-Sapfo ' last_name: Malaspinas - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Malaspinas A, Uhler C. Detecting epistasis via Markov bases. Journal of Algebraic Statistics. 2011;2(1):36-53. doi:http://dx.doi.org/10.18409/jas.v2i1.27 apa: Malaspinas, A., & Uhler, C. (2011). Detecting epistasis via Markov bases. Journal of Algebraic Statistics. Public Knowledge Project. http://dx.doi.org/10.18409/jas.v2i1.27 chicago: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” Journal of Algebraic Statistics. Public Knowledge Project, 2011. http://dx.doi.org/10.18409/jas.v2i1.27. ieee: A. Malaspinas and C. Uhler, “Detecting epistasis via Markov bases,” Journal of Algebraic Statistics, vol. 2, no. 1. Public Knowledge Project, pp. 36–53, 2011. ista: Malaspinas A, Uhler C. 2011. Detecting epistasis via Markov bases. Journal of Algebraic Statistics. 2(1), 36–53. mla: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” Journal of Algebraic Statistics, vol. 2, no. 1, Public Knowledge Project, 2011, pp. 36–53, doi:http://dx.doi.org/10.18409/jas.v2i1.27. short: A. Malaspinas, C. Uhler, Journal of Algebraic Statistics 2 (2011) 36–53. date_created: 2018-12-11T12:00:34Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:40:05Z day: '01' doi: http://dx.doi.org/10.18409/jas.v2i1.27 extern: 1 intvolume: ' 2' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1006.4929 month: '01' oa: 1 page: 36 - 53 publication: Journal of Algebraic Statistics publication_status: published publisher: Public Knowledge Project publist_id: '3764' quality_controlled: 0 status: public title: Detecting epistasis via Markov bases type: journal_article volume: 2 year: '2011' ... --- _id: '2960' abstract: - lang: eng text: Traditional statistical methods for the confidentiality protection for statistical databases do not scale well to deal with GWAS (genome-wide association studies) databases and external information on them. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual's privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially private approach to penalized logistic regression. author: - first_name: Stephen full_name: Fienberg, Stephen E last_name: Fienberg - first_name: Aleksandra full_name: Slavkovic, Aleksandra last_name: Slavkovic - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: 'Fienberg S, Slavkovic A, Uhler C. Privacy Preserving GWAS Data Sharing. In: IEEE; 2011. doi:10.1109/ICDMW.2011.140' apa: Fienberg, S., Slavkovic, A., & Uhler, C. (2011). Privacy Preserving GWAS Data Sharing. Presented at the Proceedings of the 11th IEEE International Conference on Data Mining, IEEE. https://doi.org/10.1109/ICDMW.2011.140 chicago: Fienberg, Stephen, Aleksandra Slavkovic, and Caroline Uhler. “Privacy Preserving GWAS Data Sharing.” IEEE, 2011. https://doi.org/10.1109/ICDMW.2011.140. ieee: S. Fienberg, A. Slavkovic, and C. Uhler, “Privacy Preserving GWAS Data Sharing,” presented at the Proceedings of the 11th IEEE International Conference on Data Mining, 2011. ista: Fienberg S, Slavkovic A, Uhler C. 2011. Privacy Preserving GWAS Data Sharing. Proceedings of the 11th IEEE International Conference on Data Mining. mla: Fienberg, Stephen, et al. Privacy Preserving GWAS Data Sharing. IEEE, 2011, doi:10.1109/ICDMW.2011.140. short: S. Fienberg, A. Slavkovic, C. Uhler, in:, IEEE, 2011. conference: name: Proceedings of the 11th IEEE International Conference on Data Mining date_created: 2018-12-11T12:00:34Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:40:05Z day: '01' doi: 10.1109/ICDMW.2011.140 extern: 1 month: '01' publication_status: published publisher: IEEE publist_id: '3766' quality_controlled: 0 status: public title: Privacy Preserving GWAS Data Sharing type: conference year: '2011' ... --- _id: '2975' abstract: - lang: eng text: "Zero-knowledge proofs of knowledge (ZK-PoK) for discrete logarithms and related problems are indispensable for practical cryptographic protocols. Recently, Camenisch, Kiayias, and Yung provided a specification language (the CKY-language) for such protocols which allows for a modular design and protocol analysis: for every zero-knowledge proof specified in this language, protocol designers are ensured that there exists an efficient protocol which indeed proves the specified statement.\n\nHowever, the protocols resulting from their compilation techniques only satisfy the classical notion of ZK-PoK, which is not retained are when they used as building blocks for higher-level applications or composed with other protocols.\nThis problem can be tackled by moving to the Universal Composability (UC) framework, which guarantees retention of security when composing protocols in arbitrary ways. \nWhile there exist generic transformations from $\\Sigma$-protocols to UC-secure protocols, these transformation are often too inefficient for practice.\n \nIn this paper we introduce a specification language akin to the CKY-language and a compiler such that the resulting protocols are UC-secure and efficient. \nTo this end, we propose an extension of the UC-framework addressing the \nissue that UC-secure zero-knowledge proofs are by definition proofs of knowledge, and state a special composition theorem which allows one to use the weaker -- but more efficient and often sufficient -- notion of proofs of membership in the UC-framework. \nWe believe that our contributions enable the design of practically efficient protocols that are UC-secure and thus themselves can be used as building blocks." acknowledgement: This work was in part funded by the Swiss Hasler Foundation, and the EU FP7 grants 216483 and 216499, as well as by the NSF grant CNS-0716690. alternative_title: - LNCS author: - first_name: Jan full_name: Camenisch, Jan last_name: Camenisch - first_name: Stephan full_name: Stephan Krenn id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 - first_name: Victor full_name: Shoup, Victor last_name: Shoup citation: ama: 'Camenisch J, Krenn S, Shoup V. A Framework for Practical Universally Composable Zero-Knowledge Protocols. In: Lee D, Wang X, eds. Vol 7073. Springer; 2011:449-467. doi:10.1007/978-3-642-25385-0' apa: 'Camenisch, J., Krenn, S., & Shoup, V. (2011). A Framework for Practical Universally Composable Zero-Knowledge Protocols. In D. Lee & X. Wang (Eds.) (Vol. 7073, pp. 449–467). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Springer. https://doi.org/10.1007/978-3-642-25385-0' chicago: Camenisch, Jan, Stephan Krenn, and Victor Shoup. “A Framework for Practical Universally Composable Zero-Knowledge Protocols.” edited by Dong Lee and Xiaoyun Wang, 7073:449–67. Springer, 2011. https://doi.org/10.1007/978-3-642-25385-0. ieee: 'J. Camenisch, S. Krenn, and V. Shoup, “A Framework for Practical Universally Composable Zero-Knowledge Protocols,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, 2011, vol. 7073, pp. 449–467.' ista: 'Camenisch J, Krenn S, Shoup V. 2011. A Framework for Practical Universally Composable Zero-Knowledge Protocols. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 7073, 449–467.' mla: Camenisch, Jan, et al. A Framework for Practical Universally Composable Zero-Knowledge Protocols. Edited by Dong Lee and Xiaoyun Wang, vol. 7073, Springer, 2011, pp. 449–67, doi:10.1007/978-3-642-25385-0. short: J. Camenisch, S. Krenn, V. Shoup, in:, D. Lee, X. Wang (Eds.), Springer, 2011, pp. 449–467. conference: name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security' date_created: 2018-12-11T12:00:39Z date_published: 2011-11-21T00:00:00Z date_updated: 2021-01-12T07:40:11Z day: '21' doi: 10.1007/978-3-642-25385-0 editor: - first_name: Dong full_name: Lee, Dong Hoon last_name: Lee - first_name: Xiaoyun full_name: Wang, Xiaoyun last_name: Wang extern: 1 intvolume: ' 7073' main_file_link: - open_access: '0' url: http://eprint.iacr.org/2011/228.pdf month: '11' page: 449 - 467 publication_status: published publisher: Springer publist_id: '3728' quality_controlled: 0 status: public title: A Framework for Practical Universally Composable Zero-Knowledge Protocols type: conference volume: 7073 year: '2011' ... --- _id: '2977' abstract: - lang: eng text: "Cryptographic two-party protocols are used ubiquitously in\n everyday life. While some of these protocols are easy to\n understand and implement (e.g., key exchange or transmission of\n encrypted data), many of them are much more complex (e.g.,\n e-banking and e-voting applications, or anonymous authentication\n and credential systems).\n\n For a software engineer without appropriate cryptographic skills\n the implementation of such protocols is often difficult, time\n consuming and error-prone. For this reason, a number of compilers\n supporting programmers have been published in recent\n years. However, they are either designed for very specific\n cryptographic primitives (e.g., zero-knowledge proofs of\n knowledge), or they only offer a very low level of abstraction and\n thus again demand substantial mathematical and cryptographic\n \ skills from the programmer. Finally, some of the existing\n compilers do not produce executable code, but only metacode which\n has to be instantiated with mathematical libraries, encryption\n routines, etc. before it can actually be used.\n \n In this paper we present a cryptographically aware compiler which\n is equally useful to cryptographers who want to benchmark\n protocols designed on paper, and to programmers who want to\n implement complex security sensitive protocols without having to\n understand all subtleties. Our tool offers a high level of\n abstraction and outputs well-structured and documented Java\n code. We believe that our compiler can contribute to shortening\n the development cycles of cryptographic applications and to\n reducing their error-proneness." acknowledgement: This work was in part funded by the European Community’s Seventh Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler Foundation under projects no. 09037 and 10069. author: - first_name: Endre full_name: Bangerter, Endre last_name: Bangerter - first_name: Stephan full_name: Stephan Krenn id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 - first_name: Martial full_name: Seifriz, Martial last_name: Seifriz - first_name: Ulrich full_name: Ultes-Nitsche, Ulrich last_name: Ultes Nitsche citation: ama: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. cPLC - A Cryptographic Programming Language and Compiler. In: Venter H, Coetzee M, Loock M, eds. IEEE; 2011. doi:10.1109/ISSA.2011.6027533' apa: 'Bangerter, E., Krenn, S., Seifriz, M., & Ultes Nitsche, U. (2011). cPLC - A Cryptographic Programming Language and Compiler. In H. Venter, M. Coetzee, & M. Loock (Eds.). Presented at the ISSA: Information Security South Africa, IEEE. https://doi.org/10.1109/ISSA.2011.6027533' chicago: Bangerter, Endre, Stephan Krenn, Martial Seifriz, and Ulrich Ultes Nitsche. “CPLC - A Cryptographic Programming Language and Compiler.” edited by Hein Venter, Marijke Coetzee, and Marianne Loock. IEEE, 2011. https://doi.org/10.1109/ISSA.2011.6027533. ieee: 'E. Bangerter, S. Krenn, M. Seifriz, and U. Ultes Nitsche, “cPLC - A Cryptographic Programming Language and Compiler,” presented at the ISSA: Information Security South Africa, 2011.' ista: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. 2011. cPLC - A Cryptographic Programming Language and Compiler. ISSA: Information Security South Africa.' mla: Bangerter, Endre, et al. CPLC - A Cryptographic Programming Language and Compiler. Edited by Hein Venter et al., IEEE, 2011, doi:10.1109/ISSA.2011.6027533. short: E. Bangerter, S. Krenn, M. Seifriz, U. Ultes Nitsche, in:, H. Venter, M. Coetzee, M. Loock (Eds.), IEEE, 2011. conference: name: 'ISSA: Information Security South Africa' date_created: 2018-12-11T12:00:39Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:40:12Z day: '01' doi: 10.1109/ISSA.2011.6027533 editor: - first_name: Hein full_name: Venter, Hein S. last_name: Venter - first_name: Marijke full_name: Coetzee, Marijke last_name: Coetzee - first_name: Marianne full_name: Loock, Marianne last_name: Loock extern: 1 month: '08' publication_status: published publisher: IEEE publist_id: '3726' quality_controlled: 0 status: public title: cPLC - A Cryptographic Programming Language and Compiler type: conference year: '2011' ... --- _id: '2976' abstract: - lang: eng text: |- Side channel attacks on cryptographic systems exploit information gained from physical implementations rather than theoretical weaknesses of a scheme. In recent years, major achievements were made for the class of so called access-driven cache attacks. Such attacks exploit the leakage of the memory locations accessed by a victim process. In this paper we consider the AES block cipher and present an attack which is capable of recovering the full secret key in almost realtime for AES-128, requiring only a very limited number of observed encryptions. Unlike previous attacks, we do not require any information about the plaintext (such as its distribution, etc.). Moreover, for the first time, we also show how the plaintext can be recovered without having access to the ciphertext at all. It is the first working attack on AES implementations using compressed tables. There, no efficient techniques to identify the beginning of AES rounds is known, which is the fundamental assumption underlying previous attacks. We have a fully working implementation of our attack which is able to recover AES keys after observing as little as 100 encryptions. It works against the OpenSSL 0.9.8n implementation of AES on Linux systems. Our spy process does not require any special privileges beyond those of a standard Linux user. A contribution of probably independent interest is a denial of service attack on the task scheduler of current Linux systems (CFS), which allows one to observe (on average) every single memory access of a victim process. acknowledgement: |- This work was in part funded by the European Community’s Seventh Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler Foundation. An extended abstract was also accepted for COSADE 2011. author: - first_name: David full_name: Gullasch, David last_name: Gullasch - first_name: Endre full_name: Bangerter, Endre last_name: Bangerter - first_name: Stephan full_name: Stephan Krenn id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 citation: ama: 'Gullasch D, Bangerter E, Krenn S. Cache Games - Bringing Access-Based Cache Attacks on AES to Practice. In: IEEE; 2011:490-505. doi:10.1109/SP.2011.22' apa: 'Gullasch, D., Bangerter, E., & Krenn, S. (2011). Cache Games - Bringing Access-Based Cache Attacks on AES to Practice (pp. 490–505). Presented at the S&P: IEEE Symposium on Security and Privacy, IEEE. https://doi.org/10.1109/SP.2011.22' chicago: Gullasch, David, Endre Bangerter, and Stephan Krenn. “Cache Games - Bringing Access-Based Cache Attacks on AES to Practice,” 490–505. IEEE, 2011. https://doi.org/10.1109/SP.2011.22. ieee: 'D. Gullasch, E. Bangerter, and S. Krenn, “Cache Games - Bringing Access-Based Cache Attacks on AES to Practice,” presented at the S&P: IEEE Symposium on Security and Privacy, 2011, pp. 490–505.' ista: 'Gullasch D, Bangerter E, Krenn S. 2011. Cache Games - Bringing Access-Based Cache Attacks on AES to Practice. S&P: IEEE Symposium on Security and Privacy, 490–505.' mla: Gullasch, David, et al. Cache Games - Bringing Access-Based Cache Attacks on AES to Practice. IEEE, 2011, pp. 490–505, doi:10.1109/SP.2011.22. short: D. Gullasch, E. Bangerter, S. Krenn, in:, IEEE, 2011, pp. 490–505. conference: name: 'S&P: IEEE Symposium on Security and Privacy' date_created: 2018-12-11T12:00:39Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:40:11Z day: '01' doi: 10.1109/SP.2011.22 extern: 1 main_file_link: - open_access: '0' url: http://eprint.iacr.org/2010/594.pdf month: '01' page: 490 - 505 publication_status: published publisher: IEEE publist_id: '3727' quality_controlled: 0 status: public title: Cache Games - Bringing Access-Based Cache Attacks on AES to Practice type: conference year: '2011' ... --- _id: '3092' abstract: - lang: eng text: The phytohormone auxin is vital to plant growth and development. A unique property of auxin among all other plant hormones is its cell-to-cell polar transport that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the substantial molecular insight into the cellular PIN polarization, the mechanistic understanding for developmentally and environmentally regulated PIN polarization is scarce. The long-standing belief that auxin modulates its own transport by means of a positive feedback mechanism has inspired both experimentalists and theoreticians for more than two decades. Recently, theoretical models for auxin-dependent patterning in plants include the feedback between auxin transport and the PIN protein localization. These computer models aid to assess the complexity of plant development by testing and predicting plausible scenarios for various developmental processes that occur in planta. Although the majority of these models rely on purely heuristic principles, the most recent mechanistic models tentatively integrate biologically testable components into known cellular processes that underlie the PIN polarity regulation. The existing and emerging computational approaches to describe PIN polarization are presented and discussed in the light of recent experimental data on the PIN polar targeting. author: - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Willy full_name: Govaerts, Willy last_name: Govaerts - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn citation: ama: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. Feedback models for polarized auxin transport: An emerging trend. Molecular BioSystems. 2011;7(8):2352-2359. doi:10.1039/c1mb05109a' apa: 'Wabnik, K. T., Govaerts, W., Friml, J., & Kleine Vehn, J. (2011). Feedback models for polarized auxin transport: An emerging trend. Molecular BioSystems. Royal Society of Chemistry. https://doi.org/10.1039/c1mb05109a' chicago: 'Wabnik, Krzysztof T, Willy Govaerts, Jiří Friml, and Jürgen Kleine Vehn. “Feedback Models for Polarized Auxin Transport: An Emerging Trend.” Molecular BioSystems. Royal Society of Chemistry, 2011. https://doi.org/10.1039/c1mb05109a.' ieee: 'K. T. Wabnik, W. Govaerts, J. Friml, and J. Kleine Vehn, “Feedback models for polarized auxin transport: An emerging trend,” Molecular BioSystems, vol. 7, no. 8. Royal Society of Chemistry, pp. 2352–2359, 2011.' ista: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. 2011. Feedback models for polarized auxin transport: An emerging trend. Molecular BioSystems. 7(8), 2352–2359.' mla: 'Wabnik, Krzysztof T., et al. “Feedback Models for Polarized Auxin Transport: An Emerging Trend.” Molecular BioSystems, vol. 7, no. 8, Royal Society of Chemistry, 2011, pp. 2352–59, doi:10.1039/c1mb05109a.' short: K.T. Wabnik, W. Govaerts, J. Friml, J. Kleine Vehn, Molecular BioSystems 7 (2011) 2352–2359. date_created: 2018-12-11T12:01:20Z date_published: 2011-06-10T00:00:00Z date_updated: 2021-01-12T07:41:00Z day: '10' doi: 10.1039/c1mb05109a extern: '1' external_id: pmid: - '21660355' intvolume: ' 7' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/21660355 month: '06' oa: 1 oa_version: Published Version page: 2352 - 2359 pmid: 1 publication: Molecular BioSystems publication_status: published publisher: Royal Society of Chemistry publist_id: '3608' quality_controlled: '1' status: public title: 'Feedback models for polarized auxin transport: An emerging trend' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2011' ... --- _id: '3089' abstract: - lang: eng text: The phytohormone auxin is an important determinant of plant development. Directional auxin flow within tissues depends on polar localization of PIN auxin transporters. To explore regulation of PIN-mediated auxin transport, we screened for suppressors of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase mutant (supo1), with elevated inositol trisphosphate (InsP 3) and cytosolic Ca 2+ levels. Pharmacological and genetic increases in InsP 3 or Ca 2+ levels also suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN localization, auxin transport and auxin-mediated development. In contrast, the reductions in InsP 3 levels and Ca 2+ signaling antagonized the effects of the supo1 mutation and disrupted preferentially apical PIN localization. InsP 3 and Ca 2+ are evolutionarily conserved second messengers involved in various cellular functions, particularly stress responses. Our findings implicate them as modifiers of cell polarity and polar auxin transport, and highlight a potential integration point through which Ca 2+ signaling-related stimuli could influence auxin-mediated development. author: - first_name: Jing full_name: Zhang, Jing last_name: Zhang - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Marta full_name: Michniewicz, Marta last_name: Michniewicz - first_name: Peter full_name: Peter Grones id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Christian full_name: Löfke, Christian last_name: Löfke - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Bernard full_name: Cannoot, Bernard last_name: Cannoot - first_name: Klára full_name: Hoyerová, Klára last_name: Hoyerová - first_name: Xu full_name: Xu Chen id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Hong full_name: Xue, Hong-Wei last_name: Xue - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang J, Vanneste S, Brewer P, et al. Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity. Developmental Cell. 2011;20(6):855-866. doi:10.1016/j.devcel.2011.05.013 apa: Zhang, J., Vanneste, S., Brewer, P., Michniewicz, M., Grones, P., Kleine Vehn, J., … Friml, J. (2011). Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.05.013 chicago: Zhang, Jing, Steffen Vanneste, Philip Brewer, Marta Michniewicz, Peter Grones, Jürgen Kleine Vehn, Christian Löfke, et al. “Inositol Trisphosphate-Induced Ca^2+ Signaling Modulates Auxin Transport and Pin Polarity.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.05.013. ieee: J. Zhang et al., “Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity,” Developmental Cell, vol. 20, no. 6. Cell Press, pp. 855–866, 2011. ista: Zhang J, Vanneste S, Brewer P, Michniewicz M, Grones P, Kleine Vehn J, Löfke C, Teichmann T, Bielach A, Cannoot B, Hoyerová K, Chen X, Xue H, Benková E, Zažímalová E, Friml J. 2011. Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity. Developmental Cell. 20(6), 855–866. mla: Zhang, Jing, et al. “Inositol Trisphosphate-Induced Ca^2+ Signaling Modulates Auxin Transport and Pin Polarity.” Developmental Cell, vol. 20, no. 6, Cell Press, 2011, pp. 855–66, doi:10.1016/j.devcel.2011.05.013. short: J. Zhang, S. Vanneste, P. Brewer, M. Michniewicz, P. Grones, J. Kleine Vehn, C. Löfke, T. Teichmann, A. Bielach, B. Cannoot, K. Hoyerová, X. Chen, H. Xue, E. Benková, E. Zažímalová, J. Friml, Developmental Cell 20 (2011) 855–866. date_created: 2018-12-11T12:01:18Z date_published: 2011-06-14T00:00:00Z date_updated: 2021-01-12T07:40:58Z day: '14' doi: 10.1016/j.devcel.2011.05.013 extern: 1 intvolume: ' 20' issue: '6' month: '06' page: 855 - 866 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3612' quality_controlled: 0 status: public title: Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity type: journal_article volume: 20 year: '2011' ... --- _id: '3090' abstract: - lang: eng text: The polarized transport of the phytohormone auxin [1], which is crucial for the regulation of different stages of plant development [2, 3], depends on the asymmetric plasma membrane distribution of the PIN-FORMED (PIN) auxin efflux carriers [4, 5]. The PIN polar localization results from clathrin-mediated endocytosis (CME) from the plasma membrane and subsequent polar recycling [6]. The Arabidopsis genome encodes two groups of dynamin-related proteins (DRPs) that show homology to mammalian dynamin - a protein required for fission of endocytic vesicles during CME [7, 8]. Here we show by coimmunoprecipitation (coIP), bimolecular fluorescence complementation (BiFC), and Förster resonance energy transfer (FRET) that members of the DRP1 group closely associate with PIN proteins at the cell plate. Localization and phenotypic analysis of novel drp1 mutants revealed a requirement for DRP1 function in correct PIN distribution and in auxin-mediated development. We propose that rapid and specific internalization of PIN proteins mediated by the DRP1 proteins and the associated CME machinery from the cell plate membranes during cytokinesis is an important mechanism for proper polar PIN positioning in interphase cells. author: - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Na full_name: Li, Na last_name: Li - first_name: Sjef full_name: Boeren, Sjef last_name: Boeren - first_name: Rumyana full_name: Karlova, Rumyana last_name: Karlova - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Markéta full_name: Pařezová, Markéta last_name: Pařezová - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Thomasz full_name: Nodzyński, Thomasz last_name: Nodzyński - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Sebastian full_name: Bednarek, Sebastian Y last_name: Bednarek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Sacco full_name: De Vries, Sacco last_name: De Vries - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Mravec J, Petrášek J, Li N, et al. Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis. Current Biology. 2011;21(12):1055-1060. doi:10.1016/j.cub.2011.05.018 apa: Mravec, J., Petrášek, J., Li, N., Boeren, S., Karlova, R., Kitakura, S., … Friml, J. (2011). Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.05.018 chicago: Mravec, Jozef, Jan Petrášek, Na Li, Sjef Boeren, Rumyana Karlova, Saeko Kitakura, Markéta Pařezová, et al. “Cell Plate Restricted Association of DRP1A and PIN Proteins Is Required for Cell Polarity Establishment in Arabidopsis.” Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.05.018. ieee: J. Mravec et al., “Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis,” Current Biology, vol. 21, no. 12. Cell Press, pp. 1055–1060, 2011. ista: Mravec J, Petrášek J, Li N, Boeren S, Karlova R, Kitakura S, Pařezová M, Naramoto S, Nodzyński T, Dhonukshe P, Bednarek S, Zažímalová E, De Vries S, Friml J. 2011. Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis. Current Biology. 21(12), 1055–1060. mla: Mravec, Jozef, et al. “Cell Plate Restricted Association of DRP1A and PIN Proteins Is Required for Cell Polarity Establishment in Arabidopsis.” Current Biology, vol. 21, no. 12, Cell Press, 2011, pp. 1055–60, doi:10.1016/j.cub.2011.05.018. short: J. Mravec, J. Petrášek, N. Li, S. Boeren, R. Karlova, S. Kitakura, M. Pařezová, S. Naramoto, T. Nodzyński, P. Dhonukshe, S. Bednarek, E. Zažímalová, S. De Vries, J. Friml, Current Biology 21 (2011) 1055–1060. date_created: 2018-12-11T12:01:19Z date_published: 2011-06-21T00:00:00Z date_updated: 2021-01-12T07:40:59Z day: '21' doi: 10.1016/j.cub.2011.05.018 extern: 1 intvolume: ' 21' issue: '12' month: '06' page: 1055 - 1060 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3611' quality_controlled: 0 status: public title: Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis type: journal_article volume: 21 year: '2011' ... --- _id: '3088' abstract: - lang: eng text: 'Background: Whereas the majority of animals develop toward a predetermined body plan, plants show iterative growth and continually produce new organs and structures from actively dividing meristems. This raises an intriguing question: How are these newly developed organs patterned? In Arabidopsis embryos, radial symmetry is broken by the bisymmetric specification of the cotyledons in the apical domain. Subsequently, this bisymmetry is propagated to the root promeristem. Results: Here we present a mutually inhibitory feedback loop between auxin and cytokinin that sets distinct boundaries of hormonal output. Cytokinins promote the bisymmetric distribution of the PIN-FORMED (PIN) auxin efflux proteins, which channel auxin toward a central domain. High auxin promotes transcription of the cytokinin signaling inhibitor AHP6, which closes the interaction loop. This bisymmetric auxin response domain specifies the differentiation of protoxylem in a bisymmetric pattern. In embryonic roots, cytokinin is required to translate a bisymmetric auxin response in the cotyledons to a bisymmetric vascular pattern in the root promeristem. Conclusions: Our results present an interactive feedback loop between hormonal signaling and transport by which small biases in hormonal input are propagated into distinct signaling domains to specify the vascular pattern in the root meristem. It is an intriguing possibility that such a mechanism could transform radial patterns and allow continuous vascular connections between other newly emerging organs.' author: - first_name: Anthony full_name: Bishopp, Anthony last_name: Bishopp - first_name: Hanna full_name: Help, Hanna last_name: Help - first_name: Sedeer full_name: El-Showk, Sedeer last_name: El Showk - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ari full_name: Mähönen, Ari Pekka last_name: Mähönen - first_name: Ykä full_name: Helariutta, Ykä last_name: Helariutta citation: ama: Bishopp A, Help H, El Showk S, et al. A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Current Biology. 2011;21(11):917-926. doi:10.1016/j.cub.2011.04.017 apa: Bishopp, A., Help, H., El Showk, S., Weijers, D., Scheres, B., Friml, J., … Helariutta, Y. (2011). A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.04.017 chicago: Bishopp, Anthony, Hanna Help, Sedeer El Showk, Dolf Weijers, Ben Scheres, Jiří Friml, Eva Benková, Ari Mähönen, and Ykä Helariutta. “A Mutually Inhibitory Interaction between Auxin and Cytokinin Specifies Vascular Pattern in Roots.” Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.04.017. ieee: A. Bishopp et al., “A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots,” Current Biology, vol. 21, no. 11. Cell Press, pp. 917–926, 2011. ista: Bishopp A, Help H, El Showk S, Weijers D, Scheres B, Friml J, Benková E, Mähönen A, Helariutta Y. 2011. A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Current Biology. 21(11), 917–926. mla: Bishopp, Anthony, et al. “A Mutually Inhibitory Interaction between Auxin and Cytokinin Specifies Vascular Pattern in Roots.” Current Biology, vol. 21, no. 11, Cell Press, 2011, pp. 917–26, doi:10.1016/j.cub.2011.04.017. short: A. Bishopp, H. Help, S. El Showk, D. Weijers, B. Scheres, J. Friml, E. Benková, A. Mähönen, Y. Helariutta, Current Biology 21 (2011) 917–926. date_created: 2018-12-11T12:01:18Z date_published: 2011-06-07T00:00:00Z date_updated: 2021-01-12T07:40:58Z day: '07' doi: 10.1016/j.cub.2011.04.017 extern: 1 intvolume: ' 21' issue: '11' month: '06' page: 917 - 926 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3613' quality_controlled: 0 status: public title: A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots type: journal_article volume: 21 year: '2011' ... --- _id: '3093' abstract: - lang: eng text: |2- Plants take up iron from the soil using the IRON-REGULATED TRANSPORTER 1 (IRT1) high-affinity iron transporter at the root surface. Sophisticated regulatory mechanisms allow plants to tightly control the levels of IRT1, ensuring optimal absorption of essential but toxic iron. Here, we demonstrate that overexpression of Arabidopsis thaliana IRT1 leads to constitutive IRT1 protein accumulation, metal overload, and oxidative stress. IRT1 is unexpectedly found in trans-Golgi network/early endosomes of root hair cells, and its levels and localization are unaffected by iron nutrition. Using pharmacological approaches, we show that IRT1 cycles to the plasma membrane to perform iron and metal uptake at the cell surface and is sent to the vacuole for proper turnover. We also prove that IRT1 is monoubiquitinated on several cytosol-exposed residues in vivo and that mutation of two putative monoubiquitination target residues in IRT1 triggers stabilization at the plasma membrane and leads to extreme lethality. Together, these data suggest a model in which monoubiquitin-dependent internalization/sorting and turnover keep the plasma membrane pool of IRT1 low to ensure proper iron uptake and to prevent metal toxicity. More generally, our work demonstrates the existence of monoubiquitin-dependent trafficking to lytic vacuoles in plants and points to proteasome-independent turnover of plasma membrane proteins. author: - first_name: Marie full_name: Barberon, Marie last_name: Barberon - first_name: Enric full_name: Zelazny, Enric last_name: Zelazny - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Geneviève full_name: Conéjéro, Geneviève last_name: Conéjéro - first_name: Cathy full_name: Curie, Cathy last_name: Curie - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Grégory full_name: Vert, Grégory last_name: Vert citation: ama: Barberon M, Zelazny E, Robert S, et al. Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. 2011;108(32):E450-E458. doi:10.1073/pnas.1100659108 apa: Barberon, M., Zelazny, E., Robert, S., Conéjéro, G., Curie, C., Friml, J., & Vert, G. (2011). Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1100659108 chicago: Barberon, Marie, Enric Zelazny, Stéphanie Robert, Geneviève Conéjéro, Cathy Curie, Jiří Friml, and Grégory Vert. “Monoubiquitin Dependent Endocytosis of the Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1100659108. ieee: M. Barberon et al., “Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants,” PNAS, vol. 108, no. 32. National Academy of Sciences, pp. E450–E458, 2011. ista: Barberon M, Zelazny E, Robert S, Conéjéro G, Curie C, Friml J, Vert G. 2011. Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. 108(32), E450–E458. mla: Barberon, Marie, et al. “Monoubiquitin Dependent Endocytosis of the Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” PNAS, vol. 108, no. 32, National Academy of Sciences, 2011, pp. E450–58, doi:10.1073/pnas.1100659108. short: M. Barberon, E. Zelazny, S. Robert, G. Conéjéro, C. Curie, J. Friml, G. Vert, PNAS 108 (2011) E450–E458. date_created: 2018-12-11T12:01:20Z date_published: 2011-08-09T00:00:00Z date_updated: 2021-01-12T07:41:00Z day: '09' doi: 10.1073/pnas.1100659108 extern: 1 intvolume: ' 108' issue: '32' month: '08' page: E450 - E458 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3607' quality_controlled: 0 status: public title: Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants type: journal_article volume: 108 year: '2011' ... --- _id: '3094' abstract: - lang: eng text: Summary Gravitropism aligns plant growth with gravity. It involves gravity perception and the asymmetric distribution of the phytohormone auxin. Here we provide insights into the mechanism for hypocotyl gravitropic growth. We show that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3 to the bottom side of hypocotyl endodermal cells, which correlates with an increased auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl bending require the activity of the trafficking regulator GNOM and the protein kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts the auxin flow to mediate the asymmetric distribution of auxin for gravitropic shoot bending. author: - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Javier full_name: Gallego-Bartolomé, Javier last_name: Gallego Bartolomé - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Hélène full_name: Robert, Hélène S last_name: Robert - first_name: David full_name: Alabadí, David last_name: Alabadí - first_name: Miguel full_name: Blázquez, Miguel A last_name: Blázquez - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Rakusová H, Gallego Bartolomé J, Vanstraelen M, et al. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 2011;67(5):817-826. doi:10.1111/j.1365-313X.2011.04636.x apa: Rakusová, H., Gallego Bartolomé, J., Vanstraelen, M., Robert, H., Alabadí, D., Blázquez, M., … Friml, J. (2011). Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2011.04636.x chicago: Rakusová, Hana, Javier Gallego Bartolomé, Marleen Vanstraelen, Hélène Robert, David Alabadí, Miguel Blázquez, Eva Benková, and Jiří Friml. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2011.04636.x. ieee: H. Rakusová et al., “Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana,” Plant Journal, vol. 67, no. 5. Wiley-Blackwell, pp. 817–826, 2011. ista: Rakusová H, Gallego Bartolomé J, Vanstraelen M, Robert H, Alabadí D, Blázquez M, Benková E, Friml J. 2011. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 67(5), 817–826. mla: Rakusová, Hana, et al. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” Plant Journal, vol. 67, no. 5, Wiley-Blackwell, 2011, pp. 817–26, doi:10.1111/j.1365-313X.2011.04636.x. short: H. Rakusová, J. Gallego Bartolomé, M. Vanstraelen, H. Robert, D. Alabadí, M. Blázquez, E. Benková, J. Friml, Plant Journal 67 (2011) 817–826. date_created: 2018-12-11T12:01:21Z date_published: 2011-09-01T00:00:00Z date_updated: 2021-01-12T07:41:01Z day: '01' doi: 10.1111/j.1365-313X.2011.04636.x extern: 1 intvolume: ' 67' issue: '5' month: '09' page: 817 - 826 publication: Plant Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3606' quality_controlled: 0 status: public title: Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana type: journal_article volume: 67 year: '2011' ... --- _id: '3091' author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Sauer M, Friml J. Fleeting hormone cues get stabilized for plant organogenesis. Molecular Systems Biology. 2011;7. doi:10.1038/msb.2011.45 apa: Sauer, M., & Friml, J. (2011). Fleeting hormone cues get stabilized for plant organogenesis. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2011.45 chicago: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for Plant Organogenesis.” Molecular Systems Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/msb.2011.45. ieee: M. Sauer and J. Friml, “Fleeting hormone cues get stabilized for plant organogenesis,” Molecular Systems Biology, vol. 7. Nature Publishing Group, 2011. ista: Sauer M, Friml J. 2011. Fleeting hormone cues get stabilized for plant organogenesis. Molecular Systems Biology. 7. mla: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for Plant Organogenesis.” Molecular Systems Biology, vol. 7, Nature Publishing Group, 2011, doi:10.1038/msb.2011.45. short: M. Sauer, J. Friml, Molecular Systems Biology 7 (2011). date_created: 2018-12-11T12:01:19Z date_published: 2011-07-05T00:00:00Z date_updated: 2021-01-12T07:41:00Z day: '05' doi: 10.1038/msb.2011.45 extern: '1' external_id: pmid: - '21734646' intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159970/ month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '3610' quality_controlled: '1' status: public title: Fleeting hormone cues get stabilized for plant organogenesis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2011' ... --- _id: '3102' abstract: - lang: eng text: 'Multicellular organisms depend on cell production, cell fate specification, and correct patterning to shape their adult body. In plants, auxin plays a prominent role in the timely coordination of these different cellular processes. A well-studied example is lateral root initiation, in which auxin triggers founder cell specification and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report that the E2Fa transcription factor of Arabidopsis thaliana is an essential component that regulates the asymmetric cell division marking lateral root initiation. Moreover, we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis through E2Fa transcriptional activation, whereas E2Fa expression under control of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation, vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected in auxin signaling and lbd mutants, indicating that the transcriptional induction of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle activation. Our data illustrate how a conserved mechanism driving cell cycle entry has been adapted evolutionarily to connect auxin signaling with control of processes determining plant architecture. ' author: - first_name: Barbara full_name: Berckmans, Barbara last_name: Berckmans - first_name: Valya full_name: Vassileva, Valya last_name: Vassileva - first_name: Stephan full_name: Schmid, Stephan P last_name: Schmid - first_name: Sara full_name: Maes, Sara last_name: Maes - first_name: Boris full_name: Parizot, Boris last_name: Parizot - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Zoltan full_name: Magyar, Zoltan last_name: Magyar - first_name: Claire full_name: Lessa Alvim Kamei, Claire last_name: Lessa Alvim Kamei - first_name: Csaba full_name: Koncz, Csaba last_name: Koncz - first_name: Laszlo full_name: Bögre, Laszlo last_name: Bögre - first_name: Geert full_name: Persiau, Geert last_name: Persiau - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Rüdiger full_name: Simon, Rüdiger last_name: Simon - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Lieven full_name: de Veyldera, Lieven last_name: De Veyldera citation: ama: Berckmans B, Vassileva V, Schmid S, et al. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. 2011;23(10):3671-3683. doi:10.1105/tpc.111.088377 apa: Berckmans, B., Vassileva, V., Schmid, S., Maes, S., Parizot, B., Naramoto, S., … De Veyldera, L. (2011). Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.111.088377 chicago: Berckmans, Barbara, Valya Vassileva, Stephan Schmid, Sara Maes, Boris Parizot, Satoshi Naramoto, Zoltan Magyar, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.088377. ieee: B. Berckmans et al., “Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins,” Plant Cell, vol. 23, no. 10. American Society of Plant Biologists, pp. 3671–3683, 2011. ista: Berckmans B, Vassileva V, Schmid S, Maes S, Parizot B, Naramoto S, Magyar Z, Lessa Alvim Kamei C, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon R, Beeckman T, De Veyldera L. 2011. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. 23(10), 3671–3683. mla: Berckmans, Barbara, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” Plant Cell, vol. 23, no. 10, American Society of Plant Biologists, 2011, pp. 3671–83, doi:10.1105/tpc.111.088377. short: B. Berckmans, V. Vassileva, S. Schmid, S. Maes, B. Parizot, S. Naramoto, Z. Magyar, C. Lessa Alvim Kamei, C. Koncz, L. Bögre, G. Persiau, G. De Jaeger, J. Friml, R. Simon, T. Beeckman, L. De Veyldera, Plant Cell 23 (2011) 3671–3683. date_created: 2018-12-11T12:01:24Z date_published: 2011-10-14T00:00:00Z date_updated: 2021-01-12T07:41:04Z day: '14' doi: 10.1105/tpc.111.088377 extern: 1 intvolume: ' 23' issue: '10' month: '10' page: 3671 - 3683 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3598' quality_controlled: 0 status: public title: Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins type: journal_article volume: 23 year: '2011' ... --- _id: '3103' abstract: - lang: eng text: Endocytosis in plants has an essential role not only for basic cellular functions but also for growth and development, hormonal signaling and communication with the environment including nutrient delivery, toxin avoidance, and pathogen defense. The major endocytic mechanism in plants depends on the coat protein clathrin. It starts by clathrin-coated vesicle formation at the plasma membrane, where specific cargoes are recognized and packaged for internalization. Recently, genetic, biochemical and advanced microscopy studies provided initial insights into mechanisms and roles of clathrin-mediated endocytosis in plants. Here we summarize the present state of knowledge and compare mechanisms of clathrin-mediated endocytosis in plants with animal and yeast paradigms as well as review plant-specific regulations and roles of this process. author: - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Niloufer full_name: Irani, Niloufer last_name: Irani - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Chen X, Irani N, Friml J. Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. 2011;14(6):674-682. doi:10.1016/j.pbi.2011.08.006' apa: 'Chen, X., Irani, N., & Friml, J. (2011). Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2011.08.006' chicago: 'Chen, Xu, Niloufer Irani, and Jiří Friml. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” Current Opinion in Plant Biology. Elsevier, 2011. https://doi.org/10.1016/j.pbi.2011.08.006.' ieee: 'X. Chen, N. Irani, and J. Friml, “Clathrin-mediated endocytosis: The gateway into plant cells,” Current Opinion in Plant Biology, vol. 14, no. 6. Elsevier, pp. 674–682, 2011.' ista: 'Chen X, Irani N, Friml J. 2011. Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. 14(6), 674–682.' mla: 'Chen, Xu, et al. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” Current Opinion in Plant Biology, vol. 14, no. 6, Elsevier, 2011, pp. 674–82, doi:10.1016/j.pbi.2011.08.006.' short: X. Chen, N. Irani, J. Friml, Current Opinion in Plant Biology 14 (2011) 674–682. date_created: 2018-12-11T12:01:24Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T07:41:05Z day: '01' doi: 10.1016/j.pbi.2011.08.006 extern: '1' intvolume: ' 14' issue: '6' language: - iso: eng month: '12' oa_version: None page: 674 - 682 publication: Current Opinion in Plant Biology publication_status: published publisher: Elsevier publist_id: '3596' quality_controlled: '1' status: public title: 'Clathrin-mediated endocytosis: The gateway into plant cells' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2011' ... --- _id: '3147' abstract: - lang: eng text: Cancer cell of origin is difficult to identify by analyzing cells within terminal stage tumors, whose identity could be concealed by the acquired plasticity. Thus, an ideal approach to identify the cell of origin is to analyze proliferative abnormalities in distinct lineages prior to malignancy. Here, we use mosaic analysis with double markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1 mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves. Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed salient OPC features. Finally, introducing the same p53/Nf1 mutations directly into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the cell of origin in this model, even when initial mutations occur in NSCs, and highlight the importance of analyzing premalignant stages to identify the cancer cell of origin. author: - first_name: Chong full_name: Liu, Chong last_name: Liu - first_name: Jonathan full_name: Sage, Jonathan C last_name: Sage - first_name: Michael full_name: Miller, Michael R last_name: Miller - first_name: Roel full_name: Verhaak, Roel G last_name: Verhaak - first_name: Simon full_name: Simon Hippenmeyer id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Hannes full_name: Vogel, Hannes last_name: Vogel - first_name: Oded full_name: Foreman, Oded last_name: Foreman - first_name: Roderick full_name: Bronson, Roderick T last_name: Bronson - first_name: Akiko full_name: Nishiyama, Akiko last_name: Nishiyama - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Hui full_name: Zong, Hui last_name: Zong citation: ama: Liu C, Sage J, Miller M, et al. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. 2011;146(2):209-221. doi:10.1016/j.cell.2011.06.014 apa: Liu, C., Sage, J., Miller, M., Verhaak, R., Hippenmeyer, S., Vogel, H., … Zong, H. (2011). Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. Cell Press. https://doi.org/10.1016/j.cell.2011.06.014 chicago: Liu, Chong, Jonathan Sage, Michael Miller, Roel Verhaak, Simon Hippenmeyer, Hannes Vogel, Oded Foreman, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” Cell. Cell Press, 2011. https://doi.org/10.1016/j.cell.2011.06.014. ieee: C. Liu et al., “Mosaic analysis with double markers reveals tumor cell of origin in glioma,” Cell, vol. 146, no. 2. Cell Press, pp. 209–221, 2011. ista: Liu C, Sage J, Miller M, Verhaak R, Hippenmeyer S, Vogel H, Foreman O, Bronson R, Nishiyama A, Luo L, Zong H. 2011. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. 146(2), 209–221. mla: Liu, Chong, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” Cell, vol. 146, no. 2, Cell Press, 2011, pp. 209–21, doi:10.1016/j.cell.2011.06.014. short: C. Liu, J. Sage, M. Miller, R. Verhaak, S. Hippenmeyer, H. Vogel, O. Foreman, R. Bronson, A. Nishiyama, L. Luo, H. Zong, Cell 146 (2011) 209–221. date_created: 2018-12-11T12:01:40Z date_published: 2011-07-22T00:00:00Z date_updated: 2021-01-12T07:41:23Z day: '22' doi: 10.1016/j.cell.2011.06.014 extern: 1 intvolume: ' 146' issue: '2' month: '07' page: 209 - 221 publication: Cell publication_status: published publisher: Cell Press publist_id: '3548' quality_controlled: 0 status: public title: Mosaic analysis with double markers reveals tumor cell of origin in glioma type: journal_article volume: 146 year: '2011' ... --- _id: '3204' abstract: - lang: eng text: 'We introduce a new class of functions that can be minimized in polynomial time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥ f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree. Special cases include previously studied L-convex and bisubmodular functions, which can be obtained with particular choices of trees. We present a polynomial-time algorithm for minimizing functions in the new class. It combines Murota''s steepest descent algorithm for L-convex functions with bisubmodular minimization algorithms. ' alternative_title: - LNCS author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. In: Vol 6907. Springer; 2011:400-411. doi:10.1007/978-3-642-22993-0_37' apa: 'Kolmogorov, V. (2011). Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions (Vol. 6907, pp. 400–411). Presented at the MFCS: Mathematical Foundations of Computer Science, Springer. https://doi.org/10.1007/978-3-642-22993-0_37' chicago: 'Kolmogorov, Vladimir. “Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions,” 6907:400–411. Springer, 2011. https://doi.org/10.1007/978-3-642-22993-0_37.' ieee: 'V. Kolmogorov, “Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions,” presented at the MFCS: Mathematical Foundations of Computer Science, 2011, vol. 6907, pp. 400–411.' ista: 'Kolmogorov V. 2011. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 400–411.' mla: 'Kolmogorov, Vladimir. Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions. Vol. 6907, Springer, 2011, pp. 400–11, doi:10.1007/978-3-642-22993-0_37.' short: V. Kolmogorov, in:, Springer, 2011, pp. 400–411. conference: name: 'MFCS: Mathematical Foundations of Computer Science' date_created: 2018-12-11T12:02:00Z date_published: 2011-08-09T00:00:00Z date_updated: 2021-01-12T07:41:47Z day: '09' doi: 10.1007/978-3-642-22993-0_37 extern: 1 intvolume: ' 6907' main_file_link: - open_access: '0' url: http://arxiv.org/pdf/1007.1229v3 month: '08' page: 400 - 411 publication_status: published publisher: Springer publist_id: '3478' quality_controlled: 0 status: public title: 'Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions' type: conference volume: 6907 year: '2011' ... --- _id: '3206' abstract: - lang: eng text: In this paper we address the problem of finding the most probable state of discrete Markov random field (MRF) with associative pairwise terms. Although of practical importance, this problem is known to be NP-hard in general. We propose a new type of MRF decomposition, submod-ular decomposition (SMD). Unlike existing decomposition approaches SMD decomposes the initial problem into sub-problems corresponding to a specific class label while preserving the graph structure of each subproblem. Such decomposition enables us to take into account several types of global constraints in an efficient manner. We study theoretical properties of the proposed approach and demonstrate its applicability on a number of problems. author: - first_name: Anton full_name: Osokin, Anton last_name: Osokin - first_name: Dmitry full_name: Vetrov, Dmitry last_name: Vetrov - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Osokin A, Vetrov D, Kolmogorov V. Submodular decomposition framework for inference in associative Markov networks with global constraints. In: IEEE; 2011:1889-1896. doi:10.1109/CVPR.2011.5995361' apa: 'Osokin, A., Vetrov, D., & Kolmogorov, V. (2011). Submodular decomposition framework for inference in associative Markov networks with global constraints (pp. 1889–1896). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2011.5995361' chicago: Osokin, Anton, Dmitry Vetrov, and Vladimir Kolmogorov. “Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints,” 1889–96. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995361. ieee: 'A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework for inference in associative Markov networks with global constraints,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896.' ista: 'Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework for inference in associative Markov networks with global constraints. CVPR: Computer Vision and Pattern Recognition, 1889–1896.' mla: Osokin, Anton, et al. Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints. IEEE, 2011, pp. 1889–96, doi:10.1109/CVPR.2011.5995361. short: A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:02:00Z date_published: 2011-08-22T00:00:00Z date_updated: 2021-01-12T07:41:47Z day: '22' doi: 10.1109/CVPR.2011.5995361 extern: 1 main_file_link: - open_access: '0' url: http://arxiv.org/pdf/1103.1077v1 month: '08' page: 1889 - 1896 publication_status: published publisher: IEEE publist_id: '3476' quality_controlled: 0 status: public title: Submodular decomposition framework for inference in associative Markov networks with global constraints type: conference year: '2011' ... --- _id: '3205' abstract: - lang: eng text: This paper proposes a novel Linear Programming (LP) based algorithm, called Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori (MAP) inference in probabilistic graphical models. Unlike traditional message passing algorithms, which operate uniformly on the whole factor graph, our method dynamically chooses regions of the factor graph on which to focus message-passing efforts. We propose two criteria for selecting regions, including an efficiently computable upper-bound on the increase in the objective possible by passing messages in any particular region. This bound is derived from the theory of primal-dual methods from combinatorial optimization, and the forest that maximizes the bounds can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental results show that our dynamic schedules significantly speed up state-of-the-art LP-based message-passing algorithms on a wide variety of real-world problems. author: - first_name: Daniel full_name: Tarlow, Daniel last_name: Tarlow - first_name: Druv full_name: Batra, Druv last_name: Batra - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent. In: Omnipress; 2011:113-120.' apa: 'Tarlow, D., Batra, D., Kohli, P., & Kolmogorov, V. (2011). Dynamic tree block coordinate ascent (pp. 113–120). Presented at the ICML: International Conference on Machine Learning, Omnipress.' chicago: Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011. ieee: 'D. Tarlow, D. Batra, P. Kohli, and V. Kolmogorov, “Dynamic tree block coordinate ascent,” presented at the ICML: International Conference on Machine Learning, 2011, pp. 113–120.' ista: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate ascent. ICML: International Conference on Machine Learning, 113–120.' mla: Tarlow, Daniel, et al. Dynamic Tree Block Coordinate Ascent. Omnipress, 2011, pp. 113–20. short: D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120. conference: name: 'ICML: International Conference on Machine Learning' date_created: 2018-12-11T12:02:00Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:41:47Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf month: '01' page: 113 - 120 publication_status: published publisher: Omnipress publist_id: '3475' quality_controlled: 0 status: public title: Dynamic tree block coordinate ascent type: conference year: '2011' ... --- _id: '3207' abstract: - lang: eng text: 'Cosegmentation is typically defined as the task of jointly segmenting something similar in a given set of images. Existing methods are too generic and so far have not demonstrated competitive results for any specific task. In this paper we overcome this limitation by adding two new aspects to cosegmentation: (1) the "something" has to be an object, and (2) the "similarity" measure is learned. In this way, we are able to achieve excellent results on the recently introduced iCoseg dataset, which contains small sets of images of either the same object instance or similar objects of the same class. The challenge of this dataset lies in the extreme changes in viewpoint, lighting, and object deformations within each set. We are able to considerably outperform several competitors. To achieve this performance, we borrow recent ideas from object recognition: the use of powerful features extracted from a pool of candidate object-like segmentations. We believe that our work will be beneficial to several application areas, such as image retrieval.' author: - first_name: Sara full_name: Vicente, Sara last_name: Vicente - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224. doi:10.1109/CVPR.2011.5995530' apa: 'Vicente, S., Rother, C., & Kolmogorov, V. (2011). Object cosegmentation (pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2011.5995530' chicago: Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,” 2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530. ieee: 'S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.' ista: 'Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer Vision and Pattern Recognition, 2217–2224.' mla: Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24, doi:10.1109/CVPR.2011.5995530. short: S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:02:01Z date_published: 2011-08-22T00:00:00Z date_updated: 2021-01-12T07:41:48Z day: '22' doi: 10.1109/CVPR.2011.5995530 extern: 1 month: '08' page: 2217 - 2224 publication_status: published publisher: IEEE publist_id: '3477' quality_controlled: 0 status: public title: Object cosegmentation type: conference year: '2011' ... --- _id: '3240' abstract: - lang: eng text: 'The famous Leftover Hash Lemma (LHL) states that (almost) universal hash functions are good randomness extractors. Despite its numerous applications, LHL-based extractors suffer from the following two limitations: - Large Entropy Loss: to extract v bits from distribution X of min-entropy m which are ε-close to uniform, one must set v ≤ m - 2log(1/ε), meaning that the entropy loss L = def m - v ≥ 2 log(1/ε). For many applications, such entropy loss is too large. - Large Seed Length: the seed length n of (almost) universal hash function required by the LHL must be at least n ≥ min (u - v, v + 2log(1/ε)) - O(1), where u is the length of the source, and must grow with the number of extracted bits. Quite surprisingly, we show that both limitations of the LHL - large entropy loss and large seed - can be overcome (or, at least, mitigated) in various important scenarios. First, we show that entropy loss could be reduced to L = log(1/ε) for the setting of deriving secret keys for a wide range of cryptographic applications. Specifically, the security of these schemes with an LHL-derived key gracefully degrades from ε to at most ε + √ε2-L. (Notice that, unlike standard LHL, this bound is meaningful even when one extracts more bits than the min-entropy we have!) Based on these results we build a general computational extractor that enjoys low entropy loss and can be used to instantiate a generic key derivation function for any cryptographic application. Second, we study the soundness of the natural expand-then-extract approach, where one uses a pseudorandom generator (PRG) to expand a short "input seed" S into a longer "output seed" S′, and then use the resulting S′ as the seed required by the LHL (or, more generally, by any randomness extractor). We show that, in general, the expand-then-extract approach is not sound if the Decisional Diffie-Hellman assumption is true. Despite that, we show that it is sound either: (1) when extracting a "small" (logarithmic in the security of the PRG) number of bits; or (2) in minicrypt. Implication (2) suggests that the expand-then-extract approach is likely secure when used with "practical" PRGs, despite lacking a reductionist proof of security! © 2011 International Association for Cryptologic Research.' alternative_title: - LNCS author: - first_name: Boaz full_name: Barak, Boaz last_name: Barak - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Hugo full_name: Krawczyk, Hugo last_name: Krawczyk - first_name: Olivier full_name: Pereira, Olivier last_name: Pereira - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: François full_name: Standaert, François-Xavier last_name: Standaert - first_name: Yu full_name: Yu, Yu last_name: Yu citation: ama: 'Barak B, Dodis Y, Krawczyk H, et al. Leftover hash lemma revisited. In: Vol 6841. Springer; 2011:1-20. doi: 10.1007/978-3-642-22792-9_1' apa: 'Barak, B., Dodis, Y., Krawczyk, H., Pereira, O., Pietrzak, K. Z., Standaert, F., & Yu, Y. (2011). Leftover hash lemma revisited (Vol. 6841, pp. 1–20). Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/ 10.1007/978-3-642-22792-9_1' chicago: Barak, Boaz, Yevgeniy Dodis, Hugo Krawczyk, Olivier Pereira, Krzysztof Z Pietrzak, François Standaert, and Yu Yu. “Leftover Hash Lemma Revisited,” 6841:1–20. Springer, 2011. https://doi.org/ 10.1007/978-3-642-22792-9_1. ieee: 'B. Barak et al., “Leftover hash lemma revisited,” presented at the CRYPTO: International Cryptology Conference, 2011, vol. 6841, pp. 1–20.' ista: 'Barak B, Dodis Y, Krawczyk H, Pereira O, Pietrzak KZ, Standaert F, Yu Y. 2011. Leftover hash lemma revisited. CRYPTO: International Cryptology Conference, LNCS, vol. 6841, 1–20.' mla: Barak, Boaz, et al. Leftover Hash Lemma Revisited. Vol. 6841, Springer, 2011, pp. 1–20, doi: 10.1007/978-3-642-22792-9_1. short: B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert, Y. Yu, in:, Springer, 2011, pp. 1–20. conference: name: 'CRYPTO: International Cryptology Conference' date_created: 2018-12-11T12:02:12Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:03Z day: '01' doi: ' 10.1007/978-3-642-22792-9_1' extern: 1 intvolume: ' 6841' month: '01' page: 1 - 20 publication_status: published publisher: Springer publist_id: '3440' quality_controlled: 0 status: public title: Leftover hash lemma revisited type: conference volume: 6841 year: '2011' ... --- _id: '3264' abstract: - lang: eng text: Verification of programs with procedures, multi-threaded programs, and higher-order functional programs can be effectively au- tomated using abstraction and refinement schemes that rely on spurious counterexamples for abstraction discovery. The analysis of counterexam- ples can be automated by a series of interpolation queries, or, alterna- tively, as a constraint solving query expressed by a set of recursion free Horn clauses. (A set of interpolation queries can be formulated as a single constraint over Horn clauses with linear dependency structure between the unknown relations.) In this paper we present an algorithm for solving recursion free Horn clauses over a combined theory of linear real/rational arithmetic and uninterpreted functions. Our algorithm performs resolu- tion to deal with the clausal structure and relies on partial solutions to deal with (non-local) instances of functionality axioms. alternative_title: - LNCS author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Corneliu full_name: Popeea, Corneliu last_name: Popeea - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko citation: ama: 'Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:10.1007/978-3-642-25318-8_16' apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2011). Solving recursion-free Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan: Springer. https://doi.org/10.1007/978-3-642-25318-8_16' chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011. https://doi.org/10.1007/978-3-642-25318-8_16. ieee: 'A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.' ista: 'Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS, vol. 7078, 188–203.' mla: Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF. Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16. short: A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203. conference: end_date: 2011-12-07 location: Kenting, Taiwan name: 'APLAS: Asian Symposium on Programming Languages and Systems' start_date: 2011-12-05 date_created: 2018-12-11T12:02:20Z date_published: 2011-12-05T00:00:00Z date_updated: 2021-01-12T07:42:15Z day: '05' department: - _id: ToHe doi: 10.1007/978-3-642-25318-8_16 ec_funded: 1 editor: - first_name: Hongseok full_name: Yang, Hongseok last_name: Yang intvolume: ' 7078' language: - iso: eng month: '12' oa_version: None page: 188 - 203 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '3383' quality_controlled: '1' status: public title: Solving recursion-free Horn clauses over LI+UIF type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 7078 year: '2011' ... --- _id: '3266' abstract: - lang: eng text: We present a joint image segmentation and labeling model (JSL) which, given a bag of figure-ground segment hypotheses extracted at multiple image locations and scales, constructs a joint probability distribution over both the compatible image interpretations (tilings or image segmentations) composed from those segments, and over their labeling into categories. The process of drawing samples from the joint distribution can be interpreted as first sampling tilings, modeled as maximal cliques, from a graph connecting spatially non-overlapping segments in the bag [1], followed by sampling labels for those segments, conditioned on the choice of a particular tiling. We learn the segmentation and labeling parameters jointly, based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure. The partition function over tilings and labelings is increasingly more accurately approximated by including incorrect configurations that a not-yet-competent model rates probable during learning. We show that the proposed methodologymatches the current state of the art in the Stanford dataset [2], as well as in VOC2010, where 41.7% accuracy on the test set is achieved. author: - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Joao full_name: Carreira, Joao last_name: Carreira - first_name: Cristian full_name: Sminchisescu, Cristian last_name: Sminchisescu citation: ama: 'Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation and labeling. In: NIPS Proceedings. Vol 24. Neural Information Processing Systems Foundation; 2011:1827-1835.' apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2011). Probabilistic joint image segmentation and labeling. In NIPS Proceedings (Vol. 24, pp. 1827–1835). Granada, Spain: Neural Information Processing Systems Foundation.' chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint Image Segmentation and Labeling.” In NIPS Proceedings, 24:1827–35. Neural Information Processing Systems Foundation, 2011. ieee: A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation and labeling,” in NIPS Proceedings, Granada, Spain, 2011, vol. 24, pp. 1827–1835. ista: 'Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol. 24, 1827–1835.' mla: Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.” NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation, 2011, pp. 1827–35. short: A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835. conference: end_date: 2011-12-14 location: Granada, Spain name: 'NIPS: Neural Information Processing Systems' start_date: 2011-12-12 date_created: 2018-12-11T12:02:21Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T07:42:15Z day: '01' department: - _id: HeEd intvolume: ' 24' language: - iso: eng month: '12' oa_version: None page: 1827 - 1835 publication: NIPS Proceedings publication_status: published publisher: Neural Information Processing Systems Foundation publist_id: '3381' quality_controlled: '1' scopus_import: 1 status: public title: Probabilistic joint image segmentation and labeling type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2011' ... --- _id: '3269' abstract: - lang: eng text: The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods. article_processing_charge: No article_type: original author: - first_name: Yu full_name: Sheng, Yu last_name: Sheng - first_name: Barbara full_name: Cutler, Barbara last_name: Cutler - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Joshua full_name: Nasman, Joshua last_name: Nasman citation: ama: Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 2011;30(4):1261-1268. doi:10.1111/j.1467-8659.2011.01985.x apa: Sheng, Y., Cutler, B., Chen, C., & Nasman, J. (2011). Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2011.01985.x chicago: Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” Computer Graphics Forum. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1467-8659.2011.01985.x. ieee: Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination cancellation in complex projection environments,” Computer Graphics Forum, vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011. ista: Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 30(4), 1261–1268. mla: Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” Computer Graphics Forum, vol. 30, no. 4, Wiley-Blackwell, 2011, pp. 1261–68, doi:10.1111/j.1467-8659.2011.01985.x. short: Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268. date_created: 2018-12-11T12:02:22Z date_published: 2011-07-19T00:00:00Z date_updated: 2021-01-12T07:42:16Z day: '19' department: - _id: HeEd doi: 10.1111/j.1467-8659.2011.01985.x intvolume: ' 30' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf month: '07' oa: 1 oa_version: Published Version page: 1261 - 1268 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '3377' quality_controlled: '1' scopus_import: 1 status: public title: Perceptual global illumination cancellation in complex projection environments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2011' ... --- _id: '3267' abstract: - lang: eng text: 'We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We study the problem with different measures: volume, diameter and radius. For volume, that is, the 1-norm of a cycle, two main results are presented. First, we prove that 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). The latter result leads to 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. As for the other two measures defined by pairwise geodesic distance, diameter and radius, we show that the localization problem is NP-hard for diameter but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.' author: - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Daniel full_name: Freedman, Daniel last_name: Freedman citation: ama: Chen C, Freedman D. Hardness results for homology localization. Discrete & Computational Geometry. 2011;45(3):425-448. doi:10.1007/s00454-010-9322-8 apa: Chen, C., & Freedman, D. (2011). Hardness results for homology localization. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9322-8 chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” Discrete & Computational Geometry. Springer, 2011. https://doi.org/10.1007/s00454-010-9322-8. ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete & Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011. ista: Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete & Computational Geometry. 45(3), 425–448. mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” Discrete & Computational Geometry, vol. 45, no. 3, Springer, 2011, pp. 425–48, doi:10.1007/s00454-010-9322-8. short: C. Chen, D. Freedman, Discrete & Computational Geometry 45 (2011) 425–448. date_created: 2018-12-11T12:02:21Z date_published: 2011-01-14T00:00:00Z date_updated: 2023-02-21T16:07:10Z day: '14' department: - _id: HeEd doi: 10.1007/s00454-010-9322-8 intvolume: ' 45' issue: '3' language: - iso: eng month: '01' oa_version: None page: 425 - 448 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '3379' quality_controlled: '1' related_material: record: - id: '10909' relation: earlier_version status: public scopus_import: 1 status: public title: Hardness results for homology localization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2011' ... --- _id: '3268' abstract: - lang: eng text: 'Algebraic topology is generally considered one of the purest subfield of mathematics. However, over the last decade two interesting new lines of research have emerged, one focusing on algorithms for algebraic topology, and the other on applications of algebraic topology in engineering and science. Amongst the new areas in which the techniques have been applied are computer vision and image processing. In this paper, we survey the results of these endeavours. Because algebraic topology is an area of mathematics with which most computer vision practitioners have no experience, we review the machinery behind the theories of homology and persistent homology; our review emphasizes intuitive explanations. In terms of applications to computer vision, we focus on four illustrative problems: shape signatures, natural image statistics, image denoising, and segmentation. Our hope is that this review will stimulate interest on the part of computer vision researchers to both use and extend the tools of this new field. ' alternative_title: - Computer Science, Technology and Applications author: - first_name: Daniel full_name: Freedman, Daniel last_name: Freedman - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen citation: ama: 'Freedman D, Chen C. Algebraic topology for computer vision. In: Computer Vision. Nova Science Publishers; 2011:239-268.' apa: Freedman, D., & Chen, C. (2011). Algebraic topology for computer vision. In Computer Vision (pp. 239–268). Nova Science Publishers. chicago: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” In Computer Vision, 239–68. Nova Science Publishers, 2011. ieee: D. Freedman and C. Chen, “Algebraic topology for computer vision,” in Computer Vision, Nova Science Publishers, 2011, pp. 239–268. ista: 'Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer Vision. Computer Science, Technology and Applications, , 239–268.' mla: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” Computer Vision, Nova Science Publishers, 2011, pp. 239–68. short: D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011, pp. 239–268. date_created: 2018-12-11T12:02:22Z date_published: 2011-11-30T00:00:00Z date_updated: 2021-01-12T07:42:16Z day: '30' extern: '1' language: - iso: eng main_file_link: - url: http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf month: '11' oa_version: None page: 239 - 268 publication: Computer Vision publication_status: published publisher: Nova Science Publishers publist_id: '3378' quality_controlled: '1' status: public title: Algebraic topology for computer vision type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3288' abstract: - lang: eng text: 'The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA.' acknowledgement: his work was funded by the National Health and Medical Research Council (NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship. A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the Institute for Molecular Bioscience, established with the generous support of the ACRF. author: - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Selwin full_name: Wu, Selwin last_name: Wu - first_name: Guillermo full_name: Gomez, Guillermo last_name: Gomez - first_name: Sabine full_name: Mangold, Sabine last_name: Mangold - first_name: Alpha full_name: Yap, Alpha last_name: Yap - first_name: Nicholas full_name: Hamilton, Nicholas last_name: Hamilton citation: ama: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458 apa: Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011). Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0022458 chicago: Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap, and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458. ieee: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011. ista: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 6(7). mla: Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458. short: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011). date_created: 2018-12-11T12:02:28Z date_published: 2011-07-22T00:00:00Z date_updated: 2021-01-12T07:42:25Z day: '22' ddc: - '570' department: - _id: CaHe doi: 10.1371/journal.pone.0022458 file: - access_level: open_access checksum: 57a5eb11dd05241c48c44f492b3ec3ac content_type: application/pdf creator: dernst date_created: 2019-05-10T10:51:43Z date_updated: 2020-07-14T12:46:06Z file_id: '6399' file_name: 2011_PLOS_Smutny.PDF file_size: 1984567 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 6' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3357' quality_controlled: '1' status: public title: Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2011' ... --- _id: '3286' abstract: - lang: eng text: Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes by electrostatic interactions with negatively charged lipids. It turned out that for inhibition of microbial growth a high CAMP membrane concentration is required, which can be realized by the incorporation of hydrophobic groups within the peptide. Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial over eukaryotic host membranes, thereby causing the risk of detrimental side-effects. In this study we addressed how cationic amphipathic peptides—in particular a CAMP with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics of molecules in eukaryotic membranes. We found KLK to selectively inhibit the endocytosis of a subgroup of membrane proteins and lipids by electrostatically interacting with negatively charged sialic acid moieties. Ultrastructural characterization revealed the formation of membrane invaginations representing fission or fusion intermediates, in which the sialylated proteins and lipids were immobilized. Experiments on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively arrest sialylated membrane constituents. acknowledgement: "This work was funded by the GEN-AU project of the Austrian Research Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH, Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland), Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota, USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna) for excellent technical assistance in the processing of samples for electron microscopy and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for fruitful discussions. " author: - first_name: Julian full_name: Weghuber, Julian last_name: Weghuber - first_name: Michael full_name: Aichinger, Michael C. last_name: Aichinger - first_name: Mario full_name: Brameshuber, Mario last_name: Brameshuber - first_name: Stefan full_name: Stefan Wieser id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Verena full_name: Verena Ruprecht id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Birgit full_name: Plochberger, Birgit last_name: Plochberger - first_name: Josef full_name: Madl, Josef last_name: Madl - first_name: Andreas full_name: Horner, Andreas last_name: Horner - first_name: Siegfried full_name: Reipert, Siegfried last_name: Reipert - first_name: Karl full_name: Lohner, Karl last_name: Lohner - first_name: Tamas full_name: Henics, Tamas last_name: Henics - first_name: Gerhard full_name: Schuetz, Gerhard J last_name: Schuetz citation: ama: Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590. doi:10.1016/j.bbamem.2011.06.007 apa: Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger, B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2011.06.007 chicago: Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser, Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier, 2011. https://doi.org/10.1016/j.bbamem.2011.06.007. ieee: J. Weghuber et al., “Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells,” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10. Elsevier, pp. 2581–2590, 2011. ista: Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1808(10), 2581–2590. mla: Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011, pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007. short: J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger, J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590. date_created: 2018-12-11T12:02:28Z date_published: 2011-10-01T00:00:00Z date_updated: 2021-01-12T07:42:24Z day: '01' doi: 10.1016/j.bbamem.2011.06.007 extern: 1 intvolume: ' 1808' issue: '10' license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' page: 2581 - 2590 publication: Biochimica et Biophysica Acta (BBA) - Biomembranes publication_status: published publisher: Elsevier publist_id: '3359' quality_controlled: 0 status: public title: Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 1808 year: '2011' ... --- _id: '3287' abstract: - lang: eng text: 'Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion.' author: - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Markus full_name: Axmann, Markus last_name: Axmann - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Gerhard full_name: Schuetz, Gerhard last_name: Schuetz citation: ama: Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule trajectories? Current Protein & Peptide Science. 2011;12(8):714-724. doi:10.2174/138920311798841753 apa: Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we learn from single molecule trajectories? Current Protein & Peptide Science. Bentham Science Publishers. https://doi.org/10.2174/138920311798841753 chicago: Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753. ieee: V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” Current Protein & Peptide Science, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011. ista: Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724. mla: Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753. short: V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide Science 12 (2011) 714–724. date_created: 2018-12-11T12:02:28Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T07:42:24Z day: '01' department: - _id: CaHe - _id: MiSi doi: 10.2174/138920311798841753 intvolume: ' 12' issue: '8' language: - iso: eng month: '12' oa_version: None page: 714 - 724 publication: Current Protein & Peptide Science publication_status: published publisher: Bentham Science Publishers publist_id: '3358' quality_controlled: '1' scopus_import: 1 status: public title: What can we learn from single molecule trajectories? type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2011' ... --- _id: '3285' abstract: - lang: eng text: Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents. acknowledgement: Y 250-B03/Austrian Science Fund FWF/Austria author: - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Didier full_name: Marguet, Didier last_name: Marguet - first_name: Gerhard full_name: Schuetz, Gerhard last_name: Schuetz citation: ama: Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 2011;100(11):2839-2845. doi:10.1016/j.bpj.2011.04.035 apa: Ruprecht, V., Wieser, S., Marguet, D., & Schuetz, G. (2011). Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2011.04.035 chicago: Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical Journal. Biophysical Society, 2011. https://doi.org/10.1016/j.bpj.2011.04.035. ieee: V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes,” Biophysical Journal, vol. 100, no. 11. Biophysical Society, pp. 2839–2845, 2011. ista: Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 100(11), 2839–2845. mla: Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035. short: V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011) 2839–2845. date_created: 2018-12-11T12:02:27Z date_published: 2011-06-08T00:00:00Z date_updated: 2021-01-12T07:42:23Z day: '08' doi: 10.1016/j.bpj.2011.04.035 extern: '1' intvolume: ' 100' issue: '11' language: - iso: eng month: '06' oa_version: None page: 2839 - 2845 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '3360' status: public title: Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2011' ... --- _id: '3302' abstract: - lang: eng text: Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We present a new job execution environment Flextic that exploits scal- able static scheduling techniques to provide the user with a flexible pricing model, such as a tradeoff between dif- ferent degrees of execution speed and execution price, and at the same time, reduce scheduling overhead for the cloud provider. We have evaluated a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various data parallel jobs from machine learning, im- age processing, and gene sequencing that we considered, Flextic has low scheduling overhead and reduces job du- ration by up to 15% compared to Hadoop, a dynamic cloud scheduler. author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Anmol full_name: Singh, Anmol id: 72A86902-E99F-11E9-9F62-915534D1B916 last_name: Singh - first_name: Vasu full_name: Singh, Vasu id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds. In: USENIX; 2011:1-6.' apa: 'Henzinger, T. A., Singh, A., Singh, V., Wies, T., & Zufferey, D. (2011). Static scheduling in clouds (pp. 1–6). Presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, USENIX.' chicago: Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey. “Static Scheduling in Clouds,” 1–6. USENIX, 2011. ieee: 'T. A. Henzinger, A. Singh, V. Singh, T. Wies, and D. Zufferey, “Static scheduling in clouds,” presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, 2011, pp. 1–6.' ista: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. 2011. Static scheduling in clouds. HotCloud: Workshop on Hot Topics in Cloud Computing, 1–6.' mla: Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 2011, pp. 1–6. short: T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6. conference: end_date: 2011-06-15 name: 'HotCloud: Workshop on Hot Topics in Cloud Computing' start_date: 2011-06-14 date_created: 2018-12-11T12:02:33Z date_published: 2011-06-14T00:00:00Z date_updated: 2021-01-12T07:42:31Z day: '14' ddc: - '000' - '005' department: - _id: ToHe file: - access_level: open_access checksum: 21a461ac004bb535c83320fe79b30375 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:14Z date_updated: 2020-07-14T12:46:06Z file_id: '5333' file_name: IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf file_size: 232770 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 1 - 6 publication_status: published publisher: USENIX publist_id: '3338' pubrep_id: '90' quality_controlled: '1' status: public title: Static scheduling in clouds type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3301' abstract: - lang: eng text: The chemical master equation is a differential equation describing the time evolution of the probability distribution over the possible “states” of a biochemical system. The solution of this equation is of interest within the systems biology field ever since the importance of the molec- ular noise has been acknowledged. Unfortunately, most of the systems do not have analytical solutions, and numerical solutions suffer from the course of dimensionality and therefore need to be approximated. Here, we introduce the concept of tail approximation, which retrieves an approximation of the probabilities in the tail of a distribution from the total probability of the tail and its conditional expectation. This approximation method can then be used to numerically compute the solution of the chemical master equation on a subset of the state space, thus fighting the explosion of the state space, for which this problem is renowned. author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Maria full_name: Mateescu, Maria last_name: Mateescu citation: ama: 'Henzinger TA, Mateescu M. Tail approximation for the chemical master equation. In: Tampere International Center for Signal Processing; 2011.' apa: 'Henzinger, T. A., & Mateescu, M. (2011). Tail approximation for the chemical master equation. Presented at the WCSB: Workshop on Computational Systems Biology (TICSP), Tampere International Center for Signal Processing.' chicago: Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011. ieee: 'T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP), 2011.' ista: 'Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP).' mla: Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical Master Equation. Tampere International Center for Signal Processing, 2011. short: T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal Processing, 2011. conference: name: 'WCSB: Workshop on Computational Systems Biology (TICSP)' date_created: 2018-12-11T12:02:33Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:30Z day: '01' ddc: - '005' - '570' department: - _id: ToHe file: - access_level: open_access checksum: aa4d7a832a5419e6c0090650ebff2b9a content_type: application/pdf creator: system date_created: 2018-12-12T10:18:12Z date_updated: 2020-07-14T12:46:06Z file_id: '5331' file_name: IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf file_size: 240820 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version publication_status: published publisher: Tampere International Center for Signal Processing publist_id: '3339' pubrep_id: '91' quality_controlled: '1' status: public title: Tail approximation for the chemical master equation type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3299' abstract: - lang: eng text: 'We introduce propagation models, a formalism designed to support general and efficient data structures for the transient analysis of biochemical reaction networks. We give two use cases for propagation abstract data types: the uniformization method and numerical integration. We also sketch an implementation of a propagation abstract data type, which uses abstraction to approximate states.' author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Maria full_name: Mateescu, Maria last_name: Mateescu citation: ama: 'Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction networks. In: Springer; 2011:1-3. doi:10.1145/2037509.2037510' apa: 'Henzinger, T. A., & Mateescu, M. (2011). Propagation models for computing biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational Methods in Systems Biology, Paris, France: Springer. https://doi.org/10.1145/2037509.2037510' chicago: Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing Biochemical Reaction Networks,” 1–3. Springer, 2011. https://doi.org/10.1145/2037509.2037510. ieee: 'T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical reaction networks,” presented at the CMSB: Computational Methods in Systems Biology, Paris, France, 2011, pp. 1–3.' ista: 'Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.' mla: Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510. short: T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3. conference: end_date: 2011-09-23 location: Paris, France name: 'CMSB: Computational Methods in Systems Biology' start_date: 2011-09-21 date_created: 2018-12-11T12:02:32Z date_published: 2011-09-21T00:00:00Z date_updated: 2021-01-12T07:42:29Z day: '21' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1145/2037509.2037510 file: - access_level: open_access checksum: 7f5c65509db1a9fb049abedd9663ed06 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:50Z date_updated: 2020-07-14T12:46:06Z file_id: '4649' file_name: IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf file_size: 255780 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1 - 3 publication_status: published publisher: Springer publist_id: '3341' pubrep_id: '92' quality_controlled: '1' scopus_import: 1 status: public title: Propagation models for computing biochemical reaction networks type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3316' abstract: - lang: eng text: In addition to being correct, a system should be robust, that is, it should behave reasonably even after receiving unexpected inputs. In this paper, we summarize two formal notions of robustness that we have introduced previously for reactive systems. One of the notions is based on assigning costs for failures on a user-provided notion of incorrect transitions in a specification. Here, we define a system to be robust if a finite number of incorrect inputs does not lead to an infinite number of incorrect outputs. We also give a more refined notion of robustness that aims to minimize the ratio of output failures to input failures. The second notion is aimed at liveness. In contrast to the previous notion, it has no concept of recovery from an error. Instead, it compares the ratio of the number of liveness constraints that the system violates to the number of liveness constraints that the environment violates. article_processing_charge: No author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Karin full_name: Greimel, Karin last_name: Greimel - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann citation: ama: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered robustness. In: 6th IEEE International Symposium on Industrial and Embedded Systems. IEEE; 2011:176-185. doi:10.1109/SIES.2011.5953660' apa: 'Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann, B. (2011). Specification-centered robustness. In 6th IEEE International Symposium on Industrial and Embedded Systems (pp. 176–185). Vasteras, Sweden: IEEE. https://doi.org/10.1109/SIES.2011.5953660' chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Specification-Centered Robustness.” In 6th IEEE International Symposium on Industrial and Embedded Systems, 176–85. IEEE, 2011. https://doi.org/10.1109/SIES.2011.5953660. ieee: R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered robustness,” in 6th IEEE International Symposium on Industrial and Embedded Systems, Vasteras, Sweden, 2011, pp. 176–185. ista: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered robustness. 6th IEEE International Symposium on Industrial and Embedded Systems. SIES: International Symposium on Industrial Embedded Systems, 176–185.' mla: Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660. short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–185. conference: end_date: 2011-06-17 location: Vasteras, Sweden name: ' SIES: International Symposium on Industrial Embedded Systems' start_date: 2011-06-15 date_created: 2018-12-11T12:02:38Z date_published: 2011-07-14T00:00:00Z date_updated: 2021-01-12T07:42:36Z day: '14' department: - _id: KrCh - _id: ToHe doi: 10.1109/SIES.2011.5953660 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse month: '07' oa: 1 oa_version: Published Version page: 176 - 185 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 6th IEEE International Symposium on Industrial and Embedded Systems publication_status: published publisher: IEEE publist_id: '3323' quality_controlled: '1' scopus_import: 1 status: public title: Specification-centered robustness type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3318' abstract: - lang: eng text: Parvalbumin is thought to act in a manner similar to EGTA, but how a slow Ca2+ buffer affects nanodomain-coupling regimes at GABAergic synapses is unclear. Direct measurements of parvalbumin concentration and paired recordings in rodent hippocampus and cerebellum revealed that parvalbumin affects synaptic dynamics only when expressed at high levels. Modeling suggests that, in high concentrations, parvalbumin may exert BAPTA-like effects, modulating nanodomain coupling via competition with local saturation of endogenous fixed buffers. author: - first_name: Emmanuel full_name: Eggermann, Emmanuel last_name: Eggermann - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Eggermann E, Jonas PM. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. 2011;15:20-22. doi:10.1038/nn.3002 apa: Eggermann, E., & Jonas, P. M. (2011). How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3002 chicago: Eggermann, Emmanuel, and Peter M Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.3002. ieee: E. Eggermann and P. M. Jonas, “How the ‘slow’ Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses,” Nature Neuroscience, vol. 15. Nature Publishing Group, pp. 20–22, 2011. ista: Eggermann E, Jonas PM. 2011. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. 15, 20–22. mla: Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” Nature Neuroscience, vol. 15, Nature Publishing Group, 2011, pp. 20–22, doi:10.1038/nn.3002. short: E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22. date_created: 2018-12-11T12:02:38Z date_published: 2011-12-04T00:00:00Z date_updated: 2021-01-12T07:42:37Z day: '04' department: - _id: PeJo doi: 10.1038/nn.3002 intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/ month: '12' oa: 1 oa_version: Submitted Version page: 20 - 22 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '3321' quality_controlled: '1' scopus_import: 1 status: public title: How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2011' ... --- _id: '3335' abstract: - lang: eng text: We study the topology of the Megaparsec Cosmic Web in terms of the scale-dependent Betti numbers, which formalize the topological information content of the cosmic mass distribution. While the Betti numbers do not fully quantify topology, they extend the information beyond conventional cosmological studies of topology in terms of genus and Euler characteristic. The richer information content of Betti numbers goes along the availability of fast algorithms to compute them. For continuous density fields, we determine the scale-dependence of Betti numbers by invoking the cosmologically familiar filtration of sublevel or superlevel sets defined by density thresholds. For the discrete galaxy distribution, however, the analysis is based on the alpha shapes of the particles. These simplicial complexes constitute an ordered sequence of nested subsets of the Delaunay tessellation, a filtration defined by the scale parameter, α. As they are homotopy equivalent to the sublevel sets of the distance field, they are an excellent tool for assessing the topological structure of a discrete point distribution. In order to develop an intuitive understanding for the behavior of Betti numbers as a function of α, and their relation to the morphological patterns in the Cosmic Web, we first study them within the context of simple heuristic Voronoi clustering models. These can be tuned to consist of specific morphological elements of the Cosmic Web, i.e. clusters, filaments, or sheets. To elucidate the relative prominence of the various Betti numbers in different stages of morphological evolution, we introduce the concept of alpha tracks. Subsequently, we address the topology of structures emerging in the standard LCDM scenario and in cosmological scenarios with alternative dark energy content. The evolution of the Betti numbers is shown to reflect the hierarchical evolution of the Cosmic Web. We also demonstrate that the scale-dependence of the Betti numbers yields a promising measure of cosmological parameters, with a potential to help in determining the nature of dark energy and to probe primordial non-Gaussianities. We also discuss the expected Betti numbers as a function of the density threshold for superlevel sets of a Gaussian random field. Finally, we introduce the concept of persistent homology. It measures scale levels of the mass distribution and allows us to separate small from large scale features. Within the context of the hierarchical cosmic structure formation, persistence provides a natural formalism for a multiscale topology study of the Cosmic Web. alternative_title: - LNCS author: - first_name: Rien full_name: Van De Weygaert, Rien last_name: Van De Weygaert - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Bernard full_name: Jones, Bernard last_name: Jones - first_name: Pratyush full_name: Pranav, Pratyush last_name: Pranav - first_name: Changbom full_name: Park, Changbom last_name: Park - first_name: Wojciech full_name: Hellwing, Wojciech last_name: Hellwing - first_name: Bob full_name: Eldering, Bob last_name: Eldering - first_name: Nico full_name: Kruithof, Nico last_name: Kruithof - first_name: Patrick full_name: Bos, Patrick last_name: Bos - first_name: Johan full_name: Hidding, Johan last_name: Hidding - first_name: Job full_name: Feldbrugge, Job last_name: Feldbrugge - first_name: Eline full_name: Ten Have, Eline last_name: Ten Have - first_name: Matti full_name: Van Engelen, Matti last_name: Van Engelen - first_name: Manuel full_name: Caroli, Manuel last_name: Caroli - first_name: Monique full_name: Teillaud, Monique last_name: Teillaud citation: ama: 'Van De Weygaert R, Vegter G, Edelsbrunner H, et al. Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In: Gavrilova M, Tan K, Mostafavi M, eds. Transactions on Computational Science XIV. Vol 6970. Special Issue on Voronoi Diagrams and Delaunay Triangulation. Springer; 2011:60-101. doi:10.1007/978-3-642-25249-5_3' apa: 'Van De Weygaert, R., Vegter, G., Edelsbrunner, H., Jones, B., Pranav, P., Park, C., … Teillaud, M. (2011). Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In M. Gavrilova, K. Tan, & M. Mostafavi (Eds.), Transactions on Computational Science XIV (Vol. 6970, pp. 60–101). Springer. https://doi.org/10.1007/978-3-642-25249-5_3' chicago: 'Van De Weygaert, Rien, Gert Vegter, Herbert Edelsbrunner, Bernard Jones, Pratyush Pranav, Changbom Park, Wojciech Hellwing, et al. “Alpha, Betti and the Megaparsec Universe: On the Topology of the Cosmic Web.” In Transactions on Computational Science XIV, edited by Marina Gavrilova, Kenneth Tan, and Mir Mostafavi, 6970:60–101. Special Issue on Voronoi Diagrams and Delaunay Triangulation. Springer, 2011. https://doi.org/10.1007/978-3-642-25249-5_3.' ieee: 'R. Van De Weygaert et al., “Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web,” in Transactions on Computational Science XIV, vol. 6970, M. Gavrilova, K. Tan, and M. Mostafavi, Eds. Springer, 2011, pp. 60–101.' ista: 'Van De Weygaert R, Vegter G, Edelsbrunner H, Jones B, Pranav P, Park C, Hellwing W, Eldering B, Kruithof N, Bos P, Hidding J, Feldbrugge J, Ten Have E, Van Engelen M, Caroli M, Teillaud M. 2011.Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In: Transactions on Computational Science XIV. LNCS, vol. 6970, 60–101.' mla: 'Van De Weygaert, Rien, et al. “Alpha, Betti and the Megaparsec Universe: On the Topology of the Cosmic Web.” Transactions on Computational Science XIV, edited by Marina Gavrilova et al., vol. 6970, Springer, 2011, pp. 60–101, doi:10.1007/978-3-642-25249-5_3.' short: R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park, W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi (Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101. date_created: 2018-12-11T12:02:44Z date_published: 2011-11-09T00:00:00Z date_updated: 2021-01-12T07:42:44Z day: '09' department: - _id: HeEd doi: 10.1007/978-3-642-25249-5_3 editor: - first_name: Marina full_name: Gavrilova, Marina last_name: Gavrilova - first_name: Kenneth full_name: Tan, Kenneth last_name: Tan - first_name: Mir full_name: Mostafavi, Mir last_name: Mostafavi external_id: arxiv: - '1306.3640' intvolume: ' 6970' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1306.3640 month: '11' oa: 1 oa_version: Preprint page: 60 - 101 publication: Transactions on Computational Science XIV publication_status: published publisher: Springer publist_id: '3295' quality_controlled: '1' scopus_import: 1 series_title: Special Issue on Voronoi Diagrams and Delaunay Triangulation status: public title: 'Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web' type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6970 year: '2011' ... --- _id: '3329' abstract: - lang: eng text: 'We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance µ in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution shape P; then, P''s offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(n log n)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. An alternative algorithm, based purely on rational arithmetic, answers the same deconstruction problem, up to an uncertainty parameter, and its running time depends on the parameter δ (in addition to the other input parameters: n, δ and the radius of the disk). If the input shape is found to be approximable, the rational-arithmetic algorithm also computes an approximate solution shape for the problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution shape P with at most one more vertex than a vertex-minimal one. Our study is motivated by applications from two different domains. However, since the offset operation has numerous uses, we anticipate that the reverse question that we study here will be still more broadly applicable. We present results obtained with our implementation of the rational-arithmetic algorithm.' author: - first_name: Eric full_name: Berberich, Eric last_name: Berberich - first_name: Dan full_name: Halperin, Dan last_name: Halperin - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Roza full_name: Pogalnikova, Roza last_name: Pogalnikova citation: ama: 'Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. In: Proceedings of the Twenty-Seventh Annual Symposium on Computational Geometry. ACM; 2011:187-196. doi:10.1145/1998196.1998225' apa: 'Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2011). Deconstructing approximate offsets. In Proceedings of the twenty-seventh annual symposium on Computational geometry (pp. 187–196). Paris, France: ACM. https://doi.org/10.1145/1998196.1998225' chicago: Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” In Proceedings of the Twenty-Seventh Annual Symposium on Computational Geometry, 187–96. ACM, 2011. https://doi.org/10.1145/1998196.1998225. ieee: E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” in Proceedings of the twenty-seventh annual symposium on Computational geometry, Paris, France, 2011, pp. 187–196. ista: 'Berberich E, Halperin D, Kerber M, Pogalnikova R. 2011. Deconstructing approximate offsets. Proceedings of the twenty-seventh annual symposium on Computational geometry. SCG: Symposium on Computational Geometry, 187–196.' mla: Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Proceedings of the Twenty-Seventh Annual Symposium on Computational Geometry, ACM, 2011, pp. 187–96, doi:10.1145/1998196.1998225. short: E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, in:, Proceedings of the Twenty-Seventh Annual Symposium on Computational Geometry, ACM, 2011, pp. 187–196. conference: end_date: 2011-06-15 location: Paris, France name: 'SCG: Symposium on Computational Geometry' start_date: 2011-06-13 date_created: 2018-12-11T12:02:42Z date_published: 2011-06-13T00:00:00Z date_updated: 2023-02-23T11:12:57Z day: '13' department: - _id: HeEd doi: 10.1145/1998196.1998225 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.2158 month: '06' oa: 1 oa_version: Preprint page: 187 - 196 publication: Proceedings of the twenty-seventh annual symposium on Computational geometry publication_status: published publisher: ACM publist_id: '3306' quality_controlled: '1' related_material: record: - id: '3115' relation: later_version status: public scopus_import: 1 status: public title: Deconstructing approximate offsets type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3332' abstract: - lang: eng text: Given an algebraic hypersurface O in ℝd, how many simplices are necessary for a simplicial complex isotopic to O? We address this problem and the variant where all vertices of the complex must lie on O. We give asymptotically tight worst-case bounds for algebraic plane curves. Our results gradually improve known bounds in higher dimensions; however, the question for tight bounds remains unsolved for d ≥ 3. article_processing_charge: No article_type: original author: - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Michael full_name: Sagraloff, Michael last_name: Sagraloff citation: ama: Kerber M, Sagraloff M. A note on the complexity of real algebraic hypersurfaces. Graphs and Combinatorics. 2011;27(3):419-430. doi:10.1007/s00373-011-1020-7 apa: Kerber, M., & Sagraloff, M. (2011). A note on the complexity of real algebraic hypersurfaces. Graphs and Combinatorics. Springer. https://doi.org/10.1007/s00373-011-1020-7 chicago: Kerber, Michael, and Michael Sagraloff. “A Note on the Complexity of Real Algebraic Hypersurfaces.” Graphs and Combinatorics. Springer, 2011. https://doi.org/10.1007/s00373-011-1020-7. ieee: M. Kerber and M. Sagraloff, “A note on the complexity of real algebraic hypersurfaces,” Graphs and Combinatorics, vol. 27, no. 3. Springer, pp. 419–430, 2011. ista: Kerber M, Sagraloff M. 2011. A note on the complexity of real algebraic hypersurfaces. Graphs and Combinatorics. 27(3), 419–430. mla: Kerber, Michael, and Michael Sagraloff. “A Note on the Complexity of Real Algebraic Hypersurfaces.” Graphs and Combinatorics, vol. 27, no. 3, Springer, 2011, pp. 419–30, doi:10.1007/s00373-011-1020-7. short: M. Kerber, M. Sagraloff, Graphs and Combinatorics 27 (2011) 419–430. date_created: 2018-12-11T12:02:43Z date_published: 2011-03-17T00:00:00Z date_updated: 2021-01-12T07:42:43Z day: '17' ddc: - '500' department: - _id: HeEd doi: 10.1007/s00373-011-1020-7 file: - access_level: open_access checksum: a63a1e3e885dcc68f1e3dea68dfbe213 content_type: application/pdf creator: dernst date_created: 2020-05-19T16:11:36Z date_updated: 2020-07-14T12:46:08Z file_id: '7869' file_name: 2011_GraphsCombi_Kerber.pdf file_size: 143976 relation: main_file file_date_updated: 2020-07-14T12:46:08Z has_accepted_license: '1' intvolume: ' 27' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 419 - 430 publication: Graphs and Combinatorics publication_status: published publisher: Springer publist_id: '3301' quality_controlled: '1' scopus_import: 1 status: public title: A note on the complexity of real algebraic hypersurfaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2011' ... --- _id: '3330' abstract: - lang: eng text: We consider the problem of approximating all real roots of a square-free polynomial f. Given isolating intervals, our algorithm refines each of them to a width at most 2-L, that is, each of the roots is approximated to L bits after the binary point. Our method provides a certified answer for arbitrary real polynomials, only requiring finite approximations of the polynomial coefficient and choosing a suitable working precision adaptively. In this way, we get a correct algorithm that is simple to implement and practically efficient. Our algorithm uses the quadratic interval refinement method; we adapt that method to be able to cope with inaccuracies when evaluating f, without sacrificing its quadratic convergence behavior. We prove a bound on the bit complexity of our algorithm in terms of degree, coefficient size and discriminant. Our bound improves previous work on integer polynomials by a factor of deg f and essentially matches best known theoretical bounds on root approximation which are obtained by very sophisticated algorithms. article_processing_charge: No author: - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Michael full_name: Sagraloff, Michael last_name: Sagraloff citation: ama: 'Kerber M, Sagraloff M. Root refinement for real polynomials. In: Springer; 2011:209-216. doi:10.1145/1993886.1993920' apa: 'Kerber, M., & Sagraloff, M. (2011). Root refinement for real polynomials (pp. 209–216). Presented at the ISSAC: International Symposium on Symbolic and Algebraic Computation, California, USA: Springer. https://doi.org/10.1145/1993886.1993920' chicago: Kerber, Michael, and Michael Sagraloff. “Root Refinement for Real Polynomials,” 209–16. Springer, 2011. https://doi.org/10.1145/1993886.1993920. ieee: 'M. Kerber and M. Sagraloff, “Root refinement for real polynomials,” presented at the ISSAC: International Symposium on Symbolic and Algebraic Computation, California, USA, 2011, pp. 209–216.' ista: 'Kerber M, Sagraloff M. 2011. Root refinement for real polynomials. ISSAC: International Symposium on Symbolic and Algebraic Computation, 209–216.' mla: Kerber, Michael, and Michael Sagraloff. Root Refinement for Real Polynomials. Springer, 2011, pp. 209–16, doi:10.1145/1993886.1993920. short: M. Kerber, M. Sagraloff, in:, Springer, 2011, pp. 209–216. conference: end_date: 2011-06-11 location: California, USA name: 'ISSAC: International Symposium on Symbolic and Algebraic Computation' start_date: 2011-06-08 date_created: 2018-12-11T12:02:43Z date_published: 2011-06-08T00:00:00Z date_updated: 2021-01-12T07:42:42Z day: '08' department: - _id: HeEd doi: 10.1145/1993886.1993920 external_id: arxiv: - '1104.1362' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.1362 month: '06' oa: 1 oa_version: Preprint page: 209 - 216 publication_status: published publisher: Springer publist_id: '3304' quality_controlled: '1' scopus_import: 1 status: public title: Root refinement for real polynomials type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3328' abstract: - lang: eng text: 'We report on a generic uni- and bivariate algebraic kernel that is publicly available with CGAL 3.7. It comprises complete, correct, though efficient state-of-the-art implementations on polynomials, roots of polynomial systems, and the support to analyze algebraic curves defined by bivariate polynomials. The kernel design is generic, that is, various number types and substeps can be exchanged. It is accompanied with a ready-to-use interface to enable arrangements induced by algebraic curves, that have already been used as basis for various geometric applications, as arrangements on Dupin cyclides or the triangulation of algebraic surfaces. We present two novel applications: arrangements of rotated algebraic curves and Boolean set operations on polygons bounded by segments of algebraic curves. We also provide experiments showing that our general implementation is competitive and even often clearly outperforms existing implementations that are explicitly tailored for specific types of non-linear curves that are available in CGAL.' article_processing_charge: No author: - first_name: Eric full_name: Berberich, Eric last_name: Berberich - first_name: Michael full_name: Hemmer, Michael last_name: Hemmer - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 citation: ama: 'Berberich E, Hemmer M, Kerber M. A generic algebraic kernel for non linear geometric applications. In: ACM; 2011:179-186. doi:10.1145/1998196.1998224' apa: 'Berberich, E., Hemmer, M., & Kerber, M. (2011). A generic algebraic kernel for non linear geometric applications (pp. 179–186). Presented at the SCG: Symposium on Computational Geometry, Paris, France: ACM. https://doi.org/10.1145/1998196.1998224' chicago: Berberich, Eric, Michael Hemmer, and Michael Kerber. “A Generic Algebraic Kernel for Non Linear Geometric Applications,” 179–86. ACM, 2011. https://doi.org/10.1145/1998196.1998224. ieee: 'E. Berberich, M. Hemmer, and M. Kerber, “A generic algebraic kernel for non linear geometric applications,” presented at the SCG: Symposium on Computational Geometry, Paris, France, 2011, pp. 179–186.' ista: 'Berberich E, Hemmer M, Kerber M. 2011. A generic algebraic kernel for non linear geometric applications. SCG: Symposium on Computational Geometry, 179–186.' mla: Berberich, Eric, et al. A Generic Algebraic Kernel for Non Linear Geometric Applications. ACM, 2011, pp. 179–86, doi:10.1145/1998196.1998224. short: E. Berberich, M. Hemmer, M. Kerber, in:, ACM, 2011, pp. 179–186. conference: end_date: 2011-06-15 location: Paris, France name: 'SCG: Symposium on Computational Geometry' start_date: 2011-06-13 date_created: 2018-12-11T12:02:42Z date_published: 2011-06-13T00:00:00Z date_updated: 2021-01-12T07:42:41Z day: '13' department: - _id: HeEd doi: 10.1145/1998196.1998224 language: - iso: eng main_file_link: - open_access: '1' url: https://hal.inria.fr/inria-00480031/file/RR-7274.pdf month: '06' oa: 1 oa_version: Published Version page: 179 - 186 publication_status: published publisher: ACM publist_id: '3307' quality_controlled: '1' scopus_import: 1 status: public title: A generic algebraic kernel for non linear geometric applications type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3334' article_type: letter_note author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: János full_name: Pach, János last_name: Pach - first_name: Günter full_name: Ziegler, Günter last_name: Ziegler citation: ama: Edelsbrunner H, Pach J, Ziegler G. Letter from the new editors-in-chief. Discrete & Computational Geometry. 2011;45(1):1-2. doi:10.1007/s00454-010-9313-9 apa: Edelsbrunner, H., Pach, J., & Ziegler, G. (2011). Letter from the new editors-in-chief. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9313-9 chicago: Edelsbrunner, Herbert, János Pach, and Günter Ziegler. “Letter from the New Editors-in-Chief.” Discrete & Computational Geometry. Springer, 2011. https://doi.org/10.1007/s00454-010-9313-9. ieee: H. Edelsbrunner, J. Pach, and G. Ziegler, “Letter from the new editors-in-chief,” Discrete & Computational Geometry, vol. 45, no. 1. Springer, pp. 1–2, 2011. ista: Edelsbrunner H, Pach J, Ziegler G. 2011. Letter from the new editors-in-chief. Discrete & Computational Geometry. 45(1), 1–2. mla: Edelsbrunner, Herbert, et al. “Letter from the New Editors-in-Chief.” Discrete & Computational Geometry, vol. 45, no. 1, Springer, 2011, pp. 1–2, doi:10.1007/s00454-010-9313-9. short: H. Edelsbrunner, J. Pach, G. Ziegler, Discrete & Computational Geometry 45 (2011) 1–2. date_created: 2018-12-11T12:02:44Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:44Z day: '01' department: - _id: HeEd doi: 10.1007/s00454-010-9313-9 intvolume: ' 45' issue: '1' language: - iso: eng month: '01' oa_version: None page: 1 - 2 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '3297' quality_controlled: '1' scopus_import: 1 status: public title: Letter from the new editors-in-chief type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2011' ... --- _id: '3353' abstract: - lang: eng text: 'Compositional theories are crucial when designing large and complex systems from smaller components. In this work we propose such a theory for synchronous concurrent systems. Our approach follows so-called interface theories, which use game-theoretic interpretations of composition and refinement. These are appropriate for systems with distinct inputs and outputs, and explicit conditions on inputs that must be enforced during composition. Our interfaces model systems that execute in an infinite sequence of synchronous rounds. At each round, a contract must be satisfied. The contract is simply a relation specifying the set of valid input/output pairs. Interfaces can be composed by parallel, serial or feedback composition. A refinement relation between interfaces is defined, and shown to have two main properties: (1) it is preserved by composition, and (2) it is equivalent to substitutability, namely, the ability to replace an interface by another one in any context. Shared refinement and abstraction operators, corresponding to greatest lower and least upper bounds with respect to refinement, are also defined. Input-complete interfaces, that impose no restrictions on inputs, and deterministic interfaces, that produce a unique output for any legal input, are discussed as special cases, and an interesting duality between the two classes is exposed. A number of illustrative examples are provided, as well as algorithms to compute compositions, check refinement, and so on, for finite-state interfaces.' article_number: '14' author: - first_name: Stavros full_name: Tripakis, Stavros last_name: Tripakis - first_name: Ben full_name: Lickly, Ben last_name: Lickly - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Edward full_name: Lee, Edward last_name: Lee citation: ama: Tripakis S, Lickly B, Henzinger TA, Lee E. A theory of synchronous relational interfaces. ACM Transactions on Programming Languages and Systems (TOPLAS). 2011;33(4). doi:10.1145/1985342.1985345 apa: Tripakis, S., Lickly, B., Henzinger, T. A., & Lee, E. (2011). A theory of synchronous relational interfaces. ACM Transactions on Programming Languages and Systems (TOPLAS). ACM. https://doi.org/10.1145/1985342.1985345 chicago: Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “A Theory of Synchronous Relational Interfaces.” ACM Transactions on Programming Languages and Systems (TOPLAS). ACM, 2011. https://doi.org/10.1145/1985342.1985345. ieee: S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “A theory of synchronous relational interfaces,” ACM Transactions on Programming Languages and Systems (TOPLAS), vol. 33, no. 4. ACM, 2011. ista: Tripakis S, Lickly B, Henzinger TA, Lee E. 2011. A theory of synchronous relational interfaces. ACM Transactions on Programming Languages and Systems (TOPLAS). 33(4), 14. mla: Tripakis, Stavros, et al. “A Theory of Synchronous Relational Interfaces.” ACM Transactions on Programming Languages and Systems (TOPLAS), vol. 33, no. 4, 14, ACM, 2011, doi:10.1145/1985342.1985345. short: S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, ACM Transactions on Programming Languages and Systems (TOPLAS) 33 (2011). date_created: 2018-12-11T12:02:51Z date_published: 2011-07-01T00:00:00Z date_updated: 2021-01-12T07:42:52Z day: '01' ddc: - '000' - '005' department: - _id: ToHe doi: 10.1145/1985342.1985345 ec_funded: 1 file: - access_level: open_access checksum: 5d44a8aa81e33210649beae507602138 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:45Z date_updated: 2020-07-14T12:46:09Z file_id: '5235' file_name: IST-2012-85-v1+1_A_theory_of_synchronous_relational_interfaces.pdf file_size: 775662 relation: main_file file_date_updated: 2020-07-14T12:46:09Z has_accepted_license: '1' intvolume: ' 33' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: ACM Transactions on Programming Languages and Systems (TOPLAS) publication_status: published publisher: ACM publist_id: '3263' pubrep_id: '85' quality_controlled: '1' scopus_import: 1 status: public title: A theory of synchronous relational interfaces type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2011' ... --- _id: '3355' abstract: - lang: eng text: Byzantine Fault Tolerant (BFT) protocols aim to improve the reliability of distributed systems. They enable systems to tolerate arbitrary failures in a bounded number of nodes. BFT protocols are usually proven correct for certain safety and liveness properties. However, recent studies have shown that the performance of state-of-the-art BFT protocols decreases drastically in the presence of even a single malicious node. This motivates a formal quantitative analysis of BFT protocols to investigate their performance characteristics under different scenarios. We present HyPerf, a new hybrid methodology based on model checking and simulation techniques for evaluating the performance of BFT protocols. We build a transition system corresponding to a BFT protocol and systematically explore the set of behaviors allowed by the protocol. We associate certain timing information with different operations in the protocol, like cryptographic operations and message transmission. After an elaborate state exploration, we use the time information to evaluate the performance characteristics of the protocol using simulation techniques. We integrate our framework in Mace, a tool for building and verifying distributed systems. We evaluate the performance of PBFT using our framework. We describe two different use-cases of our methodology. For the benign operation of the protocol, we use the time information as random variables to compute the probability distribution of the execution times. In the presence of faults, we estimate the worst-case performance of the protocol for various attacks that can be employed by malicious nodes. Our results show the importance of hybrid techniques in systematically analyzing the performance of large-scale systems. author: - first_name: Raluca full_name: Halalai, Raluca id: 584C6850-E996-11E9-805B-F01764644770 last_name: Halalai - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Vasu full_name: Singh, Vasu id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh citation: ama: 'Halalai R, Henzinger TA, Singh V. Quantitative evaluation of BFT protocols. In: IEEE; 2011:255-264. doi:10.1109/QEST.2011.40' apa: 'Halalai, R., Henzinger, T. A., & Singh, V. (2011). Quantitative evaluation of BFT protocols (pp. 255–264). Presented at the QEST: Quantitative Evaluation of Systems, Aachen, Germany: IEEE. https://doi.org/10.1109/QEST.2011.40' chicago: Halalai, Raluca, Thomas A Henzinger, and Vasu Singh. “Quantitative Evaluation of BFT Protocols,” 255–64. IEEE, 2011. https://doi.org/10.1109/QEST.2011.40. ieee: 'R. Halalai, T. A. Henzinger, and V. Singh, “Quantitative evaluation of BFT protocols,” presented at the QEST: Quantitative Evaluation of Systems, Aachen, Germany, 2011, pp. 255–264.' ista: 'Halalai R, Henzinger TA, Singh V. 2011. Quantitative evaluation of BFT protocols. QEST: Quantitative Evaluation of Systems, 255–264.' mla: Halalai, Raluca, et al. Quantitative Evaluation of BFT Protocols. IEEE, 2011, pp. 255–64, doi:10.1109/QEST.2011.40. short: R. Halalai, T.A. Henzinger, V. Singh, in:, IEEE, 2011, pp. 255–264. conference: end_date: 2011-09-08 location: Aachen, Germany name: 'QEST: Quantitative Evaluation of Systems' start_date: 2011-09-05 date_created: 2018-12-11T12:02:51Z date_published: 2011-10-13T00:00:00Z date_updated: 2021-01-12T07:42:53Z day: '13' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1109/QEST.2011.40 file: - access_level: open_access checksum: 4dc8750ab7921f51de992000b13d1b01 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:49Z date_updated: 2020-07-14T12:46:09Z file_id: '4648' file_name: IST-2012-84-v1+1_Quantitative_evaluation_of_BFT_protocols.pdf file_size: 272017 relation: main_file file_date_updated: 2020-07-14T12:46:09Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 255 - 264 publication_status: published publisher: IEEE publist_id: '3260' pubrep_id: '84' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative evaluation of BFT protocols type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3350' abstract: - lang: eng text: A controller for a discrete game with ω-regular objectives requires attention if, intuitively, it requires measuring the state and switching from the current control action. Minimum attention controllers are preferable in modern shared implementations of cyber-physical systems because they produce the least burden on system resources such as processor time or communication bandwidth. We give algorithms to compute minimum attention controllers for ω-regular objectives in imperfect information discrete two-player games. We show a polynomial-time reduction from minimum attention controller synthesis to synthesis of controllers for mean-payoff parity objectives in games of incomplete information. This gives an optimal EXPTIME-complete synthesis algorithm. We show that the minimum attention controller problem is decidable for infinite state systems with finite bisimulation quotients. In particular, the problem is decidable for timed and rectangular automata. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: 'Chatterjee K, Majumdar R. Minimum attention controller synthesis for omega regular objectives. In: Fahrenberg U, Tripakis S, eds. Vol 6919. Springer; 2011:145-159. doi:10.1007/978-3-642-24310-3_11' apa: 'Chatterjee, K., & Majumdar, R. (2011). Minimum attention controller synthesis for omega regular objectives. In U. Fahrenberg & S. Tripakis (Eds.) (Vol. 6919, pp. 145–159). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Aalborg, Denmark: Springer. https://doi.org/10.1007/978-3-642-24310-3_11' chicago: Chatterjee, Krishnendu, and Ritankar Majumdar. “Minimum Attention Controller Synthesis for Omega Regular Objectives.” edited by Uli Fahrenberg and Stavros Tripakis, 6919:145–59. Springer, 2011. https://doi.org/10.1007/978-3-642-24310-3_11. ieee: 'K. Chatterjee and R. Majumdar, “Minimum attention controller synthesis for omega regular objectives,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Aalborg, Denmark, 2011, vol. 6919, pp. 145–159.' ista: 'Chatterjee K, Majumdar R. 2011. Minimum attention controller synthesis for omega regular objectives. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 6919, 145–159.' mla: Chatterjee, Krishnendu, and Ritankar Majumdar. Minimum Attention Controller Synthesis for Omega Regular Objectives. Edited by Uli Fahrenberg and Stavros Tripakis, vol. 6919, Springer, 2011, pp. 145–59, doi:10.1007/978-3-642-24310-3_11. short: K. Chatterjee, R. Majumdar, in:, U. Fahrenberg, S. Tripakis (Eds.), Springer, 2011, pp. 145–159. conference: end_date: 2011-09-23 location: Aalborg, Denmark name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2011-09-21 date_created: 2018-12-11T12:02:49Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:51Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-24310-3_11 editor: - first_name: Uli full_name: Fahrenberg, Uli last_name: Fahrenberg - first_name: Stavros full_name: Tripakis, Stavros last_name: Tripakis intvolume: ' 6919' language: - iso: eng month: '01' oa_version: None page: 145 - 159 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '3271' quality_controlled: '1' scopus_import: 1 status: public title: Minimum attention controller synthesis for omega regular objectives type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6919 year: '2011' ... --- _id: '3351' abstract: - lang: eng text: In two-player games on graph, the players construct an infinite path through the game graph and get a reward computed by a payoff function over infinite paths. Over weighted graphs, the typical and most studied payoff functions compute the limit-average or the discounted sum of the rewards along the path. Besides their simple definition, these two payoff functions enjoy the property that memoryless optimal strategies always exist. In an attempt to construct other simple payoff functions, we define a class of payoff functions which compute an (infinite) weighted average of the rewards. This new class contains both the limit-average and the discounted sum functions, and we show that they are the only members of this class which induce memoryless optimal strategies, showing that there is essentially no other simple payoff functions. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Rohit full_name: Singh, Rohit last_name: Singh citation: ama: 'Chatterjee K, Doyen L, Singh R. On memoryless quantitative objectives. In: Owe O, Steffen M, Telle JA, eds. Vol 6914. Springer; 2011:148-159. doi:10.1007/978-3-642-22953-4_13' apa: 'Chatterjee, K., Doyen, L., & Singh, R. (2011). On memoryless quantitative objectives. In O. Owe, M. Steffen, & J. A. Telle (Eds.) (Vol. 6914, pp. 148–159). Presented at the FCT: Fundamentals of Computation Theory, Oslo, Norway: Springer. https://doi.org/10.1007/978-3-642-22953-4_13' chicago: Chatterjee, Krishnendu, Laurent Doyen, and Rohit Singh. “On Memoryless Quantitative Objectives.” edited by Olaf Owe, Martin Steffen, and Jan Arne Telle, 6914:148–59. Springer, 2011. https://doi.org/10.1007/978-3-642-22953-4_13. ieee: 'K. Chatterjee, L. Doyen, and R. Singh, “On memoryless quantitative objectives,” presented at the FCT: Fundamentals of Computation Theory, Oslo, Norway, 2011, vol. 6914, pp. 148–159.' ista: 'Chatterjee K, Doyen L, Singh R. 2011. On memoryless quantitative objectives. FCT: Fundamentals of Computation Theory, LNCS, vol. 6914, 148–159.' mla: Chatterjee, Krishnendu, et al. On Memoryless Quantitative Objectives. Edited by Olaf Owe et al., vol. 6914, Springer, 2011, pp. 148–59, doi:10.1007/978-3-642-22953-4_13. short: K. Chatterjee, L. Doyen, R. Singh, in:, O. Owe, M. Steffen, J.A. Telle (Eds.), Springer, 2011, pp. 148–159. conference: end_date: 2011-08-25 location: Oslo, Norway name: 'FCT: Fundamentals of Computation Theory' start_date: 2011-08-22 date_created: 2018-12-11T12:02:50Z date_published: 2011-04-16T00:00:00Z date_updated: 2021-01-12T07:42:52Z day: '16' department: - _id: KrCh doi: 10.1007/978-3-642-22953-4_13 editor: - first_name: Olaf full_name: Owe, Olaf last_name: Owe - first_name: Martin full_name: Steffen, Martin last_name: Steffen - first_name: Jan Arne full_name: Telle, Jan Arne last_name: Telle intvolume: ' 6914' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.3211 month: '04' oa: 1 oa_version: Submitted Version page: 148 - 159 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '3270' quality_controlled: '1' scopus_import: 1 status: public title: On memoryless quantitative objectives type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6914 year: '2011' ... --- _id: '3354' abstract: - lang: eng text: 'We consider two-player games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. We consider ω-regular winning conditions specified as parity objectives. Both players are allowed to use randomization when choosing their moves. We study the computation of the limit-winning set of states, consisting of the states where the sup-inf value of the game for player 1 is 1: in other words, a state is limit-winning if player 1 can ensure a probability of winning arbitrarily close to 1. We show that the limit-winning set can be computed in O(n2d+2) time, where n is the size of the game structure and 2d is the number of priorities (or colors). The membership problem of whether a state belongs to the limit-winning set can be decided in NP ∩ coNP. While this complexity is the same as for the simpler class of turn-based parity games, where in each state only one of the two players has a choice of moves, our algorithms are considerably more involved than those for turn-based games. This is because concurrent games do not satisfy two of the most fundamental properties of turn-based parity games. First, in concurrent games limit-winning strategies require randomization; and second, they require infinite memory.' article_number: '28' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, De Alfaro L, Henzinger TA. Qualitative concurrent parity games. ACM Transactions on Computational Logic (TOCL). 2011;12(4). doi:10.1145/1970398.1970404 apa: Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2011). Qualitative concurrent parity games. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/1970398.1970404 chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Qualitative Concurrent Parity Games.” ACM Transactions on Computational Logic (TOCL). ACM, 2011. https://doi.org/10.1145/1970398.1970404. ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Qualitative concurrent parity games,” ACM Transactions on Computational Logic (TOCL), vol. 12, no. 4. ACM, 2011. ista: Chatterjee K, De Alfaro L, Henzinger TA. 2011. Qualitative concurrent parity games. ACM Transactions on Computational Logic (TOCL). 12(4), 28. mla: Chatterjee, Krishnendu, et al. “Qualitative Concurrent Parity Games.” ACM Transactions on Computational Logic (TOCL), vol. 12, no. 4, 28, ACM, 2011, doi:10.1145/1970398.1970404. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, ACM Transactions on Computational Logic (TOCL) 12 (2011). date_created: 2018-12-11T12:02:51Z date_published: 2011-07-04T00:00:00Z date_updated: 2023-02-23T10:26:18Z day: '04' department: - _id: KrCh - _id: ToHe doi: 10.1145/1970398.1970404 intvolume: ' 12' issue: '4' language: - iso: eng month: '07' oa_version: None project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ACM Transactions on Computational Logic (TOCL) publication_status: published publisher: ACM publist_id: '3262' quality_controlled: '1' related_material: record: - id: '2054' relation: later_version status: public scopus_import: 1 status: public title: Qualitative concurrent parity games type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2011' ... --- _id: '3349' abstract: - lang: eng text: 'Games on graphs provide a natural model for reactive non-terminating systems. In such games, the interaction of two players on an arena results in an infinite path that describes a run of the system. Different settings are used to model various open systems in computer science, as for instance turn-based or concurrent moves, and deterministic or stochastic transitions. In this paper, we are interested in turn-based games, and specifically in deterministic parity games and stochastic reachability games (also known as simple stochastic games). We present a simple, direct and efficient reduction from deterministic parity games to simple stochastic games: it yields an arena whose size is linear up to a logarithmic factor in size of the original arena.' alternative_title: - EPTCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nathanaël full_name: Fijalkow, Nathanaël last_name: Fijalkow citation: ama: 'Chatterjee K, Fijalkow N. A reduction from parity games to simple stochastic games. In: Vol 54. EPTCS; 2011:74-86. doi:10.4204/EPTCS.54.6' apa: 'Chatterjee, K., & Fijalkow, N. (2011). A reduction from parity games to simple stochastic games (Vol. 54, pp. 74–86). Presented at the GandALF: Games, Automata, Logic, and Formal Verification, Minori, Italy: EPTCS. https://doi.org/10.4204/EPTCS.54.6' chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. “A Reduction from Parity Games to Simple Stochastic Games,” 54:74–86. EPTCS, 2011. https://doi.org/10.4204/EPTCS.54.6. ieee: 'K. Chatterjee and N. Fijalkow, “A reduction from parity games to simple stochastic games,” presented at the GandALF: Games, Automata, Logic, and Formal Verification, Minori, Italy, 2011, vol. 54, pp. 74–86.' ista: 'Chatterjee K, Fijalkow N. 2011. A reduction from parity games to simple stochastic games. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 54, 74–86.' mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. A Reduction from Parity Games to Simple Stochastic Games. Vol. 54, EPTCS, 2011, pp. 74–86, doi:10.4204/EPTCS.54.6. short: K. Chatterjee, N. Fijalkow, in:, EPTCS, 2011, pp. 74–86. conference: end_date: 2011-06-17 location: Minori, Italy name: 'GandALF: Games, Automata, Logic, and Formal Verification' start_date: 2011-06-15 date_created: 2018-12-11T12:02:49Z date_published: 2011-06-04T00:00:00Z date_updated: 2021-01-12T07:42:51Z day: '04' department: - _id: KrCh doi: 10.4204/EPTCS.54.6 intvolume: ' 54' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1106.1232 month: '06' oa: 1 oa_version: Submitted Version page: 74 - 86 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: EPTCS publist_id: '3272' scopus_import: 1 status: public title: A reduction from parity games to simple stochastic games type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2011' ... --- _id: '335' abstract: - lang: eng text: 'Recently reported synthetic routes for the production of hollow nanoparticles have stimulated significant interest for the possibilities this novel geometry offers. While advantageous properties have been found and innovative applications have been proposed, the development of the full potential of these new nanostructures is still strongly tied to the extent of control that can be accomplished over their characteristics (e.g., composition, size, shell thickness, and nanocrystalline structure). In the present work, we investigate the means and limits of control over these parameters that can be obtained by the Kirkendall effect synthetic route on cadmium chalcogenide nanocrystalline shells. We demonstrate that the selection of the reactants and oxidation conditions allows some extent of control of the nanocrystalline structure and thickness of the shell. However, the tuning range is limited by the intrinsic restrictions of the synthetic procedure and by the dependence of the particle geometry on the same reaction conditions. Thus, we further explore the range of control over the shell parameters that can be accomplished through post-synthesis processes, such as chemical etching and thermal annealing. ' article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Raquel full_name: Nafria, Raquel last_name: Nafria - first_name: Alex full_name: Carrete, Alex last_name: Carrete - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Ibáñez M, Fan J, Li W, et al. Means and limits of control of the shell parameters in hollow nanoparticles obtained by the Kirkendall effect. Chemistry of Materials. 2011;23(12):3095-3104. doi:10.1021/cm2006633 apa: Ibáñez, M., Fan, J., Li, W., Cadavid, D., Nafria, R., Carrete, A., & Cabot, A. (2011). Means and limits of control of the shell parameters in hollow nanoparticles obtained by the Kirkendall effect. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/cm2006633 chicago: Ibáñez, Maria, Jiandong Fan, Wenhua Li, Doris Cadavid, Raquel Nafria, Alex Carrete, and Andreu Cabot. “Means and Limits of Control of the Shell Parameters in Hollow Nanoparticles Obtained by the Kirkendall Effect.” Chemistry of Materials. American Chemical Society, 2011. https://doi.org/10.1021/cm2006633. ieee: M. Ibáñez et al., “Means and limits of control of the shell parameters in hollow nanoparticles obtained by the Kirkendall effect,” Chemistry of Materials, vol. 23, no. 12. American Chemical Society, pp. 3095–3104, 2011. ista: Ibáñez M, Fan J, Li W, Cadavid D, Nafria R, Carrete A, Cabot A. 2011. Means and limits of control of the shell parameters in hollow nanoparticles obtained by the Kirkendall effect. Chemistry of Materials. 23(12), 3095–3104. mla: Ibáñez, Maria, et al. “Means and Limits of Control of the Shell Parameters in Hollow Nanoparticles Obtained by the Kirkendall Effect.” Chemistry of Materials, vol. 23, no. 12, American Chemical Society, 2011, pp. 3095–104, doi:10.1021/cm2006633. short: M. Ibáñez, J. Fan, W. Li, D. Cadavid, R. Nafria, A. Carrete, A. Cabot, Chemistry of Materials 23 (2011) 3095–3104. date_created: 2018-12-11T11:45:53Z date_published: 2011-05-24T00:00:00Z date_updated: 2021-01-12T07:42:51Z day: '24' doi: 10.1021/cm2006633 extern: '1' intvolume: ' 23' issue: '12' language: - iso: eng month: '05' oa_version: None page: 3095 - 3104 publication: Chemistry of Materials publication_status: published publisher: American Chemical Society publist_id: '7492' quality_controlled: '1' status: public title: Means and limits of control of the shell parameters in hollow nanoparticles obtained by the Kirkendall effect type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2011' ... --- _id: '3352' abstract: - lang: eng text: Exploring the connection of biology with reactive systems to better understand living systems. author: - first_name: Jasmin full_name: Fisher, Jasmin last_name: Fisher - first_name: David full_name: Harel, David last_name: Harel - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Fisher J, Harel D, Henzinger TA. Biology as reactivity. Communications of the ACM. 2011;54(10):72-82. doi:10.1145/2001269.2001289 apa: Fisher, J., Harel, D., & Henzinger, T. A. (2011). Biology as reactivity. Communications of the ACM. ACM. https://doi.org/10.1145/2001269.2001289 chicago: Fisher, Jasmin, David Harel, and Thomas A Henzinger. “Biology as Reactivity.” Communications of the ACM. ACM, 2011. https://doi.org/10.1145/2001269.2001289. ieee: J. Fisher, D. Harel, and T. A. Henzinger, “Biology as reactivity,” Communications of the ACM, vol. 54, no. 10. ACM, pp. 72–82, 2011. ista: Fisher J, Harel D, Henzinger TA. 2011. Biology as reactivity. Communications of the ACM. 54(10), 72–82. mla: Fisher, Jasmin, et al. “Biology as Reactivity.” Communications of the ACM, vol. 54, no. 10, ACM, 2011, pp. 72–82, doi:10.1145/2001269.2001289. short: J. Fisher, D. Harel, T.A. Henzinger, Communications of the ACM 54 (2011) 72–82. date_created: 2018-12-11T12:02:50Z date_published: 2011-10-01T00:00:00Z date_updated: 2021-01-12T07:42:52Z day: '01' department: - _id: ToHe doi: 10.1145/2001269.2001289 ec_funded: 1 intvolume: ' 54' issue: '10' language: - iso: eng month: '10' oa_version: None page: 72 - 82 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Communications of the ACM publication_status: published publisher: ACM publist_id: '3267' quality_controlled: '1' status: public title: Biology as reactivity type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2011' ... --- _id: '3362' abstract: - lang: eng text: State-transition systems communicating by shared variables have been the underlying model of choice for applications of model checking. Such formalisms, however, have difficulty with modeling process creation or death and communication reconfigurability. Here, we introduce “dynamic reactive modules” (DRM), a state-transition modeling formalism that supports dynamic reconfiguration and creation/death of processes. The resulting formalism supports two types of variables, data variables and reference variables. Reference variables enable changing the connectivity between processes and referring to instances of processes. We show how this new formalism supports parallel composition and refinement through trace containment. DRM provide a natural language for modeling (and ultimately reasoning about) biological systems and multiple threads communicating through shared variables. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jasmin full_name: Fisher, Jasmin last_name: Fisher - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Nir full_name: Piterman, Nir last_name: Piterman - first_name: Anmol full_name: Singh, Anmol last_name: Singh - first_name: Moshe full_name: Vardi, Moshe last_name: Vardi citation: ama: 'Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. Dynamic reactive modules. In: Vol 6901. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2011:404-418. doi:10.1007/978-3-642-23217-6_27' apa: 'Fisher, J., Henzinger, T. A., Nickovic, D., Piterman, N., Singh, A., & Vardi, M. (2011). Dynamic reactive modules (Vol. 6901, pp. 404–418). Presented at the CONCUR: Concurrency Theory, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-23217-6_27' chicago: Fisher, Jasmin, Thomas A Henzinger, Dejan Nickovic, Nir Piterman, Anmol Singh, and Moshe Vardi. “Dynamic Reactive Modules,” 6901:404–18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011. https://doi.org/10.1007/978-3-642-23217-6_27. ieee: 'J. Fisher, T. A. Henzinger, D. Nickovic, N. Piterman, A. Singh, and M. Vardi, “Dynamic reactive modules,” presented at the CONCUR: Concurrency Theory, Aachen, Germany, 2011, vol. 6901, pp. 404–418.' ista: 'Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. 2011. Dynamic reactive modules. CONCUR: Concurrency Theory, LNCS, vol. 6901, 404–418.' mla: Fisher, Jasmin, et al. Dynamic Reactive Modules. Vol. 6901, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–18, doi:10.1007/978-3-642-23217-6_27. short: J. Fisher, T.A. Henzinger, D. Nickovic, N. Piterman, A. Singh, M. Vardi, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–418. conference: end_date: 2011-09-09 location: Aachen, Germany name: 'CONCUR: Concurrency Theory' start_date: 2011-09-06 date_created: 2018-12-11T12:02:54Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:57Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-642-23217-6_27 ec_funded: 1 file: - access_level: open_access checksum: 6bf2453d8e52e979ddb58d17325bad26 content_type: application/pdf creator: dernst date_created: 2020-05-19T16:17:48Z date_updated: 2020-07-14T12:46:10Z file_id: '7870' file_name: 2011_CONCUR_Fisher.pdf file_size: 337125 relation: main_file file_date_updated: 2020-07-14T12:46:10Z has_accepted_license: '1' intvolume: ' 6901' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 404 - 418 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '3253' quality_controlled: '1' scopus_import: 1 status: public title: Dynamic reactive modules type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6901 year: '2011' ... --- _id: '3365' abstract: - lang: eng text: We present the tool Quasy, a quantitative synthesis tool. Quasy takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. The user can choose between a system that satisfies and optimizes the specifications (a) under all possible environment behaviors or (b) under the most-likely environment behaviors given as a probability distribution on the possible input sequences. Quasy solves these two quantitative synthesis problems by reduction to instances of 2-player games and Markov Decision Processes (MDPs) with quantitative winning objectives. Quasy can also be seen as a game solver for quantitative games. Most notable, it can solve lexicographic mean-payoff games with 2 players, MDPs with mean-payoff objectives, and ergodic MDPs with mean-payoff parity objectives. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Rohit full_name: Singh, Rohit last_name: Singh citation: ama: 'Chatterjee K, Henzinger TA, Jobstmann B, Singh R. QUASY: quantitative synthesis tool. In: Vol 6605. Springer; 2011:267-271. doi:10.1007/978-3-642-19835-9_24' apa: 'Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Singh, R. (2011). QUASY: quantitative synthesis tool (Vol. 6605, pp. 267–271). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany: Springer. https://doi.org/10.1007/978-3-642-19835-9_24' chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “QUASY: Quantitative Synthesis Tool,” 6605:267–71. Springer, 2011. https://doi.org/10.1007/978-3-642-19835-9_24.' ieee: 'K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “QUASY: quantitative synthesis tool,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany, 2011, vol. 6605, pp. 267–271.' ista: 'Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2011. QUASY: quantitative synthesis tool. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 6605, 267–271.' mla: 'Chatterjee, Krishnendu, et al. QUASY: Quantitative Synthesis Tool. Vol. 6605, Springer, 2011, pp. 267–71, doi:10.1007/978-3-642-19835-9_24.' short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, in:, Springer, 2011, pp. 267–271. conference: end_date: 2011-04-03 location: Saarbrucken, Germany name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2011-03-26 date_created: 2018-12-11T12:02:55Z date_published: 2011-09-29T00:00:00Z date_updated: 2021-01-12T07:42:58Z day: '29' ddc: - '000' - '005' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-642-19835-9_24 file: - access_level: open_access checksum: 762e52eb296f6dbfbf2a75d98b8ebaee content_type: application/pdf creator: system date_created: 2018-12-12T10:13:37Z date_updated: 2020-07-14T12:46:10Z file_id: '5022' file_name: IST-2012-77-v1+1_QUASY-_quantitative_synthesis_tool.pdf file_size: 475661 relation: main_file file_date_updated: 2020-07-14T12:46:10Z has_accepted_license: '1' intvolume: ' 6605' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 267 - 271 publication_status: published publisher: Springer publist_id: '3248' pubrep_id: '77' quality_controlled: '1' scopus_import: 1 status: public title: 'QUASY: quantitative synthesis tool' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6605 year: '2011' ... --- _id: '3367' abstract: - lang: eng text: In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ>0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0,1), the running time is O(C(1-δ)ΓR(n)log n), where C(1-δ)Γ is the number of homology classes with persistence at least (1-δ)Γ, n is the total number of simplices, and R(n) is the complexity of computing the rank of an n x n matrix with O(n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O(C(1-δ)Γn2.376) algorithm, a O(C(1-δ)Γn2.28) Las-Vegas algorithm, or a O(C(1-δ)Γn2+ε) Monte-Carlo algorithm for an arbitrary ε>0. article_processing_charge: No author: - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 citation: ama: 'Chen C, Kerber M. An output sensitive algorithm for persistent homology. In: ACM; 2011:207-216. doi:10.1145/1998196.1998228' apa: 'Chen, C., & Kerber, M. (2011). An output sensitive algorithm for persistent homology (pp. 207–216). Presented at the SoCG: Symposium on Computational Geometry, Paris, France: ACM. https://doi.org/10.1145/1998196.1998228' chicago: Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology,” 207–16. ACM, 2011. https://doi.org/10.1145/1998196.1998228. ieee: 'C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” presented at the SoCG: Symposium on Computational Geometry, Paris, France, 2011, pp. 207–216.' ista: 'Chen C, Kerber M. 2011. An output sensitive algorithm for persistent homology. SoCG: Symposium on Computational Geometry, 207–216.' mla: Chen, Chao, and Michael Kerber. An Output Sensitive Algorithm for Persistent Homology. ACM, 2011, pp. 207–16, doi:10.1145/1998196.1998228. short: C. Chen, M. Kerber, in:, ACM, 2011, pp. 207–216. conference: end_date: 2011-06-15 location: Paris, France name: 'SoCG: Symposium on Computational Geometry' start_date: 2011-06-13 date_created: 2018-12-11T12:02:56Z date_published: 2011-06-13T00:00:00Z date_updated: 2023-02-23T11:05:04Z day: '13' department: - _id: HeEd doi: 10.1145/1998196.1998228 language: - iso: eng month: '06' oa_version: None page: 207 - 216 publication_status: published publisher: ACM publist_id: '3245' quality_controlled: '1' related_material: record: - id: '2939' relation: later_version status: public scopus_import: 1 status: public title: An output sensitive algorithm for persistent homology type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3363' abstract: - lang: eng text: We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs for probabilistic finite automata and present a complete characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems for probabilistic automata on infinite words. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Mathieu full_name: Tracol, Mathieu id: 3F54FA38-F248-11E8-B48F-1D18A9856A87 last_name: Tracol citation: ama: Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words. apa: Chatterjee, K., Henzinger, T. A., & Tracol, M. (n.d.). The decidability frontier for probabilistic automata on infinite words. ArXiv. chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Mathieu Tracol. “The Decidability Frontier for Probabilistic Automata on Infinite Words.” ArXiv, n.d. ieee: K. Chatterjee, T. A. Henzinger, and M. Tracol, “The decidability frontier for probabilistic automata on infinite words.” ArXiv. ista: Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words. mla: Chatterjee, Krishnendu, et al. The Decidability Frontier for Probabilistic Automata on Infinite Words. ArXiv. short: K. Chatterjee, T.A. Henzinger, M. Tracol, (n.d.). date_created: 2018-12-11T12:02:54Z date_published: 2011-04-01T00:00:00Z date_updated: 2020-01-21T13:20:24Z day: '01' department: - _id: KrCh - _id: ToHe ec_funded: 1 external_id: arxiv: - '1104.0127' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1104.0127 month: '04' oa: 1 oa_version: Preprint page: '19' project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems publication_status: submitted publisher: ArXiv publist_id: '3251' status: public title: The decidability frontier for probabilistic automata on infinite words type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3372' abstract: - lang: eng text: Nowak et al.1 argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues. author: - first_name: Patrick full_name: Abbot, Patrick last_name: Abbot - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: John full_name: Alcock, John last_name: Alcock - first_name: Samuel full_name: Alizon, Samuel last_name: Alizon - first_name: Joao full_name: Alpedrinha, Joao last_name: Alpedrinha - first_name: Malte full_name: Andersson, Malte last_name: Andersson - first_name: Jean full_name: Andre, Jean last_name: Andre - first_name: Minus full_name: Van Baalen, Minus last_name: Van Baalen - first_name: Francois full_name: Balloux, Francois last_name: Balloux - first_name: Sigal full_name: Balshine, Sigal last_name: Balshine - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Leo full_name: Beukeboom, Leo last_name: Beukeboom - first_name: Jay full_name: Biernaskie, Jay last_name: Biernaskie - first_name: Trine full_name: Bilde, Trine last_name: Bilde - first_name: Gerald full_name: Borgia, Gerald last_name: Borgia - first_name: Michael full_name: Breed, Michael last_name: Breed - first_name: Sam full_name: Brown, Sam last_name: Brown - first_name: Redouan full_name: Bshary, Redouan last_name: Bshary - first_name: Angus full_name: Buckling, Angus last_name: Buckling - first_name: Nancy full_name: Burley, Nancy last_name: Burley - first_name: Max full_name: Burton Chellew, Max last_name: Burton Chellew - first_name: Michael full_name: Cant, Michael last_name: Cant - first_name: Michel full_name: Chapuisat, Michel last_name: Chapuisat - first_name: Eric full_name: Charnov, Eric last_name: Charnov - first_name: Tim full_name: Clutton Brock, Tim last_name: Clutton Brock - first_name: Andrew full_name: Cockburn, Andrew last_name: Cockburn - first_name: Blaine full_name: Cole, Blaine last_name: Cole - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave - first_name: Leda full_name: Cosmides, Leda last_name: Cosmides - first_name: Iain full_name: Couzin, Iain last_name: Couzin - first_name: Jerry full_name: Coyne, Jerry last_name: Coyne - first_name: Scott full_name: Creel, Scott last_name: Creel - first_name: Bernard full_name: Crespi, Bernard last_name: Crespi - first_name: Robert full_name: Curry, Robert last_name: Curry - first_name: Sasha full_name: Dall, Sasha last_name: Dall - first_name: Troy full_name: Day, Troy last_name: Day - first_name: Janis full_name: Dickinson, Janis last_name: Dickinson - first_name: Lee full_name: Dugatkin, Lee last_name: Dugatkin - first_name: Claire full_name: El Mouden, Claire last_name: El Mouden - first_name: Stephen full_name: Emlen, Stephen last_name: Emlen - first_name: Jay full_name: Evans, Jay last_name: Evans - first_name: Regis full_name: Ferriere, Regis last_name: Ferriere - first_name: Jeremy full_name: Field, Jeremy last_name: Field - first_name: Susanne full_name: Foitzik, Susanne last_name: Foitzik - first_name: Kevin full_name: Foster, Kevin last_name: Foster - first_name: William full_name: Foster, William last_name: Foster - first_name: Charles full_name: Fox, Charles last_name: Fox - first_name: Juergen full_name: Gadau, Juergen last_name: Gadau - first_name: Sylvain full_name: Gandon, Sylvain last_name: Gandon - first_name: Andy full_name: Gardner, Andy last_name: Gardner - first_name: Michael full_name: Gardner, Michael last_name: Gardner - first_name: Thomas full_name: Getty, Thomas last_name: Getty - first_name: Michael full_name: Goodisman, Michael last_name: Goodisman - first_name: Alan full_name: Grafen, Alan last_name: Grafen - first_name: Rick full_name: Grosberg, Rick last_name: Grosberg - first_name: Christina full_name: Grozinger, Christina last_name: Grozinger - first_name: Pierre full_name: Gouyon, Pierre last_name: Gouyon - first_name: Darryl full_name: Gwynne, Darryl last_name: Gwynne - first_name: Paul full_name: Harvey, Paul last_name: Harvey - first_name: Ben full_name: Hatchwell, Ben last_name: Hatchwell - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Heikki full_name: Helantera, Heikki last_name: Helantera - first_name: Ken full_name: Helms, Ken last_name: Helms - first_name: Kim full_name: Hill, Kim last_name: Hill - first_name: Natalie full_name: Jiricny, Natalie last_name: Jiricny - first_name: Rufus full_name: Johnstone, Rufus last_name: Johnstone - first_name: Alex full_name: Kacelnik, Alex last_name: Kacelnik - first_name: E Toby full_name: Kiers, E Toby last_name: Kiers - first_name: Hanna full_name: Kokko, Hanna last_name: Kokko - first_name: Jan full_name: Komdeur, Jan last_name: Komdeur - first_name: Judith full_name: Korb, Judith last_name: Korb - first_name: Daniel full_name: Kronauer, Daniel last_name: Kronauer - first_name: Rolf full_name: Kümmerli, Rolf last_name: Kümmerli - first_name: Laurent full_name: Lehmann, Laurent last_name: Lehmann - first_name: Timothy full_name: Linksvayer, Timothy last_name: Linksvayer - first_name: Sébastien full_name: Lion, Sébastien last_name: Lion - first_name: Bruce full_name: Lyon, Bruce last_name: Lyon - first_name: James full_name: Marshall, James last_name: Marshall - first_name: Richard full_name: Mcelreath, Richard last_name: Mcelreath - first_name: Yannis full_name: Michalakis, Yannis last_name: Michalakis - first_name: Richard full_name: Michod, Richard last_name: Michod - first_name: Douglas full_name: Mock, Douglas last_name: Mock - first_name: Thibaud full_name: Monnin, Thibaud last_name: Monnin - first_name: Robert full_name: Montgomerie, Robert last_name: Montgomerie - first_name: Allen full_name: Moore, Allen last_name: Moore - first_name: Ulrich full_name: Mueller, Ulrich last_name: Mueller - first_name: Ronald full_name: Noë, Ronald last_name: Noë - first_name: Samir full_name: Okasha, Samir last_name: Okasha - first_name: Pekka full_name: Pamilo, Pekka last_name: Pamilo - first_name: Geoff full_name: Parker, Geoff last_name: Parker - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen - first_name: Ido full_name: Pen, Ido last_name: Pen - first_name: David full_name: Pfennig, David last_name: Pfennig - first_name: David full_name: Queller, David last_name: Queller - first_name: Daniel full_name: Rankin, Daniel last_name: Rankin - first_name: Sarah full_name: Reece, Sarah last_name: Reece - first_name: Hudson full_name: Reeve, Hudson last_name: Reeve - first_name: Max full_name: Reuter, Max last_name: Reuter - first_name: Gilbert full_name: Roberts, Gilbert last_name: Roberts - first_name: Simon full_name: Robson, Simon last_name: Robson - first_name: Denis full_name: Roze, Denis last_name: Roze - first_name: Francois full_name: Rousset, Francois last_name: Rousset - first_name: Olav full_name: Rueppell, Olav last_name: Rueppell - first_name: Joel full_name: Sachs, Joel last_name: Sachs - first_name: Lorenzo full_name: Santorelli, Lorenzo last_name: Santorelli - first_name: Paul full_name: Schmid Hempel, Paul last_name: Schmid Hempel - first_name: Michael full_name: Schwarz, Michael last_name: Schwarz - first_name: Tom full_name: Scott Phillips, Tom last_name: Scott Phillips - first_name: Janet full_name: Shellmann Sherman, Janet last_name: Shellmann Sherman - first_name: Paul full_name: Sherman, Paul last_name: Sherman - first_name: David full_name: Shuker, David last_name: Shuker - first_name: Jeff full_name: Smith, Jeff last_name: Smith - first_name: Joseph full_name: Spagna, Joseph last_name: Spagna - first_name: Beverly full_name: Strassmann, Beverly last_name: Strassmann - first_name: Andrew full_name: Suarez, Andrew last_name: Suarez - first_name: Liselotte full_name: Sundström, Liselotte last_name: Sundström - first_name: Michael full_name: Taborsky, Michael last_name: Taborsky - first_name: Peter full_name: Taylor, Peter last_name: Taylor - first_name: Graham full_name: Thompson, Graham last_name: Thompson - first_name: John full_name: Tooby, John last_name: Tooby - first_name: Neil full_name: Tsutsui, Neil last_name: Tsutsui - first_name: Kazuki full_name: Tsuji, Kazuki last_name: Tsuji - first_name: Stefano full_name: Turillazzi, Stefano last_name: Turillazzi - first_name: Francisco full_name: Úbeda, Francisco last_name: Úbeda - first_name: Edward full_name: Vargo, Edward last_name: Vargo - first_name: Bernard full_name: Voelkl, Bernard last_name: Voelkl - first_name: Tom full_name: Wenseleers, Tom last_name: Wenseleers - first_name: Stuart full_name: West, Stuart last_name: West - first_name: Mary full_name: West Eberhard, Mary last_name: West Eberhard - first_name: David full_name: Westneat, David last_name: Westneat - first_name: Diane full_name: Wiernasz, Diane last_name: Wiernasz - first_name: Geoff full_name: Wild, Geoff last_name: Wild - first_name: Richard full_name: Wrangham, Richard last_name: Wrangham - first_name: Andrew full_name: Young, Andrew last_name: Young - first_name: David full_name: Zeh, David last_name: Zeh - first_name: Jeanne full_name: Zeh, Jeanne last_name: Zeh - first_name: Andrew full_name: Zink, Andrew last_name: Zink citation: ama: Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831 apa: Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09831 chicago: Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831. ieee: P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011. ista: Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4. mla: Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831. short: P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-23T00:00:00Z date_updated: 2021-01-12T07:43:02Z day: '23' department: - _id: NiBa doi: 10.1038/nature09831 external_id: pmid: - '21430721' intvolume: ' 471' issue: '7339' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/ month: '03' oa: 1 oa_version: Submitted Version page: E1 - E4 pmid: 1 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3237' quality_controlled: '1' scopus_import: 1 status: public title: Inclusive fitness theory and eusociality type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2011' ... --- _id: '3371' abstract: - lang: eng text: The Minisymposium “Cell Migration and Motility” was attended by approximately 500 visitors and covered a broad range of questions in the field using diverse model systems. Topics comprised actin dynamics, cell polarity, force transduction, signal transduction, bar- rier transmigration, and chemotactic guidance. article_type: original author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Carole full_name: Parent, Carole last_name: Parent citation: ama: Sixt MK, Parent C. Cells on the move in Philadelphia. Molecular Biology and Evolution. 2011;22(6):724. doi:10.1091/mbc.E10-12-0958 apa: Sixt, M. K., & Parent, C. (2011). Cells on the move in Philadelphia. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1091/mbc.E10-12-0958 chicago: Sixt, Michael K, and Carole Parent. “Cells on the Move in Philadelphia.” Molecular Biology and Evolution. Oxford University Press, 2011. https://doi.org/10.1091/mbc.E10-12-0958. ieee: M. K. Sixt and C. Parent, “Cells on the move in Philadelphia,” Molecular Biology and Evolution, vol. 22, no. 6. Oxford University Press, p. 724, 2011. ista: Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology and Evolution. 22(6), 724. mla: Sixt, Michael K., and Carole Parent. “Cells on the Move in Philadelphia.” Molecular Biology and Evolution, vol. 22, no. 6, Oxford University Press, 2011, p. 724, doi:10.1091/mbc.E10-12-0958. short: M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-15T00:00:00Z date_updated: 2021-01-12T07:43:01Z day: '15' ddc: - '570' department: - _id: MiSi doi: 10.1091/mbc.E10-12-0958 file: - access_level: open_access checksum: 3467986ab7a64e7694ffd1013b5d9da9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:29Z date_updated: 2020-07-14T12:46:11Z file_id: '5283' file_name: IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf file_size: 105421 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 22' issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '724' publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '3238' pubrep_id: '373' quality_controlled: '1' scopus_import: 1 status: public title: Cells on the move in Philadelphia tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2011' ... --- _id: '3374' abstract: - lang: eng text: Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'. article_number: '153102' author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Aleksandra full_name: Walczak, Aleksandra last_name: Walczak citation: ama: 'Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 2011;23(15). doi:10.1088/0953-8984/23/15/153102' apa: 'Tkačik, G., & Walczak, A. (2011). Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/0953-8984/23/15/153102' chicago: 'Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2011. https://doi.org/10.1088/0953-8984/23/15/153102.' ieee: 'G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” Journal of Physics: Condensed Matter, vol. 23, no. 15. IOP Publishing Ltd., 2011.' ista: 'Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.' mla: 'Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.' short: 'G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).' date_created: 2018-12-11T12:02:58Z date_published: 2011-04-01T00:00:00Z date_updated: 2021-01-12T07:43:03Z day: '01' department: - _id: GaTk doi: 10.1088/0953-8984/23/15/153102 intvolume: ' 23' issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1101.4240 month: '04' oa: 1 oa_version: Submitted Version publication: 'Journal of Physics: Condensed Matter' publication_status: published publisher: IOP Publishing Ltd. publist_id: '3233' quality_controlled: '1' scopus_import: 1 status: public title: Information transmission in genetic regulatory networks a review type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2011' ... --- _id: '3368' abstract: - lang: eng text: Tissue surface tension (TST) is an important mechanical property influencing cell sorting and tissue envelopment. The study by Manning et al. (1) reported on a mathematical model describing TST on the basis of the balance between adhesive and tensile properties of the constituent cells. The model predicts that, in high-adhesion cell aggregates, surface cells will be stretched to maintain the same area of cell–cell contact as interior bulk cells, resulting in an elongated and flattened cell shape. The authors (1) observed flat and elongated cells at the surface of high-adhesion zebrafish germ-layer explants, which they argue are undifferentiated stretched germ-layer progenitor cells, and they use this observation as a validation of their model. author: - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Stephanie full_name: Möllmert, Stephanie id: 260FD49C-E911-11E9-B5EA-D9538404589B last_name: Möllmert - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Krens G, Möllmert S, Heisenberg C-PJ. Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants. PNAS. 2011;108(3):E9-E10. doi:10.1073/pnas.1010767108 apa: Krens, G., Möllmert, S., & Heisenberg, C.-P. J. (2011). Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1010767108 chicago: Krens, Gabriel, Stephanie Möllmert, and Carl-Philipp J Heisenberg. “Enveloping Cell Layer Differentiation at the Surface of Zebrafish Germ Layer Tissue Explants.” PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1010767108. ieee: G. Krens, S. Möllmert, and C.-P. J. Heisenberg, “Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants,” PNAS, vol. 108, no. 3. National Academy of Sciences, pp. E9–E10, 2011. ista: Krens G, Möllmert S, Heisenberg C-PJ. 2011. Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants. PNAS. 108(3), E9–E10. mla: Krens, Gabriel, et al. “Enveloping Cell Layer Differentiation at the Surface of Zebrafish Germ Layer Tissue Explants.” PNAS, vol. 108, no. 3, National Academy of Sciences, 2011, pp. E9–10, doi:10.1073/pnas.1010767108. short: G. Krens, S. Möllmert, C.-P.J. Heisenberg, PNAS 108 (2011) E9–E10. date_created: 2018-12-11T12:02:56Z date_published: 2011-01-18T00:00:00Z date_updated: 2021-01-12T07:43:00Z day: '18' department: - _id: CaHe doi: 10.1073/pnas.1010767108 external_id: pmid: - '21212360' intvolume: ' 108' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024655 month: '01' oa: 1 oa_version: Submitted Version page: E9 - E10 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3244' quality_controlled: '1' scopus_import: 1 status: public title: Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2011' ... --- _id: '3370' abstract: - lang: eng text: Supertree methods are widely applied and give rise to new conclusions about phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have been studied in greater detail, examples include shape bias (Wilkinson et al. 2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at two matrix representation methods, matrix representation with compatibility (MRC) and matrix representation with parsimony (MRP). Different null models of random data are studied and the resulting tree shapes are investigated. Thereby I consider unrooted trees and a bias in tree shape is determined by a tree balance measure. The measure for unrooted trees is a modification of a tree balance measure for rooted trees. I observe that depending on the underlying null model of random data, the methods may resolve conflict in favor of more balanced tree shapes. The analyses refer only to trees with the same taxon set, also known as the consensus setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions on how to deal with missing data. author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok citation: ama: Kupczok A. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 2011;60(2):218-225. doi:10.1093/sysbio/syq086 apa: Kupczok, A. (2011). Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. Oxford University Press. https://doi.org/10.1093/sysbio/syq086 chicago: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” Systematic Biology. Oxford University Press, 2011. https://doi.org/10.1093/sysbio/syq086. ieee: A. Kupczok, “Consequences of different null models on the tree shape bias of supertree methods,” Systematic Biology, vol. 60, no. 2. Oxford University Press, pp. 218–225, 2011. ista: Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225. mla: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” Systematic Biology, vol. 60, no. 2, Oxford University Press, 2011, pp. 218–25, doi:10.1093/sysbio/syq086. short: A. Kupczok, Systematic Biology 60 (2011) 218–225. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-01T00:00:00Z date_updated: 2021-01-12T07:43:01Z day: '01' department: - _id: JoBo doi: 10.1093/sysbio/syq086 intvolume: ' 60' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://eprints.cs.univie.ac.at/3226/ month: '03' oa: 1 oa_version: Submitted Version page: 218 - 225 publication: Systematic Biology publication_status: published publisher: Oxford University Press publist_id: '3241' quality_controlled: '1' status: public title: Consequences of different null models on the tree shape bias of supertree methods type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2011' ... --- _id: '3369' abstract: - lang: eng text: Rab3 interacting molecules (RIMs) are highly enriched in the active zones of presynaptic terminals. It is generally thought that they operate as effectors of the small G protein Rab3. Three recent papers, by Han et al. (this issue of Neuron), Deng et al. (this issue of Neuron), and Kaeser et al. (a recent issue of Cell), shed new light on the functional role of RIM in presynaptic terminals. First, RIM tethers Ca2+ channels to active zones. Second, RIM contributes to priming of synaptic vesicles by interacting with another presynaptic protein, Munc13. author: - first_name: Alejandro full_name: Pernia-Andrade, Alejandro id: 36963E98-F248-11E8-B48F-1D18A9856A87 last_name: Pernia-Andrade - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Pernia-Andrade A, Jonas PM. The multiple faces of RIM. Neuron. 2011;69(2):185-187. doi:10.1016/j.neuron.2011.01.010 apa: Pernia-Andrade, A., & Jonas, P. M. (2011). The multiple faces of RIM. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2011.01.010 chicago: Pernia-Andrade, Alejandro, and Peter M Jonas. “The Multiple Faces of RIM.” Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.01.010. ieee: A. Pernia-Andrade and P. M. Jonas, “The multiple faces of RIM,” Neuron, vol. 69, no. 2. Elsevier, pp. 185–187, 2011. ista: Pernia-Andrade A, Jonas PM. 2011. The multiple faces of RIM. Neuron. 69(2), 185–187. mla: Pernia-Andrade, Alejandro, and Peter M. Jonas. “The Multiple Faces of RIM.” Neuron, vol. 69, no. 2, Elsevier, 2011, pp. 185–87, doi:10.1016/j.neuron.2011.01.010. short: A. Pernia-Andrade, P.M. Jonas, Neuron 69 (2011) 185–187. date_created: 2018-12-11T12:02:56Z date_published: 2011-01-27T00:00:00Z date_updated: 2021-01-12T07:43:00Z day: '27' department: - _id: PeJo doi: 10.1016/j.neuron.2011.01.010 intvolume: ' 69' issue: '2' language: - iso: eng month: '01' oa_version: None page: 185 - 187 publication: Neuron publication_status: published publisher: Elsevier publist_id: '3243' quality_controlled: '1' scopus_import: 1 status: public title: The multiple faces of RIM type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2011' ... --- _id: '3396' abstract: - lang: eng text: Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain undergo a characteristic tangential migration from rhombomere (r) 4, where they are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium such that they move apically between NCs towards the midline of the neuroepithelium instead of tangentially along the basal side of the neuroepithelium towards r6/7. However, direct experimental evaluation of this hypothesis is still lacking. Here, we have used a combination of biophysical cell adhesion measurements and high-resolution time-lapse microscopy to determine the role of NC cohesion in FBMN migration. We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity results in FBMNs positioned at the basal side of the neuroepithelium moving apically towards the neural tube midline instead of tangentially towards r6/7. In embryos with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results in fusion of the bilateral FBMN clusters over the apical midline of the neural tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin 2 (Cntn2) expression in these cells has little effect on apical FBMN movement, but reduces the fusion of the bilateral FBMN clusters in embryos with strongly diminished NC cohesion. These data provide direct experimental evidence that NC cohesion functions in tangential FBMN migration by restricting their apical movement. acknowledged_ssus: - _id: Bio - _id: PreCl article_type: original author: - first_name: Petra full_name: Stockinger, Petra id: 261CB030-E90D-11E9-B182-F697D44B663C last_name: Stockinger - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 citation: ama: Stockinger P, Heisenberg C-PJ, Maître J-L. Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube. Development. 2011;138(21):4673-4683. doi:10.1242/dev.071233 apa: Stockinger, P., Heisenberg, C.-P. J., & Maître, J.-L. (2011). Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube. Development. Company of Biologists. https://doi.org/10.1242/dev.071233 chicago: Stockinger, Petra, Carl-Philipp J Heisenberg, and Jean-Léon Maître. “Defective Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” Development. Company of Biologists, 2011. https://doi.org/10.1242/dev.071233. ieee: P. Stockinger, C.-P. J. Heisenberg, and J.-L. Maître, “Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube,” Development, vol. 138, no. 21. Company of Biologists, pp. 4673–4683, 2011. ista: Stockinger P, Heisenberg C-PJ, Maître J-L. 2011. Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube. Development. 138(21), 4673–4683. mla: Stockinger, Petra, et al. “Defective Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” Development, vol. 138, no. 21, Company of Biologists, 2011, pp. 4673–83, doi:10.1242/dev.071233. short: P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 4673–4683. date_created: 2018-12-11T12:03:06Z date_published: 2011-09-28T00:00:00Z date_updated: 2021-01-12T07:43:11Z day: '28' ddc: - '570' department: - _id: CaHe doi: 10.1242/dev.071233 file: - access_level: open_access checksum: ca12b79e01ef36c1ef1aea31cf7e7139 content_type: application/pdf creator: dernst date_created: 2019-10-07T14:19:42Z date_updated: 2020-07-14T12:46:12Z file_id: '6930' file_name: 2011_Development_Stockinger.pdf file_size: 4672439 relation: main_file file_date_updated: 2020-07-14T12:46:12Z has_accepted_license: '1' intvolume: ' 138' issue: '21' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 4673 - 4683 publication: Development publication_status: published publisher: Company of Biologists publist_id: '3210' quality_controlled: '1' scopus_import: 1 status: public title: Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 138 year: '2011' ... --- _id: '3394' abstract: - lang: eng text: 'Random genetic drift shifts clines in space, alters their width, and distorts their shape. Such random fluctuations complicate inferences from cline width and position. Notably, the effect of genetic drift on the expected shape of the cline is opposite to the naive (but quite common) misinterpretation of classic results on the expected cline. While random drift on average broadens the overall cline in expected allele frequency, it narrows the width of any particular cline. The opposing effects arise because locally, drift drives alleles to fixation—but fluctuations in position widen the expected cline. The effect of genetic drift can be predicted from standardized variance in allele frequencies, averaged across the habitat: 〈F〉. A cline maintained by spatially varying selection (step change) is expected to be narrower by a factor of relative to the cline in the absence of drift. The expected cline is broader by the inverse of this factor. In a tension zone maintained by underdominance, the expected cline width is narrower by about 1 – 〈F〉relative to the width in the absence of drift. Individual clines can differ substantially from the expectation, and we give quantitative predictions for the variance in cline position and width. The predictions apply to clines in almost one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or along a coast line and give a guide to what patterns to expect in two dimensions.' author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Polechova J, Barton NH. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 2011;189(1):227-235. doi:10.1534/genetics.111.129817 apa: Polechova, J., & Barton, N. H. (2011). Genetic drift widens the expected cline but narrows the expected cline width. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129817 chicago: Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129817. ieee: J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but narrows the expected cline width,” Genetics, vol. 189, no. 1. Genetics Society of America, pp. 227–235, 2011. ista: Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 189(1), 227–235. mla: Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” Genetics, vol. 189, no. 1, Genetics Society of America, 2011, pp. 227–35, doi:10.1534/genetics.111.129817. short: J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235. date_created: 2018-12-11T12:03:05Z date_published: 2011-09-01T00:00:00Z date_updated: 2021-01-12T07:43:11Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.111.129817 ec_funded: 1 intvolume: ' 189' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/ month: '09' oa: 1 oa_version: Submitted Version page: 227 - 235 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3213' quality_controlled: '1' scopus_import: 1 status: public title: Genetic drift widens the expected cline but narrows the expected cline width type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2011' ... --- _id: '3390' abstract: - lang: eng text: 'What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a ''pedigree'' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual''s reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual''s reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual''s genetic contribution to the population can be summarized through a single number: its reproductive value.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: Barton NH, Etheridge A. The relation between reproductive value and genetic contribution. Genetics. 2011;188(4):953-973. doi:10.1534/genetics.111.127555 apa: Barton, N. H., & Etheridge, A. (2011). The relation between reproductive value and genetic contribution. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.127555 chicago: Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.127555. ieee: N. H. Barton and A. Etheridge, “The relation between reproductive value and genetic contribution,” Genetics, vol. 188, no. 4. Genetics Society of America, pp. 953–973, 2011. ista: Barton NH, Etheridge A. 2011. The relation between reproductive value and genetic contribution. Genetics. 188(4), 953–973. mla: Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” Genetics, vol. 188, no. 4, Genetics Society of America, 2011, pp. 953–73, doi:10.1534/genetics.111.127555. short: N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973. date_created: 2018-12-11T12:03:04Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:43:09Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.111.127555 ec_funded: 1 intvolume: ' 188' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/ month: '08' oa: 1 oa_version: Submitted Version page: 953 - 973 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3217' quality_controlled: '1' scopus_import: 1 status: public title: The relation between reproductive value and genetic contribution type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 188 year: '2011' ... --- _id: '3391' abstract: - lang: eng text: 'Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time' author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: de Vladar H, Barton NH. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 2011;26(8):424-432. doi:10.1016/j.tree.2011.04.002 apa: de Vladar, H., & Barton, N. H. (2011). The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2011.04.002 chicago: Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” Trends in Ecology and Evolution. Cell Press, 2011. https://doi.org/10.1016/j.tree.2011.04.002. ieee: H. de Vladar and N. H. Barton, “The contribution of statistical physics to evolutionary biology,” Trends in Ecology and Evolution, vol. 26, no. 8. Cell Press, pp. 424–432, 2011. ista: de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 26(8), 424–432. mla: de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” Trends in Ecology and Evolution, vol. 26, no. 8, Cell Press, 2011, pp. 424–32, doi:10.1016/j.tree.2011.04.002. short: H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432. date_created: 2018-12-11T12:03:04Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:43:10Z day: '01' department: - _id: NiBa doi: 10.1016/j.tree.2011.04.002 ec_funded: 1 intvolume: ' 26' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.2854 month: '08' oa: 1 oa_version: Submitted Version page: 424 - 432 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Trends in Ecology and Evolution publication_status: published publisher: Cell Press publist_id: '3216' quality_controlled: '1' scopus_import: 1 status: public title: The contribution of statistical physics to evolutionary biology type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2011' ... --- _id: '3397' abstract: - lang: eng text: Recent advances in microscopy techniques and biophysical measurements have provided novel insight into the molecular, cellular and biophysical basis of cell adhesion. However, comparably little is known about a core element of cell–cell adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss approaches to understand the nature and regulation of adhesion energy, and propose strategies to determine adhesion energy between cells in vitro and in vivo. author: - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Maître J-L, Heisenberg C-PJ. The role of adhesion energy in controlling cell-cell contacts. Current Opinion in Cell Biology. 2011;23(5):508-514. doi:10.1016/j.ceb.2011.07.004 apa: Maître, J.-L., & Heisenberg, C.-P. J. (2011). The role of adhesion energy in controlling cell-cell contacts. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2011.07.004 chicago: Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “The Role of Adhesion Energy in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology. Elsevier, 2011. https://doi.org/10.1016/j.ceb.2011.07.004. ieee: J.-L. Maître and C.-P. J. Heisenberg, “The role of adhesion energy in controlling cell-cell contacts,” Current Opinion in Cell Biology, vol. 23, no. 5. Elsevier, pp. 508–514, 2011. ista: Maître J-L, Heisenberg C-PJ. 2011. The role of adhesion energy in controlling cell-cell contacts. Current Opinion in Cell Biology. 23(5), 508–514. mla: Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “The Role of Adhesion Energy in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology, vol. 23, no. 5, Elsevier, 2011, pp. 508–14, doi:10.1016/j.ceb.2011.07.004. short: J.-L. Maître, C.-P.J. Heisenberg, Current Opinion in Cell Biology 23 (2011) 508–514. date_created: 2018-12-11T12:03:06Z date_published: 2011-10-01T00:00:00Z date_updated: 2021-01-12T07:43:12Z day: '01' department: - _id: CaHe doi: 10.1016/j.ceb.2011.07.004 intvolume: ' 23' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188705/ month: '10' oa: 1 oa_version: Submitted Version page: 508 - 514 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '3211' quality_controlled: '1' scopus_import: 1 status: public title: The role of adhesion energy in controlling cell-cell contacts type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2011' ... --- _id: '3405' abstract: - lang: eng text: Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system and gates non-selective cation channels. The origins of glutamate receptors are not well understood as they differ structurally and functionally from simple bacterial ligand-gated ion channels. Here we report the discovery of an ionotropic glutamate receptor that combines the typical eukaryotic domain architecture with the 'TXVGYG' signature sequence of the selectivity filter found in K+ channels. This receptor exhibits functional properties intermediate between bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors. author: - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Guillaume full_name: Sandoz, Guillaume last_name: Sandoz - first_name: Ehud full_name: Isacoff, Ehud last_name: Isacoff citation: ama: Janovjak HL, Sandoz G, Isacoff E. Modern ionotropic glutamate receptor with a K+ selectivity signature sequence. Nature Communications. 2011;2(232):1-6. doi:10.1038/ncomms1231 apa: Janovjak, H. L., Sandoz, G., & Isacoff, E. (2011). Modern ionotropic glutamate receptor with a K+ selectivity signature sequence. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms1231 chicago: Janovjak, Harald L, Guillaume Sandoz, and Ehud Isacoff. “Modern Ionotropic Glutamate Receptor with a K+ Selectivity Signature Sequence.” Nature Communications. Nature Publishing Group, 2011. https://doi.org/10.1038/ncomms1231. ieee: H. L. Janovjak, G. Sandoz, and E. Isacoff, “Modern ionotropic glutamate receptor with a K+ selectivity signature sequence,” Nature Communications, vol. 2, no. 232. Nature Publishing Group, pp. 1–6, 2011. ista: Janovjak HL, Sandoz G, Isacoff E. 2011. Modern ionotropic glutamate receptor with a K+ selectivity signature sequence. Nature Communications. 2(232), 1–6. mla: Janovjak, Harald L., et al. “Modern Ionotropic Glutamate Receptor with a K+ Selectivity Signature Sequence.” Nature Communications, vol. 2, no. 232, Nature Publishing Group, 2011, pp. 1–6, doi:10.1038/ncomms1231. short: H.L. Janovjak, G. Sandoz, E. Isacoff, Nature Communications 2 (2011) 1–6. date_created: 2018-12-11T12:03:09Z date_published: 2011-03-08T00:00:00Z date_updated: 2021-01-12T07:43:15Z day: '08' ddc: - '570' - '571' department: - _id: HaJa doi: 10.1038/ncomms1231 file: - access_level: open_access checksum: 6b68d65aadd97c18d663eb117a0a9d35 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:36Z date_updated: 2020-07-14T12:46:12Z file_id: '4891' file_name: IST-2017-832-v1+1_janovjak.pdf file_size: 387654 relation: main_file file_date_updated: 2020-07-14T12:46:12Z has_accepted_license: '1' intvolume: ' 2' issue: '232' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 1 - 6 publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '2997' pubrep_id: '832' quality_controlled: '1' scopus_import: 1 status: public title: Modern ionotropic glutamate receptor with a K+ selectivity signature sequence type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2011' ... --- _id: '341' abstract: - lang: eng text: An oriented attachment and growth mechanism allows an accurate control of the size and morphology of Cu2-xS nanocrystals, from spheres and disks to tetradecahedrons and dodecahedrons. The synthesis conditions and the growth mechanism are detailed here. acknowledgement: "This work was supported by the Spanish MICINN projects\r\nMAT2008-05779, MAT2008-03400-E/MAT, ENE2008-03277-E/\r\nCON, MAT2010-15138, MAT-2010-21510, CDS2009-00050 and\r\nCSD2009-00013 and by Generalitat de Catalunya 2009-SGR-770\r\nand XaRMAE." article_processing_charge: No article_type: original author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Roger full_name: Guzman, Roger last_name: Guzman - first_name: Javier full_name: Rubio Garcia, Javier last_name: Rubio Garcia - first_name: Cristina full_name: Flox, Cristina last_name: Flox - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Shavel A, Guzman R, et al. Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons. Chemical Communications. 2011;47(37):10332-10334. doi:10.1039/c1cc13803k' apa: 'Li, W., Shavel, A., Guzman, R., Rubio Garcia, J., Flox, C., Fan, J., … Cabot, A. (2011). Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons. Chemical Communications. Royal Society of Chemistry (RSC) . https://doi.org/10.1039/c1cc13803k' chicago: 'Li, Wenhua, Alexey Shavel, Roger Guzman, Javier Rubio Garcia, Cristina Flox, Jiandong Fan, Doris Cadavid, et al. “Morphology Evolution of Cu2−xS Nanoparticles: From Spheres to Dodecahedrons.” Chemical Communications. Royal Society of Chemistry (RSC) , 2011. https://doi.org/10.1039/c1cc13803k.' ieee: 'W. Li et al., “Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons,” Chemical Communications, vol. 47, no. 37. Royal Society of Chemistry (RSC) , pp. 10332–10334, 2011.' ista: 'Li W, Shavel A, Guzman R, Rubio Garcia J, Flox C, Fan J, Cadavid D, Ibáñez M, Arbiol J, Morante J, Cabot A. 2011. Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons. Chemical Communications. 47(37), 10332–10334.' mla: 'Li, Wenhua, et al. “Morphology Evolution of Cu2−xS Nanoparticles: From Spheres to Dodecahedrons.” Chemical Communications, vol. 47, no. 37, Royal Society of Chemistry (RSC) , 2011, pp. 10332–34, doi:10.1039/c1cc13803k.' short: W. Li, A. Shavel, R. Guzman, J. Rubio Garcia, C. Flox, J. Fan, D. Cadavid, M. Ibáñez, J. Arbiol, J. Morante, A. Cabot, Chemical Communications 47 (2011) 10332–10334. date_created: 2018-12-11T11:45:55Z date_published: 2011-10-07T00:00:00Z date_updated: 2021-01-12T07:43:17Z day: '07' doi: 10.1039/c1cc13803k extern: '1' intvolume: ' 47' issue: '37' language: - iso: eng month: '10' oa_version: None page: 10332 - 10334 publication: Chemical Communications publication_status: published publisher: 'Royal Society of Chemistry (RSC) ' publist_id: '7491' quality_controlled: '1' status: public title: 'Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2011' ... --- _id: '3429' abstract: - lang: eng text: Transcription factors are central to sustaining pluripotency, yet little is known about transcription factor dynamics in defining pluripotency in the early mammalian embryo. Here, we establish a fluorescence decay after photoactivation (FDAP) assay to quantitatively study the kinetic behaviour of Oct4, a key transcription factor controlling pre-implantation development in the mouse embryo. FDAP measurements reveal that each cell in a developing embryo shows one of two distinct Oct4 kinetics, before there are any morphologically distinguishable differences or outward signs of lineage patterning. The differences revealed by FDAP are due to differences in the accessibility of Oct4 to its DNA binding sites in the nucleus. Lineage tracing of the cells in the two distinct sub-populations demonstrates that the Oct4 kinetics predict lineages of the early embryo. Cells with slower Oct4 kinetics are more likely to give rise to the pluripotent cell lineage that contributes to the inner cell mass. Those with faster Oct4 kinetics contribute mostly to the extra-embryonic lineage. Our findings identify Oct4 kinetics, rather than differences in total transcription factor expression levels, as a predictive measure of developmental cell lineage patterning in the early mouse embryo. acknowledgement: This work was supported by the Beckman Institute and Biological Imaging Center at the California Institute of Technology and by the NHGRI Center of Excellence in Genomic Science grant P50HG004071. author: - first_name: Nicolas full_name: Plachta, Nicolas last_name: Plachta - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Shirley full_name: Pease, Shirley last_name: Pease - first_name: Scott full_name: Fraser, Scott last_name: Fraser - first_name: Periklis full_name: Pantazis, Periklis last_name: Pantazis citation: ama: Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology. 2011;13(2):117-123. doi:10.1038/ncb2154 apa: Plachta, N., Bollenbach, M. T., Pease, S., Fraser, S., & Pantazis, P. (2011). Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2154 chicago: Plachta, Nicolas, Mark Tobias Bollenbach, Shirley Pease, Scott Fraser, and Periklis Pantazis. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early Mammalian Embryo.” Nature Cell Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/ncb2154. ieee: N. Plachta, M. T. Bollenbach, S. Pease, S. Fraser, and P. Pantazis, “Oct4 kinetics predict cell lineage patterning in the early mammalian embryo,” Nature Cell Biology, vol. 13, no. 2. Nature Publishing Group, pp. 117–123, 2011. ista: Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. 2011. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology. 13(2), 117–123. mla: Plachta, Nicolas, et al. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early Mammalian Embryo.” Nature Cell Biology, vol. 13, no. 2, Nature Publishing Group, 2011, pp. 117–23, doi:10.1038/ncb2154. short: N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell Biology 13 (2011) 117–123. date_created: 2018-12-11T12:03:17Z date_published: 2011-01-23T00:00:00Z date_updated: 2021-01-12T07:43:24Z day: '23' department: - _id: ToBo doi: 10.1038/ncb2154 intvolume: ' 13' issue: '2' language: - iso: eng month: '01' oa_version: None page: 117 - 123 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '2971' scopus_import: 1 status: public title: Oct4 kinetics predict cell lineage patterning in the early mammalian embryo type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2011' ... --- _id: '3505' abstract: - lang: eng text: Cell migration on two-dimensional (2D) substrates follows entirely different rules than cell migration in three-dimensional (3D) environments. This is especially relevant for leukocytes that are able to migrate in the absence of adhesion receptors within the confined geometry of artificial 3D extracellular matrix scaffolds and within the interstitial space in vivo. Here, we describe in detail a simple and economical protocol to visualize dendritic cell migration in 3D collagen scaffolds along chemotactic gradients. This method can be adapted to other cell types and may serve as a physiologically relevant paradigm for the directed locomotion of most amoeboid cells. alternative_title: - Methods in Molecular Biology article_processing_charge: No article_type: original author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann citation: ama: Sixt MK, Lämmermann T. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 2011;769:149-165. doi:10.1007/978-1-61779-207-6_11 apa: Sixt, M. K., & Lämmermann, T. (2011). In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. Springer. https://doi.org/10.1007/978-1-61779-207-6_11 chicago: Sixt, Michael K, and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” Cell Migration. Springer, 2011. https://doi.org/10.1007/978-1-61779-207-6_11. ieee: M. K. Sixt and T. Lämmermann, “In vitro analysis of chemotactic leukocyte migration in 3D environments,” Cell Migration, vol. 769. Springer, pp. 149–165, 2011. ista: Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 769, 149–165. mla: Sixt, Michael K., and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” Cell Migration, vol. 769, Springer, 2011, pp. 149–65, doi:10.1007/978-1-61779-207-6_11. short: M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165. date_created: 2018-12-11T12:03:41Z date_published: 2011-05-17T00:00:00Z date_updated: 2021-01-12T07:43:55Z day: '17' department: - _id: MiSi doi: 10.1007/978-1-61779-207-6_11 intvolume: ' 769' language: - iso: eng main_file_link: - open_access: '1' url: https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf month: '05' oa: 1 oa_version: Published Version page: 149 - 165 publication: Cell Migration publication_status: published publisher: Springer publist_id: '2882' quality_controlled: '1' status: public title: In vitro analysis of chemotactic leukocyte migration in 3D environments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 769 year: '2011' ... --- _id: '3784' abstract: - lang: eng text: Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus. article_processing_charge: No article_type: original author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Guillermo full_name: Guerao, Guillermo last_name: Guerao - first_name: Paul full_name: Clark, Paul last_name: Clark - first_name: Pere full_name: Abello, Pere last_name: Abello citation: ama: 'Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 2011;91(2):485-492. doi:10.1017/S0025315410000287' apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287' chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.' ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description,” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492, 2011.' ista: 'Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 91(2), 485–492.' mla: 'Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287.' short: F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492. date_created: 2018-12-11T12:05:09Z date_published: 2011-03-01T00:00:00Z date_updated: 2021-01-12T07:52:10Z day: '01' department: - _id: NiBa doi: 10.1017/S0025315410000287 intvolume: ' 91' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf month: '03' oa: 1 oa_version: Published Version page: 485 - 492 publication: Journal of the Marine Biological Association of the United Kingdom publication_status: published publisher: Cambridge University Press publist_id: '2443' quality_controlled: '1' scopus_import: 1 status: public title: 'Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2011' ... --- _id: '3781' abstract: - lang: eng text: We bound the difference in length of two curves in terms of their total curvatures and the Fréchet distance. The bound is independent of the dimension of the ambient Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and it generalizes a result by Fáry and Chakerian. acknowledgement: Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship. author: - first_name: Brittany Terese full_name: Fasy, Brittany Terese id: F65D502E-E68D-11E9-9252-C644099818F6 last_name: Fasy citation: ama: Fasy BT. The difference in length of curves in R^n. Acta Sci Math (Szeged). 2011;77(1-2):359-367. apa: Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Sci. Math. (Szeged). Szegedi Tudományegyetem. chicago: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta Sci. Math. (Szeged). Szegedi Tudományegyetem, 2011. ieee: B. T. Fasy, “The difference in length of curves in R^n,” Acta Sci. Math. (Szeged), vol. 77, no. 1–2. Szegedi Tudományegyetem, pp. 359–367, 2011. ista: Fasy BT. 2011. The difference in length of curves in R^n. Acta Sci. Math. (Szeged). 77(1–2), 359–367. mla: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta Sci. Math. (Szeged), vol. 77, no. 1–2, Szegedi Tudományegyetem, 2011, pp. 359–67. short: B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367. date_created: 2018-12-11T12:05:08Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:52:09Z day: '01' department: - _id: HeEd intvolume: ' 77' issue: 1-2 language: - iso: eng month: '01' oa_version: None page: 359 - 367 publication: Acta Sci. Math. (Szeged) publication_status: published publisher: Szegedi Tudományegyetem publist_id: '2446' quality_controlled: '1' status: public title: The difference in length of curves in R^n type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2011' ... --- _id: '3796' abstract: - lang: eng text: We address the problem of covering ℝ n with congruent balls, while minimizing the number of balls that contain an average point. Considering the 1-parameter family of lattices defined by stretching or compressing the integer grid in diagonal direction, we give a closed formula for the covering density that depends on the distortion parameter. We observe that our family contains the thinnest lattice coverings in dimensions 2 to 5. We also consider the problem of packing congruent balls in ℝ n , for which we give a closed formula for the packing density as well. Again we observe that our family contains optimal configurations, this time densest packings in dimensions 2 and 3. alternative_title: - LNCS author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 citation: ama: 'Edelsbrunner H, Kerber M. Covering and packing with spheres by diagonal distortion in R^n. In: Calude C, Rozenberg G, Salomaa A, eds. Rainbow of Computer Science. Vol 6570. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer; 2011:20-35. doi:10.1007/978-3-642-19391-0_2' apa: Edelsbrunner, H., & Kerber, M. (2011). Covering and packing with spheres by diagonal distortion in R^n. In C. Calude, G. Rozenberg, & A. Salomaa (Eds.), Rainbow of Computer Science (Vol. 6570, pp. 20–35). Springer. https://doi.org/10.1007/978-3-642-19391-0_2 chicago: Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” In Rainbow of Computer Science, edited by Cristian Calude, Grzegorz Rozenberg, and Arto Salomaa, 6570:20–35. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer, 2011. https://doi.org/10.1007/978-3-642-19391-0_2. ieee: H. Edelsbrunner and M. Kerber, “Covering and packing with spheres by diagonal distortion in R^n,” in Rainbow of Computer Science, vol. 6570, C. Calude, G. Rozenberg, and A. Salomaa, Eds. Springer, 2011, pp. 20–35. ista: 'Edelsbrunner H, Kerber M. 2011.Covering and packing with spheres by diagonal distortion in R^n. In: Rainbow of Computer Science. LNCS, vol. 6570, 20–35.' mla: Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” Rainbow of Computer Science, edited by Cristian Calude et al., vol. 6570, Springer, 2011, pp. 20–35, doi:10.1007/978-3-642-19391-0_2. short: H. Edelsbrunner, M. Kerber, in:, C. Calude, G. Rozenberg, A. Salomaa (Eds.), Rainbow of Computer Science, Springer, 2011, pp. 20–35. date_created: 2018-12-11T12:05:13Z date_published: 2011-05-03T00:00:00Z date_updated: 2021-01-12T07:52:15Z day: '03' ddc: - '000' department: - _id: HeEd doi: 10.1007/978-3-642-19391-0_2 editor: - first_name: Cristian full_name: Calude, Cristian last_name: Calude - first_name: Grzegorz full_name: Rozenberg, Grzegorz last_name: Rozenberg - first_name: Arto full_name: Salomaa, Arto last_name: Salomaa file: - access_level: open_access checksum: aaf22b4d7bd4277ffe8db532119cf474 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:42Z date_updated: 2020-07-14T12:46:16Z file_id: '4640' file_name: IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf file_size: 436875 relation: main_file file_date_updated: 2020-07-14T12:46:16Z has_accepted_license: '1' intvolume: ' 6570' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 20 - 35 publication: Rainbow of Computer Science publication_status: published publisher: Springer publist_id: '2427' pubrep_id: '539' quality_controlled: '1' series_title: Dedicated to Hermann Maurer on the Occasion of His 70th Birthday status: public title: Covering and packing with spheres by diagonal distortion in R^n type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6570 year: '2011' ... --- _id: '3381' abstract: - lang: eng text: In this survey, we compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. All these languages — matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models — describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, and ease of use. Moreover, they provide different support for checking the well-formedness of a model and for analyzing a model. author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Verena full_name: Wolf, Verena last_name: Wolf citation: ama: 'Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 2011;22(4):823-841. doi:10.1142/S0129054111008441' apa: 'Henzinger, T. A., Jobstmann, B., & Wolf, V. (2011). Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054111008441' chicago: 'Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models.” IJFCS: International Journal of Foundations of Computer Science. World Scientific Publishing, 2011. https://doi.org/10.1142/S0129054111008441.' ieee: 'T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” IJFCS: International Journal of Foundations of Computer Science, vol. 22, no. 4. World Scientific Publishing, pp. 823–841, 2011.' ista: 'Henzinger TA, Jobstmann B, Wolf V. 2011. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 22(4), 823–841.' mla: 'Henzinger, Thomas A., et al. “Formalisms for Specifying Markovian Population Models.” IJFCS: International Journal of Foundations of Computer Science, vol. 22, no. 4, World Scientific Publishing, 2011, pp. 823–41, doi:10.1142/S0129054111008441.' short: 'T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations of Computer Science 22 (2011) 823–841.' date_created: 2018-12-11T12:03:00Z date_published: 2011-06-01T00:00:00Z date_updated: 2023-02-23T11:45:03Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1142/S0129054111008441 file: - access_level: open_access checksum: df88431872586c773fbcfea37d7b36a2 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:45Z date_updated: 2020-07-14T12:46:11Z file_id: '4707' file_name: IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf file_size: 222840 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 22' issue: '4' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 823 - 841 publication: 'IJFCS: International Journal of Foundations of Computer Science' publication_status: published publisher: World Scientific Publishing publist_id: '3226' pubrep_id: '628' quality_controlled: '1' related_material: record: - id: '3841' relation: earlier_version status: public scopus_import: 1 status: public title: Formalisms for specifying Markovian population models type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2011' ... --- _id: '386' abstract: - lang: eng text: 'We present a detailed study of the local density of states (LDOS) associated with the surface-state band near a step edge of the strong topological insulator Bi2Te3 and reveal a one-dimensional bound state that runs parallel to the step edge and is bound to it at some characteristic distance. This bound state is clearly observed in the bulk gap region, while it becomes entangled with the oscillations of the warped surface band at high energy, and with the valence-band states near the Dirac point. We obtain excellent fits to theoretical predictions [Alpichshev, 2011] that properly incorporate the three-dimensional nature of the problem to the surface state. Fitting the data at different energies, we can recalculate the LDOS originating from the Dirac band without the contribution of the bulk bands or incoherent tunneling effects. ' article_processing_charge: No article_type: original author: - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: J G full_name: Analytis, J G last_name: Analytis - first_name: J H full_name: Chu, J H last_name: Chu - first_name: I R full_name: Fisher, I R last_name: Fisher - first_name: A full_name: Kapitulnik, A last_name: Kapitulnik citation: ama: Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. 2011;84(4). doi:10.1103/PhysRevB.84.041104 apa: Alpichshev, Z., Analytis, J. G., Chu, J. H., Fisher, I. R., & Kapitulnik, A. (2011). STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.041104 chicago: Alpichshev, Zhanybek, J G Analytis, J H Chu, I R Fisher, and A Kapitulnik. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.041104. ieee: Z. Alpichshev, J. G. Analytis, J. H. Chu, I. R. Fisher, and A. Kapitulnik, “STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3,” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 4. American Physical Society, 2011. ista: Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. 2011. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. 84(4). mla: Alpichshev, Zhanybek, et al. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 4, American Physical Society, 2011, doi:10.1103/PhysRevB.84.041104. short: Z. Alpichshev, J.G. Analytis, J.H. Chu, I.R. Fisher, A. Kapitulnik, Physical Review B - Condensed Matter and Materials Physics 84 (2011). date_created: 2018-12-11T11:46:10Z date_published: 2011-07-21T00:00:00Z date_updated: 2021-01-12T07:52:44Z day: '21' doi: 10.1103/PhysRevB.84.041104 extern: '1' external_id: arxiv: - '1003.2233' intvolume: ' 84' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1003.2233 month: '07' oa: 1 oa_version: Preprint publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '7443' quality_controlled: '1' status: public title: STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 84 year: '2011' ... --- _id: '3315' abstract: - lang: eng text: We consider two-player games played in real time on game structures with clocks where the objectives of players are described using parity conditions. The games are concurrent in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to play strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to turn-based (i.e., not concurrent) finite-state (i.e., untimed) parity games. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. The states of the resulting game are based on clock regions of the original game, and the state space of the finite game is linear in the size of the region graph. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust winning strategies. Using a limit-robust winning strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust winning. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust winning strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: 'Chatterjee K, Henzinger TA, Prabhu V. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 2011;7(4). doi:10.2168/LMCS-7(4:8)2011' apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2011). Timed parity games: Complexity and robustness. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-7(4:8)2011' chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Timed Parity Games: Complexity and Robustness.” Logical Methods in Computer Science. International Federation of Computational Logic, 2011. https://doi.org/10.2168/LMCS-7(4:8)2011.' ieee: 'K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Timed parity games: Complexity and robustness,” Logical Methods in Computer Science, vol. 7, no. 4. International Federation of Computational Logic, 2011.' ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 7(4).' mla: 'Chatterjee, Krishnendu, et al. “Timed Parity Games: Complexity and Robustness.” Logical Methods in Computer Science, vol. 7, no. 4, International Federation of Computational Logic, 2011, doi:10.2168/LMCS-7(4:8)2011.' short: K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science 7 (2011). date_created: 2018-12-11T12:02:37Z date_published: 2011-12-14T00:00:00Z date_updated: 2023-02-23T11:46:35Z day: '14' ddc: - '000' - '005' department: - _id: KrCh - _id: ToHe doi: 10.2168/LMCS-7(4:8)2011 ec_funded: 1 file: - access_level: open_access checksum: 3480e1594bbef25ff7462fa93a8a814e content_type: application/pdf creator: system date_created: 2018-12-12T10:16:42Z date_updated: 2020-07-14T12:46:07Z file_id: '5231' file_name: IST-2016-86-v2+1_1011.0688_3_.pdf file_size: 588863 relation: main_file file_date_updated: 2020-07-14T12:46:07Z has_accepted_license: '1' intvolume: ' 7' issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '12' oa: 1 oa_version: Published Version project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques publication: Logical Methods in Computer Science publication_status: published publisher: International Federation of Computational Logic publist_id: '3324' pubrep_id: '506' quality_controlled: '1' related_material: record: - id: '3876' relation: earlier_version status: public scopus_import: 1 status: public title: 'Timed parity games: Complexity and robustness' tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2011' ... --- _id: '3965' abstract: - lang: eng text: The elevation function on a smoothly embedded 2-manifold in R-3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in identifying coarse docking configurations for protein pairs. Transporting the concept from the smooth to the piecewise linear category, this paper describes an algorithm for finding all local maxima. While its worst-case running time is the same as of the algorithm used in prior work, its performance in practice is orders of magnitudes superior. We cast light on this improvement by relating the running time to the total absolute Gaussian curvature of the 2-manifold. author: - first_name: Bei full_name: Wang, Bei last_name: Wang - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov citation: ama: Wang B, Edelsbrunner H, Morozov D. Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. 2011;16(2.2):1-13. doi:10.1145/1963190.1970375 apa: Wang, B., Edelsbrunner, H., & Morozov, D. (2011). Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. ACM. https://doi.org/10.1145/1963190.1970375 chicago: Wang, Bei, Herbert Edelsbrunner, and Dmitriy Morozov. “Computing Elevation Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics. ACM, 2011. https://doi.org/10.1145/1963190.1970375. ieee: B. Wang, H. Edelsbrunner, and D. Morozov, “Computing elevation maxima by searching the Gauss sphere,” Journal of Experimental Algorithmics, vol. 16, no. 2.2. ACM, pp. 1–13, 2011. ista: Wang B, Edelsbrunner H, Morozov D. 2011. Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. 16(2.2), 1–13. mla: Wang, Bei, et al. “Computing Elevation Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics, vol. 16, no. 2.2, ACM, 2011, pp. 1–13, doi:10.1145/1963190.1970375. short: B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics 16 (2011) 1–13. date_created: 2018-12-11T12:06:09Z date_published: 2011-05-01T00:00:00Z date_updated: 2021-01-12T07:53:31Z day: '01' department: - _id: HeEd doi: 10.1145/1963190.1970375 intvolume: ' 16' issue: '2.2' language: - iso: eng month: '05' oa_version: None page: 1 - 13 publication: Journal of Experimental Algorithmics publication_status: published publisher: ACM publist_id: '2161' quality_controlled: '1' scopus_import: 1 status: public title: Computing elevation maxima by searching the Gauss sphere type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2011' ... --- _id: '3086' abstract: - lang: eng text: PIN-FORMED (PIN)-dependent auxin transport is essential for plant development and its modulation in response to the environment or endogenous signals. A NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3)-like protein, MACCHI-BOU 4 (MAB4), has been shown to control PIN1 localization during organ formation, but its contribution is limited. The Arabidopsis genome contains four genes, MAB4/ENP/NPY1-LIKE1 (MEL1), MEL2, MEL3 and MEL4, highly homologous to MAB4. Genetic analysis disclosed functional redundancy between MAB4 and MEL genes in regulation of not only organ formation but also of root gravitropism, revealing that NPH3 family proteins have a wider range of functions than previously suspected. Multiple mutants showed severe reduction in PIN abundance and PIN polar localization, leading to defective expression of an auxin responsive marker DR5rev::GFP. Pharmacological analyses and fluorescence recovery after photo-bleaching experiments showed that mel mutations increase PIN2 internalization from the plasma membrane, but affect neither intracellular PIN2 trafficking nor PIN2 lateral diffusion at the plasma membrane. Notably, all MAB4 subfamily proteins show polar localization at the cell periphery in plants. The MAB4 polarity was almost identical to PIN polarity. Our results suggest that the MAB4 subfamily proteins specifically retain PIN proteins in a polarized manner at the plasma membrane, thus controlling directional auxin transport and plant development. author: - first_name: Masahiko full_name: Furutani, Masahiko last_name: Furutani - first_name: Norihito full_name: Sakamoto, Norihito last_name: Sakamoto - first_name: Shuhei full_name: Yoshida, Shuhei last_name: Yoshida - first_name: Takahito full_name: Kajiwara, Takahito last_name: Kajiwara - first_name: Hélène full_name: Robert, Hélène S last_name: Robert - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Masao full_name: Tasaka, Masao last_name: Tasaka citation: ama: Furutani M, Sakamoto N, Yoshida S, et al. Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers. Development. 2011;138(10):2069-2078. doi:10.1242/dev.057745 apa: Furutani, M., Sakamoto, N., Yoshida, S., Kajiwara, T., Robert, H., Friml, J., & Tasaka, M. (2011). Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers. Development. Company of Biologists. https://doi.org/10.1242/dev.057745 chicago: Furutani, Masahiko, Norihito Sakamoto, Shuhei Yoshida, Takahito Kajiwara, Hélène Robert, Jiří Friml, and Masao Tasaka. “Polar Localized NPH3-like Proteins Regulate Polarity and Endocytosis of PIN-FORMED Auxin Efflux Carriers.” Development. Company of Biologists, 2011. https://doi.org/10.1242/dev.057745. ieee: M. Furutani et al., “Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers,” Development, vol. 138, no. 10. Company of Biologists, pp. 2069–2078, 2011. ista: Furutani M, Sakamoto N, Yoshida S, Kajiwara T, Robert H, Friml J, Tasaka M. 2011. Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers. Development. 138(10), 2069–2078. mla: Furutani, Masahiko, et al. “Polar Localized NPH3-like Proteins Regulate Polarity and Endocytosis of PIN-FORMED Auxin Efflux Carriers.” Development, vol. 138, no. 10, Company of Biologists, 2011, pp. 2069–78, doi:10.1242/dev.057745. short: M. Furutani, N. Sakamoto, S. Yoshida, T. Kajiwara, H. Robert, J. Friml, M. Tasaka, Development 138 (2011) 2069–2078. date_created: 2018-12-11T12:01:17Z date_published: 2011-05-01T00:00:00Z date_updated: 2021-01-12T07:40:57Z day: '01' doi: 10.1242/dev.057745 extern: 1 intvolume: ' 138' issue: '10' month: '05' page: 2069 - 2078 publication: Development publication_status: published publisher: Company of Biologists publist_id: '3615' quality_controlled: 0 status: public title: Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers type: journal_article volume: 138 year: '2011' ... --- _id: '3087' abstract: - lang: eng text: Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrinmediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type-specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants. author: - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Christian full_name: Löfke, Christian last_name: Löfke - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kitakura S, Vanneste S, Robert S, et al. Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis. Plant Cell. 2011;23(5):1920-1931. doi:10.1105/tpc.111.083030 apa: Kitakura, S., Vanneste, S., Robert, S., Löfke, C., Teichmann, T., Tanaka, H., & Friml, J. (2011). Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.111.083030 chicago: Kitakura, Saeko, Steffen Vanneste, Stéphanie Robert, Christian Löfke, Thomas Teichmann, Hirokazu Tanaka, and Jiří Friml. “Clathrin Mediates Endocytosis and Polar Distribution of PIN Auxin Transporters in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.083030. ieee: S. Kitakura et al., “Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis,” Plant Cell, vol. 23, no. 5. American Society of Plant Biologists, pp. 1920–1931, 2011. ista: Kitakura S, Vanneste S, Robert S, Löfke C, Teichmann T, Tanaka H, Friml J. 2011. Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis. Plant Cell. 23(5), 1920–1931. mla: Kitakura, Saeko, et al. “Clathrin Mediates Endocytosis and Polar Distribution of PIN Auxin Transporters in Arabidopsis.” Plant Cell, vol. 23, no. 5, American Society of Plant Biologists, 2011, pp. 1920–31, doi:10.1105/tpc.111.083030. short: S. Kitakura, S. Vanneste, S. Robert, C. Löfke, T. Teichmann, H. Tanaka, J. Friml, Plant Cell 23 (2011) 1920–1931. date_created: 2018-12-11T12:01:18Z date_published: 2011-05-01T00:00:00Z date_updated: 2021-01-12T07:40:57Z day: '01' doi: 10.1105/tpc.111.083030 extern: 1 intvolume: ' 23' issue: '5' month: '05' page: 1920 - 1931 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3614' quality_controlled: 0 status: public title: Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis type: journal_article volume: 23 year: '2011' ... --- _id: '3085' abstract: - lang: eng text: Phototropism is an adaptation response, through which plants grow towards the light. It involves light perception and asymmetric distribution of the plant hormone auxin. Here we identify a crucial part of the mechanism for phototropism, revealing how light perception initiates auxin redistribution that leads to directional growth. We show that light polarizes the cellular localization of the auxin efflux carrier PIN3 in hypocotyl endodermis cells, resulting in changes in auxin distribution and differential growth. In the dark, high expression and activity of the PINOID (PID) kinase correlates with apolar targeting of PIN3 to all cell sides. Following illumination, light represses PINOID transcription and PIN3 is polarized specifically to the inner cell sides by GNOM ARF GTPase GEF (guanine nucleotide exchange factor)-dependent trafficking. Thus, differential trafficking at the shaded and illuminated hypocotyl side aligns PIN3 polarity with the light direction, and presumably redirects auxin flow towards the shaded side, where auxin promotes growth, causing hypocotyls to bend towards the light. Our results imply that PID phosphorylation-dependent recruitment of PIN proteins into distinct trafficking pathways is a mechanism to polarize auxin fluxes in response to different environmental and endogenous cues. author: - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding - first_name: Carlos full_name: Galván-Ampudia, Carlos S last_name: Galván Ampudia - first_name: Emilie full_name: Demarsy, Emilie last_name: Demarsy - first_name: Łukasz full_name: Łangowski, Łukasz last_name: Łangowski - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Yuanwei full_name: Fan, Yuanwei last_name: Fan - first_name: Miyo full_name: Morita, Miyo T last_name: Morita - first_name: Masao full_name: Tasaka, Masao last_name: Tasaka - first_name: Christian full_name: Fankhauser, Christian last_name: Fankhauser - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Ding Z, Galván Ampudia C, Demarsy E, et al. Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature Cell Biology. 2011;13(4):447-453. doi:10.1038/ncb2208 apa: Ding, Z., Galván Ampudia, C., Demarsy, E., Łangowski, Ł., Kleine Vehn, J., Fan, Y., … Friml, J. (2011). Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2208 chicago: Ding, Zhaojun, Carlos Galván Ampudia, Emilie Demarsy, Łukasz Łangowski, Jürgen Kleine Vehn, Yuanwei Fan, Miyo Morita, et al. “Light-Mediated Polarization of the PIN3 Auxin Transporter for the Phototropic Response in Arabidopsis.” Nature Cell Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/ncb2208. ieee: Z. Ding et al., “Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis,” Nature Cell Biology, vol. 13, no. 4. Nature Publishing Group, pp. 447–453, 2011. ista: Ding Z, Galván Ampudia C, Demarsy E, Łangowski Ł, Kleine Vehn J, Fan Y, Morita M, Tasaka M, Fankhauser C, Offringa R, Friml J. 2011. Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature Cell Biology. 13(4), 447–453. mla: Ding, Zhaojun, et al. “Light-Mediated Polarization of the PIN3 Auxin Transporter for the Phototropic Response in Arabidopsis.” Nature Cell Biology, vol. 13, no. 4, Nature Publishing Group, 2011, pp. 447–53, doi:10.1038/ncb2208. short: Z. Ding, C. Galván Ampudia, E. Demarsy, Ł. Łangowski, J. Kleine Vehn, Y. Fan, M. Morita, M. Tasaka, C. Fankhauser, R. Offringa, J. Friml, Nature Cell Biology 13 (2011) 447–453. date_created: 2018-12-11T12:01:17Z date_published: 2011-04-01T00:00:00Z date_updated: 2021-01-12T07:40:57Z day: '01' doi: 10.1038/ncb2208 extern: 1 intvolume: ' 13' issue: '4' month: '04' page: 447 - 453 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '3616' quality_controlled: 0 status: public title: Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis type: journal_article volume: 13 year: '2011' ... --- _id: '3084' abstract: - lang: eng text: |2- A central question in developmental biology concerns the mechanism of generation and maintenance of cell polarity, because these processes are essential for many cellular functions and multicellular development [1]. In plants, cell polarity has an additional role in mediating directional transport of the plant hormone auxin that is crucial for multiple developmental processes [2-4]. In addition, plant cells have a complex extracellular matrix, the cell wall [5, 6], whose role in regulating cellular processes, including cell polarity, is unexplored. We have found that polar distribution of PIN auxin transporters [7] in plant cells is maintained by connections between polar domains at the plasma membrane and the cell wall. Genetic and pharmacological interference with cellulose, the major component of the cell wall, or mechanical interference with the cell wall disrupts these connections and leads to increased lateral diffusion and loss of polar distribution of PIN transporters for the phytohormone auxin. Our results reveal a plant-specific mechanism for cell polarity maintenance and provide a conceptual framework for modulating cell polarity and plant development via endogenous and environmental manipulations of the cellulose-based extracellular matrix. author: - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Mugurel full_name: Feraru, Mugurel I last_name: Feraru - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Alexandre full_name: Martinière, Alexandre last_name: Martinière - first_name: Grégory full_name: Mouille, Grégory last_name: Mouille - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Samantha full_name: Vernhettes, Samantha last_name: Vernhettes - first_name: John full_name: Runions, John last_name: Runions - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Feraru E, Feraru M, Kleine Vehn J, et al. PIN polarity maintenance by the cell wall in Arabidopsis. Current Biology. 2011;21(4):338-343. doi:10.1016/j.cub.2011.01.036 apa: Feraru, E., Feraru, M., Kleine Vehn, J., Martinière, A., Mouille, G., Vanneste, S., … Friml, J. (2011). PIN polarity maintenance by the cell wall in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.01.036 chicago: Feraru, Elena, Mugurel Feraru, Jürgen Kleine Vehn, Alexandre Martinière, Grégory Mouille, Steffen Vanneste, Samantha Vernhettes, John Runions, and Jiří Friml. “PIN Polarity Maintenance by the Cell Wall in Arabidopsis.” Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.01.036. ieee: E. Feraru et al., “PIN polarity maintenance by the cell wall in Arabidopsis,” Current Biology, vol. 21, no. 4. Cell Press, pp. 338–343, 2011. ista: Feraru E, Feraru M, Kleine Vehn J, Martinière A, Mouille G, Vanneste S, Vernhettes S, Runions J, Friml J. 2011. PIN polarity maintenance by the cell wall in Arabidopsis. Current Biology. 21(4), 338–343. mla: Feraru, Elena, et al. “PIN Polarity Maintenance by the Cell Wall in Arabidopsis.” Current Biology, vol. 21, no. 4, Cell Press, 2011, pp. 338–43, doi:10.1016/j.cub.2011.01.036. short: E. Feraru, M. Feraru, J. Kleine Vehn, A. Martinière, G. Mouille, S. Vanneste, S. Vernhettes, J. Runions, J. Friml, Current Biology 21 (2011) 338–343. date_created: 2018-12-11T12:01:17Z date_published: 2011-02-22T00:00:00Z date_updated: 2021-01-12T07:40:56Z day: '22' doi: 10.1016/j.cub.2011.01.036 extern: 1 intvolume: ' 21' issue: '4' month: '02' page: 338 - 343 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3618' quality_controlled: 0 status: public title: PIN polarity maintenance by the cell wall in Arabidopsis type: journal_article volume: 21 year: '2011' ... --- _id: '3082' abstract: - lang: eng text: Shoot branching is one of the major determinants of plant architecture. Polar auxin transport in stems is necessary for the control of bud outgrowth by a dominant apex. Here, we show that following decapitation in pea (Pisum sativum L.), the axillary buds establish directional auxin export by subcellular polarization of PIN auxin transporters. Apical auxin application on the decapitated stem prevents this PIN polarization and canalization of laterally applied auxin. These results support a model in which the apical and lateral auxin sources compete for primary channels of auxin transport in the stem to control the outgrowth of axillary buds. author: - first_name: Jozef full_name: Balla, Jozef last_name: Balla - first_name: Petr full_name: Kalousek, Petr last_name: Kalousek - first_name: Vilém full_name: Reinöhl, Vilém last_name: Reinöhl - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Stanislav full_name: Procházka, Stanislav last_name: Procházka citation: ama: Balla J, Kalousek P, Reinöhl V, Friml J, Procházka S. Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant Journal. 2011;65(4):571-577. doi:10.1111/j.1365-313X.2010.04443.x apa: Balla, J., Kalousek, P., Reinöhl, V., Friml, J., & Procházka, S. (2011). Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2010.04443.x chicago: Balla, Jozef, Petr Kalousek, Vilém Reinöhl, Jiří Friml, and Stanislav Procházka. “Competitive Canalization of PIN Dependent Auxin Flow from Axillary Buds Controls Pea Bud Outgrowth.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2010.04443.x. ieee: J. Balla, P. Kalousek, V. Reinöhl, J. Friml, and S. Procházka, “Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth,” Plant Journal, vol. 65, no. 4. Wiley-Blackwell, pp. 571–577, 2011. ista: Balla J, Kalousek P, Reinöhl V, Friml J, Procházka S. 2011. Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant Journal. 65(4), 571–577. mla: Balla, Jozef, et al. “Competitive Canalization of PIN Dependent Auxin Flow from Axillary Buds Controls Pea Bud Outgrowth.” Plant Journal, vol. 65, no. 4, Wiley-Blackwell, 2011, pp. 571–77, doi:10.1111/j.1365-313X.2010.04443.x. short: J. Balla, P. Kalousek, V. Reinöhl, J. Friml, S. Procházka, Plant Journal 65 (2011) 571–577. date_created: 2018-12-11T12:01:16Z date_published: 2011-02-01T00:00:00Z date_updated: 2021-01-12T07:40:56Z day: '01' doi: 10.1111/j.1365-313X.2010.04443.x extern: 1 intvolume: ' 65' issue: '4' month: '02' page: 571 - 577 publication: Plant Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3619' quality_controlled: 0 status: public title: Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth type: journal_article volume: 65 year: '2011' ... --- _id: '3083' author: - first_name: David full_name: Robinson, David G last_name: Robinson - first_name: David full_name: Scheuring, David last_name: Scheuring - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Robinson D, Scheuring D, Naramoto S, Friml J. ARF1 localizes to the golgi and the trans Golgi network. Plant Cell. 2011;23(3):846-849. doi:10.1105/tpc.110.082099 apa: Robinson, D., Scheuring, D., Naramoto, S., & Friml, J. (2011). ARF1 localizes to the golgi and the trans Golgi network. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.110.082099 chicago: Robinson, David, David Scheuring, Satoshi Naramoto, and Jiří Friml. “ARF1 Localizes to the Golgi and the Trans Golgi Network.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.110.082099. ieee: D. Robinson, D. Scheuring, S. Naramoto, and J. Friml, “ARF1 localizes to the golgi and the trans Golgi network,” Plant Cell, vol. 23, no. 3. American Society of Plant Biologists, pp. 846–849, 2011. ista: Robinson D, Scheuring D, Naramoto S, Friml J. 2011. ARF1 localizes to the golgi and the trans Golgi network. Plant Cell. 23(3), 846–849. mla: Robinson, David, et al. “ARF1 Localizes to the Golgi and the Trans Golgi Network.” Plant Cell, vol. 23, no. 3, American Society of Plant Biologists, 2011, pp. 846–49, doi:10.1105/tpc.110.082099. short: D. Robinson, D. Scheuring, S. Naramoto, J. Friml, Plant Cell 23 (2011) 846–849. date_created: 2018-12-11T12:01:16Z date_published: 2011-03-01T00:00:00Z date_updated: 2021-01-12T07:40:56Z day: '01' doi: 10.1105/tpc.110.082099 extern: 1 intvolume: ' 23' issue: '3' month: '03' page: 846 - 849 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3617' quality_controlled: 0 status: public title: ARF1 localizes to the golgi and the trans Golgi network type: journal_article volume: 23 year: '2011' ... --- _id: '3101' abstract: - lang: eng text: Subcellular trafficking is required for a multitude of functions in eukaryotic cells. It involves regulation of cargo sorting, vesicle formation, trafficking and fusion processes at multiple levels. Adaptor protein (AP) complexes are key regulators of cargo sorting into vesicles in yeast and mammals but their existence and function in plants have not been demonstrated. Here we report the identification of the protein-affected trafficking 4 (pat4) mutant defective in the putative δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same GFP imaging-based forward genetic screen that lacks a functional putative AP-3 β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable phenotypes characterized by largely normal morphology and development, but strong intracellular accumulation of membrane proteins in aberrant vacuolar structures. All mutants are defective in morphology and function of lytic and protein storage vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation experiments and genetic studies revealed tight functional and physical associations of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely linked with putative AP-3 μ and σ subunits and several components of the clathrin and dynamin machineries. Taken together, these results demonstrate that AP complexes, similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific role in the regulation of biogenesis and function of vacuoles in plant cells. © 2011 IBCB, SIBS, CAS All rights reserved author: - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Barbara full_name: Möller, Barbara last_name: Möller - first_name: Inhwan full_name: Hwang, Inhwan last_name: Hwang - first_name: Mugurel full_name: Feraru, Mugurel I last_name: Feraru - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zwiewka M, Feraru E, Möller B, et al. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. 2011;21(12):1711-1722. doi:10.1038/cr.2011.99 apa: Zwiewka, M., Feraru, E., Möller, B., Hwang, I., Feraru, M., Kleine Vehn, J., … Friml, J. (2011). The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2011.99 chicago: Zwiewka, Marta, Elena Feraru, Barbara Möller, Inhwan Hwang, Mugurel Feraru, Jürgen Kleine Vehn, Dolf Weijers, and Jiří Friml. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” Cell Research. Nature Publishing Group, 2011. https://doi.org/10.1038/cr.2011.99. ieee: M. Zwiewka et al., “The AP 3 adaptor complex is required for vacuolar function in Arabidopsis,” Cell Research, vol. 21, no. 12. Nature Publishing Group, pp. 1711–1722, 2011. ista: Zwiewka M, Feraru E, Möller B, Hwang I, Feraru M, Kleine Vehn J, Weijers D, Friml J. 2011. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. 21(12), 1711–1722. mla: Zwiewka, Marta, et al. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” Cell Research, vol. 21, no. 12, Nature Publishing Group, 2011, pp. 1711–22, doi:10.1038/cr.2011.99. short: M. Zwiewka, E. Feraru, B. Möller, I. Hwang, M. Feraru, J. Kleine Vehn, D. Weijers, J. Friml, Cell Research 21 (2011) 1711–1722. date_created: 2018-12-11T12:01:23Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:41:04Z day: '01' doi: 10.1038/cr.2011.99 extern: 1 intvolume: ' 21' issue: '12' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357998/ month: '01' oa: 1 page: 1711 - 1722 publication: Cell Research publication_status: published publisher: Nature Publishing Group publist_id: '3597' quality_controlled: 0 status: public title: The AP 3 adaptor complex is required for vacuolar function in Arabidopsis type: journal_article volume: 21 year: '2011' ... --- _id: '3098' abstract: - lang: eng text: Cell polarity reflected by asymmetric distribution of proteins at the plasma membrane is a fundamental feature of unicellular and multicellular organisms. It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated plant cells. We have used super-resolution and semi-quantitative live-cell imaging in combination with pharmacological, genetic, and computational approaches to reveal insights into the mechanism of cell polarity maintenance in Arabidopsis thaliana. We show that polar-competent PIN transporters for the phytohormone auxin are delivered to the center of polar domains by super-polar recycling. Within the plasma membrane, PINs are recruited into non-mobile membrane clusters and their lateral diffusion is dramatically reduced, which ensures longer polar retention. At the circumventing edges of the polar domain, spatially defined internalization of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations confirm that the combination of these processes provides a robust mechanism for polarity maintenance in plant cells. Moreover, our study suggests that the regulation of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis have primary importance for PIN polarity maintenance. author: - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Krzysztof T full_name: Krzysztof Wabnik id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Alexandre full_name: Martinière, Alexandre last_name: Martinière - first_name: Łukasz full_name: Łangowski, Łukasz last_name: Łangowski - first_name: Katrin full_name: Willig, Katrin last_name: Willig - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Johannes full_name: Leitner, Johannes last_name: Leitner - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Stefan full_name: Jakobs, Stefan last_name: Jakobs - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Willy full_name: Govaerts, Willy J last_name: Govaerts - first_name: Stefan full_name: Hell, Stefan W last_name: Hell - first_name: John full_name: Runions, John last_name: Runions - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kleine Vehn J, Wabnik KT, Martinière A, et al. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. 2011;7. doi:10.1038/msb.2011.72 apa: Kleine Vehn, J., Wabnik, K. T., Martinière, A., Łangowski, Ł., Willig, K., Naramoto, S., … Friml, J. (2011). Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2011.72 chicago: Kleine Vehn, Jürgen, Krzysztof T Wabnik, Alexandre Martinière, Łukasz Łangowski, Katrin Willig, Satoshi Naramoto, Johannes Leitner, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” Molecular Systems Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/msb.2011.72. ieee: J. Kleine Vehn et al., “Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane,” Molecular Systems Biology, vol. 7. Nature Publishing Group, 2011. ista: Kleine Vehn J, Wabnik KT, Martinière A, Łangowski Ł, Willig K, Naramoto S, Leitner J, Tanaka H, Jakobs S, Robert S, Luschnig C, Govaerts W, Hell S, Runions J, Friml J. 2011. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. 7. mla: Kleine Vehn, Jürgen, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” Molecular Systems Biology, vol. 7, Nature Publishing Group, 2011, doi:10.1038/msb.2011.72. short: J. Kleine Vehn, K.T. Wabnik, A. Martinière, Ł. Łangowski, K. Willig, S. Naramoto, J. Leitner, H. Tanaka, S. Jakobs, S. Robert, C. Luschnig, W. Govaerts, S. Hell, J. Runions, J. Friml, Molecular Systems Biology 7 (2011). date_created: 2018-12-11T12:01:22Z date_published: 2011-10-25T00:00:00Z date_updated: 2021-01-12T07:41:02Z day: '25' doi: 10.1038/msb.2011.72 extern: 1 intvolume: ' 7' month: '10' publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '3601' quality_controlled: 0 status: public title: Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane type: journal_article volume: 7 year: '2011' ... --- _id: '3100' abstract: - lang: eng text: In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development. author: - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Frederik full_name: Coppens, Frederik last_name: Coppens - first_name: Eunkyoung full_name: Lee, EunKyoung last_name: Lee - first_name: Tyler full_name: Donner, Tyler J last_name: Donner - first_name: Zidian full_name: Xie, Zidian last_name: Xie - first_name: Gert full_name: Van Isterdael, Gert last_name: Van Isterdael - first_name: Stijn full_name: Dhondt, Stijn last_name: Dhondt - first_name: Freya full_name: De Winter, Freya last_name: De Winter - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Marnik full_name: Vuylsteke, Marnik last_name: Vuylsteke - first_name: Lieven full_name: De Veylder, Lieven last_name: De Veylder - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dirk full_name: Inzé, Dirk last_name: Inzé - first_name: Erich full_name: Grotewold, Erich last_name: Grotewold - first_name: Enrico full_name: Scarpella, Enrico last_name: Scarpella - first_name: Fred full_name: Sack, Fred last_name: Sack - first_name: Gerrit full_name: Beemster, Gerrit T last_name: Beemster - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman citation: ama: Vanneste S, Coppens F, Lee E, et al. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. 2011;30(16):3430-3441. doi:10.1038/emboj.2011.240 apa: Vanneste, S., Coppens, F., Lee, E., Donner, T., Xie, Z., Van Isterdael, G., … Beeckman, T. (2011). Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2011.240 chicago: Vanneste, Steffen, Frederik Coppens, Eunkyoung Lee, Tyler Donner, Zidian Xie, Gert Van Isterdael, Stijn Dhondt, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal. Wiley-Blackwell, 2011. https://doi.org/10.1038/emboj.2011.240. ieee: S. Vanneste et al., “Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ,” EMBO Journal, vol. 30, no. 16. Wiley-Blackwell, pp. 3430–3441, 2011. ista: Vanneste S, Coppens F, Lee E, Donner T, Xie Z, Van Isterdael G, Dhondt S, De Winter F, De Rybel B, Vuylsteke M, De Veylder L, Friml J, Inzé D, Grotewold E, Scarpella E, Sack F, Beemster G, Beeckman T. 2011. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. 30(16), 3430–3441. mla: Vanneste, Steffen, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal, vol. 30, no. 16, Wiley-Blackwell, 2011, pp. 3430–41, doi:10.1038/emboj.2011.240. short: S. Vanneste, F. Coppens, E. Lee, T. Donner, Z. Xie, G. Van Isterdael, S. Dhondt, F. De Winter, B. De Rybel, M. Vuylsteke, L. De Veylder, J. Friml, D. Inzé, E. Grotewold, E. Scarpella, F. Sack, G. Beemster, T. Beeckman, EMBO Journal 30 (2011) 3430–3441. date_created: 2018-12-11T12:01:23Z date_published: 2011-08-17T00:00:00Z date_updated: 2021-01-12T07:41:04Z day: '17' doi: 10.1038/emboj.2011.240 extern: 1 intvolume: ' 30' issue: '16' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160660/ month: '08' oa: 1 page: 3430 - 3441 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3600' quality_controlled: 0 status: public title: 'Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ' type: journal_article volume: 30 year: '2011' ... --- _id: '3099' abstract: - lang: eng text: Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery. author: - first_name: Georgia full_name: Drakakaki, Georgia last_name: Drakakaki - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Anna full_name: Szatmári, Anna-Maria last_name: Szatmári - first_name: Michelle full_name: Brown, Michelle Q last_name: Brown - first_name: Shingo full_name: Nagawa, Shingo last_name: Nagawa - first_name: Daniël full_name: Van Damme, Daniël last_name: Van Damme - first_name: Marylin full_name: Leonard, Marylin last_name: Leonard - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang - first_name: Thomas full_name: Girke, Thomas last_name: Girke - first_name: Sandra full_name: Schmid, Sandra L last_name: Schmid - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Natasha full_name: Raikhel, Natasha V last_name: Raikhel - first_name: Glen full_name: Hicks, Glen R last_name: Hicks citation: ama: Drakakaki G, Robert S, Szatmári A, et al. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. 2011;108(43):17850-17855. doi:10.1073/pnas.1108581108 apa: Drakakaki, G., Robert, S., Szatmári, A., Brown, M., Nagawa, S., Van Damme, D., … Hicks, G. (2011). Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1108581108 chicago: Drakakaki, Georgia, Stéphanie Robert, Anna Szatmári, Michelle Brown, Shingo Nagawa, Daniël Van Damme, Marylin Leonard, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1108581108. ieee: G. Drakakaki et al., “Clusters of bioactive compounds target dynamic endomembrane networks in vivo,” PNAS, vol. 108, no. 43. National Academy of Sciences, pp. 17850–17855, 2011. ista: Drakakaki G, Robert S, Szatmári A, Brown M, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid S, Russinova E, Friml J, Raikhel N, Hicks G. 2011. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. 108(43), 17850–17855. mla: Drakakaki, Georgia, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” PNAS, vol. 108, no. 43, National Academy of Sciences, 2011, pp. 17850–55, doi:10.1073/pnas.1108581108. short: G. Drakakaki, S. Robert, A. Szatmári, M. Brown, S. Nagawa, D. Van Damme, M. Leonard, Z. Yang, T. Girke, S. Schmid, E. Russinova, J. Friml, N. Raikhel, G. Hicks, PNAS 108 (2011) 17850–17855. date_created: 2018-12-11T12:01:23Z date_published: 2011-10-25T00:00:00Z date_updated: 2021-01-12T07:41:02Z day: '25' doi: 10.1073/pnas.1108581108 extern: 1 intvolume: ' 108' issue: '43' month: '10' page: 17850 - 17855 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3602' quality_controlled: 0 status: public title: Clusters of bioactive compounds target dynamic endomembrane networks in vivo type: journal_article volume: 108 year: '2011' ... --- _id: '3095' abstract: - lang: eng text: Root system architecture depends on lateral root (LR) initiation that takes place in a relatively narrow developmental window (DW). Here, we analyzed the role of auxin gradients established along the parent root in defining this DW for LR initiation. Correlations between auxin distribution and response, and spatiotemporal control of LR initiation were analyzed in Arabidopsis thaliana and tomato (Solanum lycopersicum). In both Arabidopsis and tomato roots, a well defined zone, where auxin content and response are minimal, demarcates the position of a DW for founder cell specification and LR initiation. We show that in the zone of auxin minimum pericycle cells have highest probability to become founder cells and that auxin perception via the TIR1/AFB pathway, and polar auxin transport, are essential for the establishment of this zone. Altogether, this study reveals that the same morphogen-like molecule, auxin, can act simultaneously as a morphogenetic trigger of LR founder cell identity and as a gradient-dependent signal defining positioning of the founder cell specification. This auxin minimum zone might represent an important control mechanism ensuring the LR initiation steadiness and the acropetal LR initiation pattern. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust. author: - first_name: Joseph full_name: Dubrovsky, Joseph G last_name: Dubrovsky - first_name: Selene full_name: Napsucialy-Mendivil, Selene last_name: Napsucialy Mendivil - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Yan full_name: Cheng, Yan last_name: Cheng - first_name: Svetlana full_name: Shishkova, Svetlana O last_name: Shishkova - first_name: Maria full_name: Ivanchenko, Maria G last_name: Ivanchenko - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Angus full_name: Murphy, Angus S last_name: Murphy - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Dubrovsky J, Napsucialy Mendivil S, Duclercq J, et al. Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. 2011;191(4):970-983. doi: 10.1111/j.1469-8137.2011.03757.x apa: Dubrovsky, J., Napsucialy Mendivil, S., Duclercq, J., Cheng, Y., Shishkova, S., Ivanchenko, M., … Benková, E. (2011). Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. Wiley-Blackwell. https://doi.org/ 10.1111/j.1469-8137.2011.03757.x chicago: Dubrovsky, Joseph, Selene Napsucialy Mendivil, Jérôme Duclercq, Yan Cheng, Svetlana Shishkova, Maria Ivanchenko, Jiří Friml, Angus Murphy, and Eva Benková. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” New Phytologist. Wiley-Blackwell, 2011. https://doi.org/ 10.1111/j.1469-8137.2011.03757.x. ieee: J. Dubrovsky et al., “Auxin minimum defines a developmental window for lateral root initiation,” New Phytologist, vol. 191, no. 4. Wiley-Blackwell, pp. 970–983, 2011. ista: Dubrovsky J, Napsucialy Mendivil S, Duclercq J, Cheng Y, Shishkova S, Ivanchenko M, Friml J, Murphy A, Benková E. 2011. Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. 191(4), 970–983. mla: Dubrovsky, Joseph, et al. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” New Phytologist, vol. 191, no. 4, Wiley-Blackwell, 2011, pp. 970–83, doi: 10.1111/j.1469-8137.2011.03757.x. short: J. Dubrovsky, S. Napsucialy Mendivil, J. Duclercq, Y. Cheng, S. Shishkova, M. Ivanchenko, J. Friml, A. Murphy, E. Benková, New Phytologist 191 (2011) 970–983. date_created: 2018-12-11T12:01:21Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:41:01Z day: '01' doi: ' 10.1111/j.1469-8137.2011.03757.x' extern: 1 intvolume: ' 191' issue: '4' month: '01' page: 970 - 983 publication: New Phytologist publication_status: published publisher: Wiley-Blackwell publist_id: '3605' quality_controlled: 0 status: public title: Auxin minimum defines a developmental window for lateral root initiation type: journal_article volume: 191 year: '2011' ... --- _id: '3097' abstract: - lang: eng text: Cytokinin is an important regulator of plant growth and development. In Arabidopsis thaliana, the two-component phosphorelay mediated through a family of histidine kinases and response regulators is recognized as the principal cytokinin signal transduction mechanism activating the complex transcriptional response to control various developmental processes. Here, we identified an alternative mode of cytokinin action that uses endocytic trafficking as a means to direct plant organogenesis. This activity occurs downstream of known cytokinin receptors but through a branch of the cytokinin signaling pathway that does not involve transcriptional regulation. We show that cytokinin regulates endocytic recycling of the auxin efflux carrier PINFORMED1 (PIN1) by redirecting it for lytic degradation in vacuoles. Stimulation of the lytic PIN1 degradation is not a default effect for general downregulation of proteins from plasma membranes, but a specific mechanism to rapidly modulate the auxin distribution in cytokinin-mediated developmental processes. author: - first_name: Peter full_name: Peter Marhavy id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Lindy full_name: Abas, Lindy last_name: Abas - first_name: Anas full_name: Abuzeineh, Anas last_name: Abuzeineh - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Markéta full_name: Pařezová, Markéta last_name: Pařezová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Marhavý P, Bielach A, Abas L, et al. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. 2011;21(4):796-804. doi:10.1016/j.devcel.2011.08.014 apa: Marhavý, P., Bielach, A., Abas, L., Abuzeineh, A., Duclercq, J., Tanaka, H., … Benková, E. (2011). Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.08.014 chicago: Marhavý, Peter, Agnieszka Bielach, Lindy Abas, Anas Abuzeineh, Jérôme Duclercq, Hirokazu Tanaka, Markéta Pařezová, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.08.014. ieee: P. Marhavý et al., “Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis,” Developmental Cell, vol. 21, no. 4. Cell Press, pp. 796–804, 2011. ista: Marhavý P, Bielach A, Abas L, Abuzeineh A, Duclercq J, Tanaka H, Pařezová M, Petrášek J, Friml J, Kleine Vehn J, Benková E. 2011. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. 21(4), 796–804. mla: Marhavý, Peter, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” Developmental Cell, vol. 21, no. 4, Cell Press, 2011, pp. 796–804, doi:10.1016/j.devcel.2011.08.014. short: P. Marhavý, A. Bielach, L. Abas, A. Abuzeineh, J. Duclercq, H. Tanaka, M. Pařezová, J. Petrášek, J. Friml, J. Kleine Vehn, E. Benková, Developmental Cell 21 (2011) 796–804. date_created: 2018-12-11T12:01:22Z date_published: 2011-10-18T00:00:00Z date_updated: 2021-01-12T07:41:02Z day: '18' doi: 10.1016/j.devcel.2011.08.014 extern: 1 intvolume: ' 21' issue: '4' month: '10' page: 796 - 804 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3603' quality_controlled: 0 status: public title: Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis type: journal_article volume: 21 year: '2011' ... --- _id: '3096' abstract: - lang: eng text: Carrier-dependent, intercellular auxin transport is central to the developmental patterning of higher plants (tracheophytes). The evolution of this polar auxin transport might be linked to the translocation of some PIN auxin efflux carriers from their presumably ancestral localization at the endoplasmic reticulum (ER) to the polar domains at the plasma membrane. Here we propose an eventually ancient mechanism of intercellular auxin distribution by ER-localized auxin transporters involving intracellular auxin retention and switch-like release from the ER. The proposed model integrates feedback circuits utilizing the conserved nuclear auxin signaling for the regulation of PIN transcription and a hypothetical ER-based signaling for the regulation of PIN-dependent transport activity at the ER. Computer simulations of the model revealed its plausibility for generating auxin channels and localized auxin maxima highlighting the possibility of this alternative mechanism for polar auxin transport. author: - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Willy full_name: Govaerts, Willy last_name: Govaerts - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. 2011;16(9):468-475. doi:10.1016/j.tplants.2011.05.002 apa: Wabnik, K. T., Kleine Vehn, J., Govaerts, W., & Friml, J. (2011). Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2011.05.002 chicago: Wabnik, Krzysztof T, Jürgen Kleine Vehn, Willy Govaerts, and Jiří Friml. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” Trends in Plant Science. Cell Press, 2011. https://doi.org/10.1016/j.tplants.2011.05.002. ieee: K. T. Wabnik, J. Kleine Vehn, W. Govaerts, and J. Friml, “Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization,” Trends in Plant Science, vol. 16, no. 9. Cell Press, pp. 468–475, 2011. ista: Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. 2011. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. 16(9), 468–475. mla: Wabnik, Krzysztof T., et al. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” Trends in Plant Science, vol. 16, no. 9, Cell Press, 2011, pp. 468–75, doi:10.1016/j.tplants.2011.05.002. short: K.T. Wabnik, J. Kleine Vehn, W. Govaerts, J. Friml, Trends in Plant Science 16 (2011) 468–475. date_created: 2018-12-11T12:01:21Z date_published: 2011-09-01T00:00:00Z date_updated: 2021-01-12T07:41:01Z day: '01' doi: 10.1016/j.tplants.2011.05.002 extern: '1' intvolume: ' 16' issue: '9' language: - iso: eng month: '09' oa_version: None page: 468 - 475 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '3604' quality_controlled: '1' status: public title: Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2011' ... --- _id: '3138' abstract: - lang: eng text: Hippocampal sharp waves (SPWs) and associated fast ("ripple") oscillations (SPW-Rs) in the CA1 region are among the most synchronous physiological patterns in the mammalian brain. Using two-dimensional arrays of electrodes for recording local field potentials and unit discharges in freely moving rats, we studied the emergence of ripple oscillations (140-220 Hz) and compared their origin and cellular-synaptic mechanisms with fast gamma oscillations (90-140 Hz). We show that (1) hippocampal SPW-Rs and fast gamma oscillations are quantitatively distinct patterns but involve the same networks and share similar mechanisms; (2) both the frequency and magnitude of fast oscillations are positively correlated with the magnitude of SPWs; (3) during both ripples and fast gamma oscillations the frequency of network oscillation is higher in CA1 than in CA3; and (4) the emergence of CA3 population bursts, a prerequisite for SPW-Rs, is biased by activity patterns in the dentate gyrus and entorhinal cortex, with the highest probability of ripples associated with an "optimum" level of dentate gamma power. We hypothesize that each hippocampal subnetwork possesses distinct resonant properties, tuned by the magnitude of the excitatory drive. author: - first_name: David full_name: Sullivan, David W last_name: Sullivan - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Kenji full_name: Mizuseki, Kenji last_name: Mizuseki - first_name: Sean full_name: Montgomery, Sean M last_name: Montgomery - first_name: Kamran full_name: Diba, Kamran last_name: Diba - first_name: György full_name: Buzsáki, György last_name: Buzsáki citation: ama: Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. 2011;31(23):8605-8616. doi:10.1523/JNEUROSCI.0294-11.2011 apa: Sullivan, D., Csicsvari, J. L., Mizuseki, K., Montgomery, S., Diba, K., & Buzsáki, G. (2011). Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0294-11.2011 chicago: Sullivan, David, Jozsef L Csicsvari, Kenji Mizuseki, Sean Montgomery, Kamran Diba, and György Buzsáki. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” Journal of Neuroscience. Society for Neuroscience, 2011. https://doi.org/10.1523/JNEUROSCI.0294-11.2011. ieee: D. Sullivan, J. L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, and G. Buzsáki, “Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity,” Journal of Neuroscience, vol. 31, no. 23. Society for Neuroscience, pp. 8605–8616, 2011. ista: Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. 2011. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. 31(23), 8605–8616. mla: Sullivan, David, et al. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” Journal of Neuroscience, vol. 31, no. 23, Society for Neuroscience, 2011, pp. 8605–16, doi:10.1523/JNEUROSCI.0294-11.2011. short: D. Sullivan, J.L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, G. Buzsáki, Journal of Neuroscience 31 (2011) 8605–8616. date_created: 2018-12-11T12:01:36Z date_published: 2011-06-08T00:00:00Z date_updated: 2021-01-12T07:41:19Z day: '08' doi: 10.1523/JNEUROSCI.0294-11.2011 extern: 1 intvolume: ' 31' issue: '23' month: '06' page: 8605 - 8616 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '3559' quality_controlled: 0 status: public title: Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity type: journal_article volume: 31 year: '2011' ... --- _id: '3145' abstract: - lang: eng text: Microinjection of recombinant DNA into zygotic pronuclei has been widely used for producing transgenic mice. However, with this method, the insertion site, integrity, and copy number of the transgene cannot be controlled. Here, we present an integrase-based approach to produce transgenic mice via pronuclear injection, whereby an intact single-copy transgene can be inserted into predetermined chromosomal loci with high efficiency (up to 40%), and faithfully transmitted through generations. We show that neighboring transgenic elements and bacterial DNA within the transgene cause profound silencing and expression variability of the transgenic marker. Removal of these undesirable elements leads to global high-level marker expression from transgenes driven by a ubiquitous promoter. We also obtained faithful marker expression from a tissue-specific promoter. The technique presented here will greatly facilitate murine transgenesis and precise structure/function dissection of mammalian gene function and regulation in vivo. author: - first_name: Bosiljka full_name: Tasic, Bosiljka last_name: Tasic - first_name: Simon full_name: Simon Hippenmeyer id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Charlene full_name: Wang, Charlene last_name: Wang - first_name: Matthew full_name: Gamboa, Matthew last_name: Gamboa - first_name: Hui full_name: Zong, Hui last_name: Zong - first_name: Yanru full_name: Chen-Tsai, Yanru last_name: Chen Tsai - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: ama: Tasic B, Hippenmeyer S, Wang C, et al. Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. 2011;108(19):7902-7907. doi:10.1073/pnas.1019507108 apa: Tasic, B., Hippenmeyer, S., Wang, C., Gamboa, M., Zong, H., Chen Tsai, Y., & Luo, L. (2011). Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1019507108 chicago: Tasic, Bosiljka, Simon Hippenmeyer, Charlene Wang, Matthew Gamboa, Hui Zong, Yanru Chen Tsai, and Liqun Luo. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019507108. ieee: B. Tasic et al., “Site specific integrase mediated transgenesis in mice via pronuclear injection,” PNAS, vol. 108, no. 19. National Academy of Sciences, pp. 7902–7907, 2011. ista: Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen Tsai Y, Luo L. 2011. Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. 108(19), 7902–7907. mla: Tasic, Bosiljka, et al. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” PNAS, vol. 108, no. 19, National Academy of Sciences, 2011, pp. 7902–07, doi:10.1073/pnas.1019507108. short: B. Tasic, S. Hippenmeyer, C. Wang, M. Gamboa, H. Zong, Y. Chen Tsai, L. Luo, PNAS 108 (2011) 7902–7907. date_created: 2018-12-11T12:01:39Z date_published: 2011-05-10T00:00:00Z date_updated: 2021-01-12T07:41:22Z day: '10' doi: 10.1073/pnas.1019507108 extern: 1 intvolume: ' 108' issue: '19' month: '05' page: 7902 - 7907 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3549' quality_controlled: 0 status: public title: Site specific integrase mediated transgenesis in mice via pronuclear injection type: journal_article volume: 108 year: '2011' ... --- _id: '3154' abstract: - lang: eng text: Regulated adhesion between cells and their environment is critical for normal cell migration. We have identified mutations in a gene encoding the Drosophila hydrogen peroxide (H2O2)-degrading enzyme Jafrac1, which lead to germ cell adhesion defects. During gastrulation, primordial germ cells (PGCs) associate tightly with the invaginating midgut primordium as it enters the embryo; however, in embryos from jafrac1 mutant mothers this association is disrupted, leaving some PGCs trailing on the outside of the embryo. We observed similar phenotypes in embryos from DE-cadherin/shotgun (shg) mutant mothers and were able to rescue the jafrac1 phenotype by increasing DE-cadherin levels. This and our biochemical evidence strongly suggest that Jafrac1-mediated reduction of H2O2 is required to maintain DE-cadherin protein levels in the early embryo. Our results present in vivo evidence of a peroxiredoxin regulating DE-cadherin-mediated adhesion. author: - first_name: Matthew full_name: DeGennaro, Matthew last_name: Degennaro - first_name: Thomas full_name: Hurd, Thomas R last_name: Hurd - first_name: Daria E full_name: Daria Siekhaus id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Benoit full_name: Biteau, Benoit last_name: Biteau - first_name: Heinrich full_name: Jasper, Heinrich last_name: Jasper - first_name: Ruth full_name: Lehmann, Ruth last_name: Lehmann citation: ama: Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. 2011;20(2):233-243. doi:10.1016/j.devcel.2010.12.007 apa: Degennaro, M., Hurd, T., Siekhaus, D. E., Biteau, B., Jasper, H., & Lehmann, R. (2011). Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2010.12.007 chicago: Degennaro, Matthew, Thomas Hurd, Daria E Siekhaus, Benoit Biteau, Heinrich Jasper, and Ruth Lehmann. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2010.12.007. ieee: M. Degennaro, T. Hurd, D. E. Siekhaus, B. Biteau, H. Jasper, and R. Lehmann, “Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion,” Developmental Cell, vol. 20, no. 2. Cell Press, pp. 233–243, 2011. ista: Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. 2011. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. 20(2), 233–243. mla: Degennaro, Matthew, et al. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” Developmental Cell, vol. 20, no. 2, Cell Press, 2011, pp. 233–43, doi:10.1016/j.devcel.2010.12.007. short: M. Degennaro, T. Hurd, D.E. Siekhaus, B. Biteau, H. Jasper, R. Lehmann, Developmental Cell 20 (2011) 233–243. date_created: 2018-12-11T12:01:42Z date_published: 2011-02-15T00:00:00Z date_updated: 2021-01-12T07:41:26Z day: '15' doi: 10.1016/j.devcel.2010.12.007 extern: 1 intvolume: ' 20' issue: '2' month: '02' page: 233 - 243 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3541' quality_controlled: 0 status: public title: Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion type: journal_article volume: 20 year: '2011' ... --- _id: '3239' abstract: - lang: eng text: Tampering attacks are cryptanalytic attacks on the implementation of cryptographic algorithms (e.g., smart cards), where an adversary introduces faults with the hope that the tampered device will reveal secret information. Inspired by the work of Ishai et al. [Eurocrypt'06], we propose a compiler that transforms any circuit into a new circuit with the same functionality, but which is resilient against a well-defined and powerful tampering adversary. More concretely, our transformed circuits remain secure even if the adversary can adaptively tamper with every wire in the circuit as long as the tampering fails with some probability δ>0. This additional requirement is motivated by practical tampering attacks, where it is often difficult to guarantee the success of a specific attack. Formally, we show that a q-query tampering attack against the transformed circuit can be "simulated" with only black-box access to the original circuit and log(q) bits of additional auxiliary information. Thus, if the implemented cryptographic scheme is secure against log(q) bits of leakage, then our implementation is tamper-proof in the above sense. Surprisingly, allowing for this small amount of information leakage allows for much more efficient compilers, which moreover do not require randomness during evaluation. Similar to earlier works our compiler requires small, stateless and computation-independent tamper-proof gadgets. Thus, our result can be interpreted as reducing the problem of shielding arbitrary complex computation to protecting simple components. © 2011 Springer-Verlag. alternative_title: - LNCS author: - first_name: Sebastian full_name: Faust, Sebastian last_name: Faust - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniele full_name: Venturi, Daniele last_name: Venturi citation: ama: 'Faust S, Pietrzak KZ, Venturi D. Tamper proof circuits How to trade leakage for tamper resilience. In: Vol 6755. Springer; 2011:391-402. doi:10.1007/978-3-642-22006-7_33' apa: 'Faust, S., Pietrzak, K. Z., & Venturi, D. (2011). Tamper proof circuits How to trade leakage for tamper resilience (Vol. 6755, pp. 391–402). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-642-22006-7_33' chicago: Faust, Sebastian, Krzysztof Z Pietrzak, and Daniele Venturi. “Tamper Proof Circuits How to Trade Leakage for Tamper Resilience,” 6755:391–402. Springer, 2011. https://doi.org/10.1007/978-3-642-22006-7_33. ieee: 'S. Faust, K. Z. Pietrzak, and D. Venturi, “Tamper proof circuits How to trade leakage for tamper resilience,” presented at the ICALP: Automata, Languages and Programming, 2011, vol. 6755, no. Part 1, pp. 391–402.' ista: 'Faust S, Pietrzak KZ, Venturi D. 2011. Tamper proof circuits How to trade leakage for tamper resilience. ICALP: Automata, Languages and Programming, LNCS, vol. 6755, 391–402.' mla: Faust, Sebastian, et al. Tamper Proof Circuits How to Trade Leakage for Tamper Resilience. Vol. 6755, no. Part 1, Springer, 2011, pp. 391–402, doi:10.1007/978-3-642-22006-7_33. short: S. Faust, K.Z. Pietrzak, D. Venturi, in:, Springer, 2011, pp. 391–402. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:02:12Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:02Z day: '01' doi: 10.1007/978-3-642-22006-7_33 extern: 1 issue: Part 1 month: '01' page: 391 - 402 publication_status: published publisher: Springer publist_id: '3441' quality_controlled: 0 status: public title: Tamper proof circuits How to trade leakage for tamper resilience type: conference volume: '6755 ' year: '2011' ... --- _id: '3236' abstract: - lang: eng text: 'If a cryptographic primitive remains secure even if ℓ bits about the secret key are leaked to the adversary, one would expect that at least one of n independent instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition has been proven true for schemes satisfying some special information-theoretic properties by Alwen et al. [Eurocrypt''10]. On the negative side, Lewko and Waters [FOCS''10] construct a CPA secure public-key encryption scheme for which this intuition fails. The counterexample of Lewko and Waters leaves open the interesting possibility that for any scheme there exists a constant c>0, such that n fold repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample requires the n copies of the encryption scheme to share a common reference parameter, leaving open the possibility that the intuition is true for all schemes without common setup. In this work we give a stronger counterexample ruling out these possibilities. We construct a signature scheme such that: 1. a single instantiation remains secure given ℓ = log(k) bits of leakage where k is a security parameter. 2. any polynomial number of independent instantiations can be broken (in the strongest sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not depend on the number of instances. The computational assumption underlying our counterexample is that non-interactive computationally sound proofs exist. Moreover, under a stronger (non-standard) assumption about such proofs, our counterexample does not require a common reference parameter. The underlying idea of our counterexample is rather generic and can be applied to other primitives like encryption schemes. © 2011 International Association for Cryptologic Research.' alternative_title: - LNCS author: - first_name: Abhishek full_name: Jain, Abhishek last_name: Jain - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification revisited. In: Vol 6597. Springer; 2011:58-69. doi:10.1007/978-3-642-19571-6_5' apa: 'Jain, A., & Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-19571-6_5' chicago: Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. https://doi.org/10.1007/978-3-642-19571-6_5. ieee: 'A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol. 6597, pp. 58–69.' ista: 'Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69.' mla: Jain, Abhishek, and Krzysztof Z. Pietrzak. Parallel Repetition for Leakage Resilience Amplification Revisited. Vol. 6597, Springer, 2011, pp. 58–69, doi:10.1007/978-3-642-19571-6_5. short: A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69. conference: name: 'TCC: Theory of Cryptography Conference' date_created: 2018-12-11T12:02:11Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:00Z day: '01' doi: 10.1007/978-3-642-19571-6_5 extern: 1 month: '01' page: 58 - 69 publication_status: published publisher: Springer publist_id: '3443' quality_controlled: 0 status: public title: Parallel repetition for leakage resilience amplification revisited type: conference volume: '6597 ' year: '2011' ... --- _id: '3276' abstract: - lang: eng text: 'We present an algorithm to identify individual neural spikes observed on high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers of distinct neural units, even when spikes overlap, and accounts for intrinsic variability of spikes from each unit. As MEAs grow larger, it is important to find spike-identification methods that are scalable, that is, the computational cost of spike fitting should scale well with the number of units observed. Our algorithm accomplishes this goal, and is fast, because it exploits the spatial locality of each unit and the basic biophysics of extracellular signal propagation. Human interaction plays a key role in our method; but effort is minimized and streamlined via a graphical interface. We illustrate our method on data from guinea pig retinal ganglion cells and document its performance on simulated data consisting of spikes added to experimentally measured background noise. We present several tests demonstrating that the algorithm is highly accurate: it exhibits low error rates on fits to synthetic data, low refractory violation rates, good receptive field coverage, and consistency across users.' acknowledgement: |+ This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04. Michael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior. author: - first_name: Jason full_name: Prentice, Jason S last_name: Prentice - first_name: Jan full_name: Homann, Jan last_name: Homann - first_name: Kristina full_name: Simmons, Kristina D last_name: Simmons - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian - first_name: Philip full_name: Nelson, Philip C last_name: Nelson citation: ama: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0019884 apa: Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., & Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0019884 chicago: Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian, and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884. ieee: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011. ista: Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 6(7). mla: Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884. short: J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011). date_created: 2018-12-11T12:02:24Z date_published: 2011-07-20T00:00:00Z date_updated: 2021-01-12T07:42:19Z day: '20' doi: 10.1371/journal.pone.0019884 extern: 1 file: - access_level: open_access checksum: 654464e99683b55a699734213d5356f1 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:38Z date_updated: 2020-07-14T12:46:06Z file_id: '4894' file_name: IST-2015-381-v1+1_journal.pone.0019884.pdf file_size: 885464 relation: main_file file_date_updated: 2020-07-14T12:46:06Z intvolume: ' 6' issue: '7' month: '07' oa: 1 publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3370' pubrep_id: '381' quality_controlled: 0 status: public title: Fast, scalable, Bayesian spike identification for multi-electrode arrays tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2011' ... ... --- _id: '3271' abstract: - lang: eng text: In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets. alternative_title: - Theory, Algorithms, and Applications author: - first_name: Hubert full_name: Wagner, Hubert last_name: Wagner - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Erald full_name: Vuçini, Erald last_name: Vuçini citation: ama: 'Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. Topological Methods in Data Analysis and Visualization II. Springer; 2011:91-106. doi:10.1007/978-3-642-23175-9_7' apa: Wagner, H., Chen, C., & Vuçini, E. (2011). Efficient computation of persistent homology for cubical data. In R. Peikert, H. Hauser, H. Carr, & R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II (pp. 91–106). Springer. https://doi.org/10.1007/978-3-642-23175-9_7 chicago: Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of Persistent Homology for Cubical Data.” In Topological Methods in Data Analysis and Visualization II, edited by Ronald Peikert, Helwig Hauser, Hamish Carr, and Raphael Fuchs, 91–106. Springer, 2011. https://doi.org/10.1007/978-3-642-23175-9_7. ieee: H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology for cubical data,” in Topological Methods in Data Analysis and Visualization II, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp. 91–106. ista: 'Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology for cubical data. In: Topological Methods in Data Analysis and Visualization II. Theory, Algorithms, and Applications, , 91–106.' mla: Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical Data.” Topological Methods in Data Analysis and Visualization II, edited by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:10.1007/978-3-642-23175-9_7. short: H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106. date_created: 2018-12-11T12:02:23Z date_published: 2011-11-14T00:00:00Z date_updated: 2021-01-12T07:42:18Z day: '14' department: - _id: HeEd doi: 10.1007/978-3-642-23175-9_7 editor: - first_name: Ronald full_name: Peikert, Ronald last_name: Peikert - first_name: Helwig full_name: Hauser, Helwig last_name: Hauser - first_name: Hamish full_name: Carr, Hamish last_name: Carr - first_name: Raphael full_name: Fuchs, Raphael last_name: Fuchs language: - iso: eng month: '11' oa_version: None page: 91 - 106 publication: Topological Methods in Data Analysis and Visualization II publication_status: published publisher: Springer publist_id: '3375' quality_controlled: '1' scopus_import: 1 status: public title: Efficient computation of persistent homology for cubical data type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3278' abstract: - lang: eng text: |- Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species. We find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies. author: - first_name: Roger full_name: Vila, Roger last_name: Vila - first_name: Naomi full_name: Pierce, Naomi E last_name: Pierce - first_name: David full_name: Nash, David R last_name: Nash - first_name: Line V full_name: Line Ugelvig id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 citation: ama: 'Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 2011;61(1):237-243. doi:10.1016/j.ympev.2011.05.016' apa: 'Vila, R., Pierce, N., Nash, D., & Ugelvig, L. V. (2011). A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. Elsevier. https://doi.org/10.1016/j.ympev.2011.05.016' chicago: 'Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution. Elsevier, 2011. https://doi.org/10.1016/j.ympev.2011.05.016.' ieee: 'R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade,” Molecular Phylogenetics and Evolution, vol. 61, no. 1. Elsevier, pp. 237–243, 2011.' ista: 'Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 61(1), 237–243.' mla: 'Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:10.1016/j.ympev.2011.05.016.' short: R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution 61 (2011) 237–243. date_created: 2018-12-11T12:02:25Z date_published: 2011-10-01T00:00:00Z date_updated: 2021-01-12T07:42:20Z day: '01' doi: 10.1016/j.ympev.2011.05.016 extern: 1 intvolume: ' 61' issue: '1' month: '10' page: 237 - 243 publication: Molecular Phylogenetics and Evolution publication_status: published publisher: Elsevier publist_id: '3368' quality_controlled: 0 status: public title: 'A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade' type: journal_article volume: 61 year: '2011' ...