[{"abstract":[{"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. ","lang":"eng"}],"intvolume":" 6907","month":"08","main_file_link":[{"open_access":"0","url":"http://arxiv.org/pdf/1007.1229v3"}],"quality_controlled":0,"alternative_title":["LNCS"],"publisher":"Springer","day":"09","year":"2011","publication_status":"published","date_created":"2018-12-11T12:02:00Z","doi":"10.1007/978-3-642-22993-0_37","volume":6907,"date_published":"2011-08-09T00:00:00Z","page":"400 - 411","_id":"3204","status":"public","conference":{"name":"MFCS: Mathematical Foundations of Computer Science"},"type":"conference","extern":1,"date_updated":"2021-01-12T07:41:47Z","citation":{"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.","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","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.","short":"V. Kolmogorov, in:, Springer, 2011, pp. 400–411.","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.","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."},"title":"Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions","publist_id":"3478","author":[{"last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}]},{"date_updated":"2021-01-12T07:41:47Z","citation":{"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.","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.","short":"A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896.","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.","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."},"extern":1,"author":[{"full_name":"Osokin, Anton","last_name":"Osokin","first_name":"Anton"},{"first_name":"Dmitry","last_name":"Vetrov","full_name":"Vetrov, Dmitry"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"}],"publist_id":"3476","title":"Submodular decomposition framework for inference in associative Markov networks with global constraints","_id":"3206","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","status":"public","publication_status":"published","year":"2011","day":"22","page":"1889 - 1896","date_created":"2018-12-11T12:02:00Z","doi":"10.1109/CVPR.2011.5995361","date_published":"2011-08-22T00:00:00Z","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."}],"main_file_link":[{"open_access":"0","url":"http://arxiv.org/pdf/1103.1077v1"}],"publisher":"IEEE","quality_controlled":0,"month":"08"},{"_id":"3205","conference":{"name":"ICML: International Conference on Machine Learning"},"type":"conference","status":"public","citation":{"ista":"Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate ascent. ICML: International Conference on Machine Learning, 113–120.","chicago":"Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011.","short":"D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120.","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.","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.","mla":"Tarlow, Daniel, et al. Dynamic Tree Block Coordinate Ascent. Omnipress, 2011, pp. 113–20."},"date_updated":"2021-01-12T07:41:47Z","extern":1,"author":[{"first_name":"Daniel","last_name":"Tarlow","full_name":"Tarlow, Daniel"},{"first_name":"Druv","last_name":"Batra","full_name":"Batra, Druv"},{"first_name":"Pushmeet","full_name":"Kohli, Pushmeet","last_name":"Kohli"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"}],"publist_id":"3475","title":"Dynamic tree block coordinate ascent","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"open_access":"0","url":"http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf"}],"quality_controlled":0,"publisher":"Omnipress","month":"01","year":"2011","publication_status":"published","day":"01","page":"113 - 120","date_created":"2018-12-11T12:02:00Z","date_published":"2011-01-01T00:00:00Z"},{"page":"2217 - 2224","date_created":"2018-12-11T12:02:01Z","date_published":"2011-08-22T00:00:00Z","doi":"10.1109/CVPR.2011.5995530","year":"2011","publication_status":"published","day":"22","quality_controlled":0,"publisher":"IEEE","month":"08","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":[{"last_name":"Vicente","full_name":"Vicente, Sara","first_name":"Sara"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"}],"publist_id":"3477","title":"Object cosegmentation","date_updated":"2021-01-12T07:41:48Z","citation":{"ieee":"S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.","short":"S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.","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","ama":"Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224. doi:10.1109/CVPR.2011.5995530","mla":"Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24, doi:10.1109/CVPR.2011.5995530.","ista":"Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer Vision and Pattern Recognition, 2217–2224.","chicago":"Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,” 2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530."},"extern":1,"conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","status":"public","_id":"3207"},{"doi":" 10.1007/978-3-642-22792-9_1","date_published":"2011-01-01T00:00:00Z","volume":6841,"date_created":"2018-12-11T12:02:12Z","page":"1 - 20","day":"01","year":"2011","publication_status":"published","month":"01","intvolume":" 6841","publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":0,"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."}],"title":"Leftover hash lemma revisited","publist_id":"3440","author":[{"first_name":"Boaz","full_name":"Barak, Boaz","last_name":"Barak"},{"first_name":"Yevgeniy","last_name":"Dodis","full_name":"Dodis, Yevgeniy"},{"last_name":"Krawczyk","full_name":"Krawczyk, Hugo","first_name":"Hugo"},{"last_name":"Pereira","full_name":"Pereira, Olivier","first_name":"Olivier"},{"orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Standaert, François-Xavier","last_name":"Standaert","first_name":"François"},{"first_name":"Yu","last_name":"Yu","full_name":"Yu, Yu"}],"extern":1,"citation":{"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.","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.","short":"B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert, Y. Yu, in:, Springer, 2011, pp. 1–20.","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","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."},"date_updated":"2021-01-12T07:42:03Z","status":"public","type":"conference","conference":{"name":"CRYPTO: International Cryptology Conference"},"_id":"3240"},{"_id":"3264","status":"public","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"type":"conference","conference":{"name":"APLAS: Asian Symposium on Programming Languages and Systems","start_date":"2011-12-05","location":"Kenting, Taiwan","end_date":"2011-12-07"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203.","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.","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","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","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."},"date_updated":"2021-01-12T07:42:15Z","editor":[{"first_name":"Hongseok","full_name":"Yang, Hongseok","last_name":"Yang"}],"department":[{"_id":"ToHe"}],"title":"Solving recursion-free Horn clauses over LI+UIF","publist_id":"3383","author":[{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Popeea, Corneliu","last_name":"Popeea","first_name":"Corneliu"},{"first_name":"Andrey","last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey"}],"oa_version":"None","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."}],"month":"12","intvolume":" 7078","publisher":"Springer","quality_controlled":"1","alternative_title":["LNCS"],"day":"05","language":[{"iso":"eng"}],"year":"2011","publication_status":"published","doi":"10.1007/978-3-642-25318-8_16","date_published":"2011-12-05T00:00:00Z","volume":7078,"date_created":"2018-12-11T12:02:20Z","ec_funded":1,"page":"188 - 203"},{"publication":"NIPS Proceedings","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2011","date_created":"2018-12-11T12:02:21Z","volume":24,"date_published":"2011-12-01T00:00:00Z","page":"1827 - 1835","oa_version":"None","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."}],"intvolume":" 24","month":"12","publisher":"Neural Information Processing Systems Foundation","scopus_import":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835.","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.","mla":"Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.” NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation, 2011, pp. 1827–35."},"date_updated":"2021-01-12T07:42:15Z","department":[{"_id":"HeEd"}],"title":"Probabilistic joint image segmentation and labeling","publist_id":"3381","author":[{"id":"29F89302-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian","last_name":"Ion","full_name":"Ion, Adrian"},{"first_name":"Joao","last_name":"Carreira","full_name":"Carreira, Joao"},{"first_name":"Cristian","last_name":"Sminchisescu","full_name":"Sminchisescu, Cristian"}],"_id":"3266","status":"public","conference":{"start_date":"2011-12-12","location":"Granada, Spain","end_date":"2011-12-14","name":"NIPS: Neural Information Processing Systems"},"type":"conference"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268.","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"},"title":"Perceptual global illumination cancellation in complex projection environments","author":[{"first_name":"Yu","full_name":"Sheng, Yu","last_name":"Sheng"},{"last_name":"Cutler","full_name":"Cutler, Barbara","first_name":"Barbara"},{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen"},{"full_name":"Nasman, Joshua","last_name":"Nasman","first_name":"Joshua"}],"publist_id":"3377","article_processing_charge":"No","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"day":"19","publication":"Computer Graphics Forum","year":"2011","date_published":"2011-07-19T00:00:00Z","doi":"10.1111/j.1467-8659.2011.01985.x","date_created":"2018-12-11T12:02:22Z","page":"1261 - 1268","_id":"3269","status":"public","type":"journal_article","article_type":"original","date_updated":"2021-01-12T07:42:16Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","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."}],"month":"07","intvolume":" 30","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":30},{"year":"2011","publication_status":"published","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}],"day":"14","page":"425 - 448","date_created":"2018-12-11T12:02:21Z","date_published":"2011-01-14T00:00:00Z","volume":45,"doi":"10.1007/s00454-010-9322-8","issue":"3","related_material":{"record":[{"id":"10909","status":"public","relation":"earlier_version"}]},"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."}],"oa_version":"None","publisher":"Springer","scopus_import":1,"quality_controlled":"1","intvolume":" 45","month":"01","citation":{"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.","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.","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete & Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011.","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"},"date_updated":"2023-02-21T16:07:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3379","author":[{"full_name":"Chen, Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"first_name":"Daniel","last_name":"Freedman","full_name":"Freedman, Daniel"}],"department":[{"_id":"HeEd"}],"title":"Hardness results for homology localization","_id":"3267","type":"journal_article","status":"public"},{"publist_id":"3378","author":[{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"},{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen"}],"title":"Algebraic topology for computer vision","citation":{"ista":"Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer Vision. Computer Science, Technology and Applications, , 239–268.","chicago":"Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” In Computer Vision, 239–68. Nova Science Publishers, 2011.","short":"D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011, pp. 239–268.","ieee":"D. Freedman and C. Chen, “Algebraic topology for computer vision,” in Computer Vision, Nova Science Publishers, 2011, pp. 239–268.","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.","mla":"Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” Computer Vision, Nova Science Publishers, 2011, pp. 239–68."},"date_updated":"2021-01-12T07:42:16Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"book_chapter","status":"public","_id":"3268","page":"239 - 268","date_created":"2018-12-11T12:02:22Z","date_published":"2011-11-30T00:00:00Z","publication_status":"published","year":"2011","publication":"Computer Vision","language":[{"iso":"eng"}],"day":"30","main_file_link":[{"url":"http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf"}],"alternative_title":["Computer Science, Technology and Applications"],"quality_controlled":"1","publisher":"Nova Science Publishers","month":"11","abstract":[{"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. ","lang":"eng"}],"oa_version":"None"},{"publication_status":"published","file":[{"file_size":1984567,"date_updated":"2020-07-14T12:46:06Z","creator":"dernst","file_name":"2011_PLOS_Smutny.PDF","date_created":"2019-05-10T10:51:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6399","checksum":"57a5eb11dd05241c48c44f492b3ec3ac"}],"language":[{"iso":"eng"}],"volume":6,"issue":"7","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."}],"oa_version":"Published Version","month":"07","intvolume":" 6","date_updated":"2021-01-12T07:42:25Z","ddc":["570"],"department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:46:06Z","_id":"3288","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2011","day":"22","publication":"PLoS One","date_published":"2011-07-22T00:00:00Z","doi":"10.1371/journal.pone.0022458","date_created":"2018-12-11T12:02:28Z","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.","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"citation":{"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).","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.","short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3357","author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael"},{"full_name":"Wu, Selwin","last_name":"Wu","first_name":"Selwin"},{"first_name":"Guillermo","full_name":"Gomez, Guillermo","last_name":"Gomez"},{"first_name":"Sabine","full_name":"Mangold, Sabine","last_name":"Mangold"},{"first_name":"Alpha","last_name":"Yap","full_name":"Yap, Alpha"},{"full_name":"Hamilton, Nicholas","last_name":"Hamilton","first_name":"Nicholas"}],"title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens"},{"_id":"3286","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","status":"public","citation":{"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.","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.","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.","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","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","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."},"date_updated":"2021-01-12T07:42:24Z","extern":1,"author":[{"first_name":"Julian","last_name":"Weghuber","full_name":"Weghuber, Julian"},{"full_name":"Aichinger, Michael C.","last_name":"Aichinger","first_name":"Michael"},{"full_name":"Brameshuber, Mario","last_name":"Brameshuber","first_name":"Mario"},{"first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","full_name":"Stefan Wieser","orcid":"0000-0002-2670-2217"},{"last_name":"Ruprecht","orcid":"0000-0003-4088-8633","full_name":"Verena Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Birgit","full_name":"Plochberger, Birgit","last_name":"Plochberger"},{"first_name":"Josef","full_name":"Madl, Josef","last_name":"Madl"},{"full_name":"Horner, Andreas","last_name":"Horner","first_name":"Andreas"},{"first_name":"Siegfried","full_name":"Reipert, Siegfried","last_name":"Reipert"},{"first_name":"Karl","last_name":"Lohner","full_name":"Lohner, Karl"},{"first_name":"Tamas","full_name":"Henics, Tamas","last_name":"Henics"},{"full_name":"Schuetz, Gerhard J","last_name":"Schuetz","first_name":"Gerhard"}],"publist_id":"3359","title":"Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells","abstract":[{"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.","lang":"eng"}],"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. ","quality_controlled":0,"publisher":"Elsevier","intvolume":" 1808","month":"10","year":"2011","publication_status":"published","publication":"Biochimica et Biophysica Acta (BBA) - Biomembranes","day":"01","page":"2581 - 2590","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2018-12-11T12:02:28Z","volume":1808,"doi":"10.1016/j.bbamem.2011.06.007","issue":"10","date_published":"2011-10-01T00:00:00Z"},{"type":"journal_article","status":"public","_id":"3287","publist_id":"3358","author":[{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht"},{"first_name":"Markus","last_name":"Axmann","full_name":"Axmann, Markus"},{"orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"last_name":"Schuetz","full_name":"Schuetz, Gerhard","first_name":"Gerhard"}],"title":"What can we learn from single molecule trajectories?","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"citation":{"short":"V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide Science 12 (2011) 714–724.","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.","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","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.","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.","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."},"date_updated":"2021-01-12T07:42:24Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"quality_controlled":"1","publisher":"Bentham Science Publishers","month":"12","intvolume":" 12","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."}],"oa_version":"None","page":"714 - 724","date_published":"2011-12-01T00:00:00Z","volume":12,"issue":"8","doi":"10.2174/138920311798841753","date_created":"2018-12-11T12:02:28Z","year":"2011","publication_status":"published","day":"01","publication":"Current Protein & Peptide Science","language":[{"iso":"eng"}]},{"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."}],"oa_version":"None","acknowledgement":"Y 250-B03/Austrian Science Fund FWF/Austria","publisher":"Biophysical Society","month":"06","intvolume":" 100","publication_status":"published","year":"2011","day":"08","publication":"Biophysical Journal","language":[{"iso":"eng"}],"page":"2839 - 2845","issue":"11","date_published":"2011-06-08T00:00:00Z","volume":100,"doi":"10.1016/j.bpj.2011.04.035","date_created":"2018-12-11T12:02:27Z","_id":"3285","type":"journal_article","status":"public","citation":{"short":"V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011) 2839–2845.","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.","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","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","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.","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.","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."},"date_updated":"2021-01-12T07:42:23Z","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3360","author":[{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","last_name":"Wieser"},{"last_name":"Marguet","full_name":"Marguet, Didier","first_name":"Didier"},{"full_name":"Schuetz, Gerhard","last_name":"Schuetz","first_name":"Gerhard"}],"title":"Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes"},{"title":"Static scheduling in clouds","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:06Z","publist_id":"3338","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Singh, Anmol","last_name":"Singh","first_name":"Anmol","id":"72A86902-E99F-11E9-9F62-915534D1B916"},{"last_name":"Singh","full_name":"Singh, Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu"},{"last_name":"Wies","full_name":"Wies, Thomas","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","last_name":"Zufferey","first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000","005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:31Z","citation":{"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.","ama":"Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds. In: USENIX; 2011:1-6.","short":"T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6.","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.","mla":"Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 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.","chicago":"Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey. “Static Scheduling in Clouds,” 1–6. USENIX, 2011."},"status":"public","pubrep_id":"90","type":"conference","conference":{"end_date":"2011-06-15","start_date":"2011-06-14","name":"HotCloud: Workshop on Hot Topics in Cloud Computing"},"_id":"3302","date_published":"2011-06-14T00:00:00Z","date_created":"2018-12-11T12:02:33Z","page":"1 - 6","day":"14","file":[{"file_id":"5333","checksum":"21a461ac004bb535c83320fe79b30375","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:14Z","file_name":"IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf","date_updated":"2020-07-14T12:46:06Z","file_size":232770,"creator":"system"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication_status":"published","year":"2011","month":"06","quality_controlled":"1","publisher":"USENIX","oa":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:46:06Z","title":"Tail approximation for the chemical master equation","department":[{"_id":"ToHe"}],"author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Maria","full_name":"Mateescu, Maria","last_name":"Mateescu"}],"publist_id":"3339","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ddc":["005","570"],"date_updated":"2021-01-12T07:42:30Z","citation":{"mla":"Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical Master Equation. Tampere International Center for Signal Processing, 2011.","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.","short":"T.A. Henzinger, M. Mateescu, in:, 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.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011.","ista":"Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP)."},"pubrep_id":"91","status":"public","conference":{"name":"WCSB: Workshop on Computational Systems Biology (TICSP)"},"type":"conference","_id":"3301","date_created":"2018-12-11T12:02:33Z","date_published":"2011-01-01T00:00:00Z","language":[{"iso":"eng"}],"file":[{"file_id":"5331","checksum":"aa4d7a832a5419e6c0090650ebff2b9a","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:12Z","file_name":"IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf","date_updated":"2020-07-14T12:46:06Z","file_size":240820,"creator":"system"}],"day":"01","year":"2011","publication_status":"published","has_accepted_license":"1","month":"01","oa":1,"quality_controlled":"1","publisher":"Tampere International Center for Signal Processing","oa_version":"Submitted Version","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."}]},{"title":"Propagation models for computing biochemical reaction networks","author":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria"}],"publist_id":"3341","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","short":"T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.","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."},"date_published":"2011-09-21T00:00:00Z","doi":"10.1145/2037509.2037510","date_created":"2018-12-11T12:02:32Z","page":"1 - 3","day":"21","has_accepted_license":"1","year":"2011","quality_controlled":"1","publisher":"Springer","oa":1,"file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"ToHe"}],"ddc":["000","004"],"date_updated":"2021-01-12T07:42:29Z","status":"public","pubrep_id":"92","type":"conference","conference":{"start_date":"2011-09-21","end_date":"2011-09-23","location":"Paris, France","name":"CMSB: Computational Methods in Systems Biology"},"_id":"3299","file":[{"file_name":"IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf","date_created":"2018-12-12T10:07:50Z","file_size":255780,"date_updated":"2020-07-14T12:46:06Z","creator":"system","file_id":"4649","checksum":"7f5c65509db1a9fb049abedd9663ed06","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"09","scopus_import":1,"oa_version":"Submitted Version","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."}]},{"date_updated":"2021-01-12T07:42:36Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"3316","status":"public","type":"conference","conference":{"name":" SIES: International Symposium on Industrial Embedded Systems","end_date":"2011-06-17","location":"Vasteras, Sweden","start_date":"2011-06-15"},"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"oa_version":"Published Version","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."}],"month":"07","scopus_import":1,"main_file_link":[{"url":"https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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.","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.","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."},"title":"Specification-centered robustness","publist_id":"3323","author":[{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Greimel","full_name":"Greimel, Karin","first_name":"Karin"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"}],"article_processing_charge":"No","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","name":"Design for Embedded Systems"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"day":"14","publication":"6th IEEE International Symposium on Industrial and Embedded Systems","year":"2011","doi":"10.1109/SIES.2011.5953660","date_published":"2011-07-14T00:00:00Z","date_created":"2018-12-11T12:02:38Z","page":"176 - 185","quality_controlled":"1","publisher":"IEEE","oa":1},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:37Z","citation":{"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.","short":"E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22.","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","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","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.","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.","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."},"department":[{"_id":"PeJo"}],"title":"How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses","publist_id":"3321","author":[{"first_name":"Emmanuel","full_name":"Eggermann, Emmanuel","last_name":"Eggermann"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"_id":"3318","status":"public","type":"journal_article","publication":"Nature Neuroscience","language":[{"iso":"eng"}],"day":"04","year":"2011","publication_status":"published","date_created":"2018-12-11T12:02:38Z","date_published":"2011-12-04T00:00:00Z","volume":15,"doi":"10.1038/nn.3002","page":"20 - 22","oa_version":"Submitted Version","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."}],"intvolume":" 15","month":"12","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/","open_access":"1"}],"quality_controlled":"1","publisher":"Nature Publishing Group","scopus_import":1},{"external_id":{"arxiv":["1306.3640"]},"author":[{"full_name":"Van De Weygaert, Rien","last_name":"Van De Weygaert","first_name":"Rien"},{"first_name":"Gert","full_name":"Vegter, Gert","last_name":"Vegter"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"last_name":"Jones","full_name":"Jones, Bernard","first_name":"Bernard"},{"full_name":"Pranav, Pratyush","last_name":"Pranav","first_name":"Pratyush"},{"first_name":"Changbom","full_name":"Park, Changbom","last_name":"Park"},{"first_name":"Wojciech","last_name":"Hellwing","full_name":"Hellwing, Wojciech"},{"first_name":"Bob","last_name":"Eldering","full_name":"Eldering, Bob"},{"last_name":"Kruithof","full_name":"Kruithof, Nico","first_name":"Nico"},{"full_name":"Bos, Patrick","last_name":"Bos","first_name":"Patrick"},{"last_name":"Hidding","full_name":"Hidding, Johan","first_name":"Johan"},{"full_name":"Feldbrugge, Job","last_name":"Feldbrugge","first_name":"Job"},{"full_name":"Ten Have, Eline","last_name":"Ten Have","first_name":"Eline"},{"first_name":"Matti","full_name":"Van Engelen, Matti","last_name":"Van Engelen"},{"first_name":"Manuel","last_name":"Caroli","full_name":"Caroli, Manuel"},{"last_name":"Teillaud","full_name":"Teillaud, Monique","first_name":"Monique"}],"publist_id":"3295","title":"Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web","editor":[{"full_name":"Gavrilova, Marina","last_name":"Gavrilova","first_name":"Marina"},{"last_name":"Tan","full_name":"Tan, Kenneth","first_name":"Kenneth"},{"first_name":"Mir","last_name":"Mostafavi","full_name":"Mostafavi, Mir"}],"citation":{"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.","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","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.","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"60 - 101","date_created":"2018-12-11T12:02:44Z","doi":"10.1007/978-3-642-25249-5_3","date_published":"2011-11-09T00:00:00Z","year":"2011","publication":"Transactions on Computational Science XIV","day":"09","oa":1,"publisher":"Springer","quality_controlled":"1","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:42:44Z","type":"book_chapter","status":"public","series_title":"Special Issue on Voronoi Diagrams and Delaunay Triangulation","_id":"3335","volume":6970,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1306.3640","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 6970","month":"11","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint"},{"status":"public","conference":{"name":"SCG: Symposium on Computational Geometry","start_date":"2011-06-13","location":"Paris, France","end_date":"2011-06-15"},"type":"conference","_id":"3329","title":"Deconstructing approximate offsets","department":[{"_id":"HeEd"}],"author":[{"last_name":"Berberich","full_name":"Berberich, Eric","first_name":"Eric"},{"last_name":"Halperin","full_name":"Halperin, Dan","first_name":"Dan"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roza","full_name":"Pogalnikova, Roza","last_name":"Pogalnikova"}],"publist_id":"3306","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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.","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."},"date_updated":"2023-02-23T11:12:57Z","month":"06","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1109.2158","open_access":"1"}],"scopus_import":1,"quality_controlled":"1","publisher":"ACM","oa_version":"Preprint","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."}],"date_created":"2018-12-11T12:02:42Z","related_material":{"record":[{"id":"3115","status":"public","relation":"later_version"}]},"date_published":"2011-06-13T00:00:00Z","doi":"10.1145/1998196.1998225","page":"187 - 196","language":[{"iso":"eng"}],"publication":"Proceedings of the twenty-seventh annual symposium on Computational geometry","day":"13","year":"2011","publication_status":"published"},{"file_date_updated":"2020-07-14T12:46:08Z","department":[{"_id":"HeEd"}],"ddc":["500"],"date_updated":"2021-01-12T07:42:43Z","status":"public","article_type":"original","type":"journal_article","_id":"3332","issue":"3","volume":27,"language":[{"iso":"eng"}],"file":[{"checksum":"a63a1e3e885dcc68f1e3dea68dfbe213","file_id":"7869","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-19T16:11:36Z","file_name":"2011_GraphsCombi_Kerber.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:08Z","file_size":143976}],"publication_status":"published","intvolume":" 27","month":"03","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"title":"A note on the complexity of real algebraic hypersurfaces","article_processing_charge":"No","author":[{"last_name":"Kerber","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Sagraloff, Michael","last_name":"Sagraloff"}],"publist_id":"3301","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kerber M, Sagraloff M. 2011. A note on the complexity of real algebraic hypersurfaces. Graphs and Combinatorics. 27(3), 419–430.","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.","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","short":"M. Kerber, M. Sagraloff, Graphs and Combinatorics 27 (2011) 419–430.","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.","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."},"date_created":"2018-12-11T12:02:43Z","doi":"10.1007/s00373-011-1020-7","date_published":"2011-03-17T00:00:00Z","page":"419 - 430","publication":"Graphs and Combinatorics","day":"17","year":"2011","has_accepted_license":"1","oa":1,"publisher":"Springer","quality_controlled":"1"},{"main_file_link":[{"url":"http://arxiv.org/abs/1104.1362","open_access":"1"}],"oa":1,"scopus_import":1,"publisher":"Springer","quality_controlled":"1","month":"06","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."}],"oa_version":"Preprint","page":"209 - 216","date_created":"2018-12-11T12:02:43Z","date_published":"2011-06-08T00:00:00Z","doi":"10.1145/1993886.1993920","publication_status":"published","year":"2011","language":[{"iso":"eng"}],"day":"08","conference":{"name":"ISSAC: International Symposium on Symbolic and Algebraic Computation","end_date":"2011-06-11","location":"California, USA","start_date":"2011-06-08"},"type":"conference","status":"public","_id":"3330","external_id":{"arxiv":["1104.1362"]},"article_processing_charge":"No","author":[{"first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","last_name":"Kerber"},{"first_name":"Michael","full_name":"Sagraloff, Michael","last_name":"Sagraloff"}],"publist_id":"3304","department":[{"_id":"HeEd"}],"title":"Root refinement for real polynomials","date_updated":"2021-01-12T07:42:42Z","citation":{"mla":"Kerber, Michael, and Michael Sagraloff. Root Refinement for Real Polynomials. Springer, 2011, pp. 209–16, 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","ama":"Kerber M, Sagraloff M. Root refinement for real polynomials. In: Springer; 2011:209-216. doi:10.1145/1993886.1993920","short":"M. Kerber, M. Sagraloff, in:, Springer, 2011, pp. 209–216.","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.","chicago":"Kerber, Michael, and Michael Sagraloff. “Root Refinement for Real Polynomials,” 209–16. Springer, 2011. https://doi.org/10.1145/1993886.1993920.","ista":"Kerber M, Sagraloff M. 2011. Root refinement for real polynomials. ISSAC: International Symposium on Symbolic and Algebraic Computation, 209–216."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"status":"public","type":"conference","conference":{"start_date":"2011-06-13","location":"Paris, France","end_date":"2011-06-15","name":"SCG: Symposium on Computational Geometry"},"_id":"3328","title":"A generic algebraic kernel for non linear geometric applications","department":[{"_id":"HeEd"}],"author":[{"full_name":"Berberich, Eric","last_name":"Berberich","first_name":"Eric"},{"full_name":"Hemmer, Michael","last_name":"Hemmer","first_name":"Michael"},{"last_name":"Kerber","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"publist_id":"3307","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:41Z","citation":{"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.","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.","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.","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"},"month":"06","publisher":"ACM","scopus_import":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/inria-00480031/file/RR-7274.pdf"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"date_published":"2011-06-13T00:00:00Z","doi":"10.1145/1998196.1998224","date_created":"2018-12-11T12:02:42Z","page":"179 - 186","day":"13","language":[{"iso":"eng"}],"year":"2011","publication_status":"published"},{"article_type":"letter_note","type":"journal_article","status":"public","_id":"3334","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pach","full_name":"Pach, János","first_name":"János"},{"full_name":"Ziegler, Günter","last_name":"Ziegler","first_name":"Günter"}],"publist_id":"3297","department":[{"_id":"HeEd"}],"title":"Letter from the new editors-in-chief","date_updated":"2021-01-12T07:42:44Z","citation":{"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.","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.","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","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","short":"H. Edelsbrunner, J. Pach, G. Ziegler, Discrete & Computational Geometry 45 (2011) 1–2.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer","scopus_import":1,"month":"01","intvolume":" 45","oa_version":"None","page":"1 - 2","issue":"1","date_published":"2011-01-01T00:00:00Z","doi":"10.1007/s00454-010-9313-9","volume":45,"date_created":"2018-12-11T12:02:44Z","publication_status":"published","year":"2011","day":"01","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}]},{"ec_funded":1,"issue":"4","volume":33,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:45Z","file_name":"IST-2012-85-v1+1_A_theory_of_synchronous_relational_interfaces.pdf","creator":"system","date_updated":"2020-07-14T12:46:09Z","file_size":775662,"checksum":"5d44a8aa81e33210649beae507602138","file_id":"5235","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 33","month":"07","scopus_import":1,"oa_version":"Submitted Version","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."}],"file_date_updated":"2020-07-14T12:46:09Z","department":[{"_id":"ToHe"}],"ddc":["000","005"],"date_updated":"2021-01-12T07:42:52Z","pubrep_id":"85","status":"public","type":"journal_article","_id":"3353","date_created":"2018-12-11T12:02:51Z","date_published":"2011-07-01T00:00:00Z","doi":"10.1145/1985342.1985345","publication":"ACM Transactions on Programming Languages and Systems (TOPLAS)","day":"01","year":"2011","has_accepted_license":"1","oa":1,"publisher":"ACM","quality_controlled":"1","title":"A theory of synchronous relational interfaces","publist_id":"3263","author":[{"first_name":"Stavros","last_name":"Tripakis","full_name":"Tripakis, Stavros"},{"first_name":"Ben","last_name":"Lickly","full_name":"Lickly, Ben"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Lee","full_name":"Lee, Edward","first_name":"Edward"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, ACM Transactions on Programming Languages and Systems (TOPLAS) 33 (2011).","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","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","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."},"project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"14"},{"title":"Quantitative evaluation of BFT protocols","author":[{"id":"584C6850-E996-11E9-805B-F01764644770","first_name":"Raluca","last_name":"Halalai","full_name":"Halalai, Raluca"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Singh","full_name":"Singh, Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu"}],"publist_id":"3260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Halalai, Raluca, et al. Quantitative Evaluation of BFT Protocols. IEEE, 2011, pp. 255–64, doi:10.1109/QEST.2011.40.","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","short":"R. Halalai, T.A. Henzinger, V. Singh, in:, IEEE, 2011, pp. 255–264.","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.","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.","ista":"Halalai R, Henzinger TA, Singh V. 2011. Quantitative evaluation of BFT protocols. QEST: Quantitative Evaluation of Systems, 255–264."},"publisher":"IEEE","quality_controlled":"1","oa":1,"date_published":"2011-10-13T00:00:00Z","doi":"10.1109/QEST.2011.40","date_created":"2018-12-11T12:02:51Z","page":"255 - 264","day":"13","has_accepted_license":"1","year":"2011","status":"public","pubrep_id":"84","type":"conference","conference":{"name":"QEST: Quantitative Evaluation of Systems","start_date":"2011-09-05","location":"Aachen, Germany","end_date":"2011-09-08"},"_id":"3355","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:09Z","ddc":["000","004"],"date_updated":"2021-01-12T07:42:53Z","month":"10","scopus_import":1,"oa_version":"Submitted Version","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."}],"file":[{"creator":"system","file_size":272017,"date_updated":"2020-07-14T12:46:09Z","file_name":"IST-2012-84-v1+1_Quantitative_evaluation_of_BFT_protocols.pdf","date_created":"2018-12-12T10:07:49Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4648","checksum":"4dc8750ab7921f51de992000b13d1b01"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"publication_status":"published","year":"2011","language":[{"iso":"eng"}],"day":"01","page":"145 - 159","date_created":"2018-12-11T12:02:49Z","date_published":"2011-01-01T00:00:00Z","volume":6919,"doi":"10.1007/978-3-642-24310-3_11","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."}],"oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"Springer","alternative_title":["LNCS"],"intvolume":" 6919","month":"01","citation":{"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.","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","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.","short":"K. Chatterjee, R. Majumdar, in:, U. Fahrenberg, S. Tripakis (Eds.), Springer, 2011, pp. 145–159.","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.","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."},"date_updated":"2021-01-12T07:42:51Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar","last_name":"Majumdar"}],"publist_id":"3271","editor":[{"first_name":"Uli","last_name":"Fahrenberg","full_name":"Fahrenberg, Uli"},{"full_name":"Tripakis, Stavros","last_name":"Tripakis","first_name":"Stavros"}],"title":"Minimum attention controller synthesis for omega regular objectives","department":[{"_id":"KrCh"}],"_id":"3350","conference":{"location":"Aalborg, Denmark","end_date":"2011-09-23","start_date":"2011-09-21","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"type":"conference","status":"public","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}]},{"_id":"3351","conference":{"end_date":"2011-08-25","location":"Oslo, Norway","start_date":"2011-08-22","name":"FCT: Fundamentals of Computation Theory"},"type":"conference","status":"public","date_updated":"2021-01-12T07:42:52Z","department":[{"_id":"KrCh"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1104.3211","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 6914","month":"04","publication_status":"published","language":[{"iso":"eng"}],"volume":6914,"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"citation":{"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.","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","short":"K. Chatterjee, L. Doyen, R. Singh, in:, O. Owe, M. Steffen, J.A. Telle (Eds.), Springer, 2011, pp. 148–159.","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.","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.","ista":"Chatterjee K, Doyen L, Singh R. 2011. On memoryless quantitative objectives. FCT: Fundamentals of Computation Theory, LNCS, vol. 6914, 148–159."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"3270","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Singh","full_name":"Singh, Rohit","first_name":"Rohit"}],"title":"On memoryless quantitative objectives","editor":[{"full_name":"Owe, Olaf","last_name":"Owe","first_name":"Olaf"},{"full_name":"Steffen, Martin","last_name":"Steffen","first_name":"Martin"},{"first_name":"Jan Arne","full_name":"Telle, Jan Arne","last_name":"Telle"}],"oa":1,"quality_controlled":"1","publisher":"Springer","year":"2011","day":"16","page":"148 - 159","date_created":"2018-12-11T12:02:50Z","date_published":"2011-04-16T00:00:00Z","doi":"10.1007/978-3-642-22953-4_13"},{"month":"07","intvolume":" 12","quality_controlled":"1","scopus_import":1,"publisher":"ACM","oa_version":"None","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."}],"volume":12,"doi":"10.1145/1970398.1970404","issue":"4","date_published":"2011-07-04T00:00:00Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"2054"}]},"date_created":"2018-12-11T12:02:51Z","day":"04","language":[{"iso":"eng"}],"publication":"ACM Transactions on Computational Logic (TOCL)","publication_status":"published","year":"2011","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"journal_article","article_number":"28","_id":"3354","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Qualitative concurrent parity games","publist_id":"3262","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"De Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, ACM Transactions on Computational Logic (TOCL) 12 (2011).","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"},"date_updated":"2023-02-23T10:26:18Z"},{"_id":"3349","type":"conference","conference":{"start_date":"2011-06-15","end_date":"2011-06-17","location":"Minori, Italy","name":"GandALF: Games, Automata, Logic, and Formal Verification"},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","date_updated":"2021-01-12T07:42:51Z","citation":{"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.","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.","short":"K. Chatterjee, N. Fijalkow, in:, EPTCS, 2011, pp. 74–86.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow","first_name":"Nathanaël"}],"publist_id":"3272","department":[{"_id":"KrCh"}],"title":"A reduction from parity games to simple stochastic games","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["EPTCS"],"scopus_import":1,"publisher":"EPTCS","main_file_link":[{"url":"http://arxiv.org/abs/1106.1232","open_access":"1"}],"oa":1,"month":"06","intvolume":" 54","year":"2011","publication_status":"published","day":"04","language":[{"iso":"eng"}],"page":"74 - 86","volume":54,"date_published":"2011-06-04T00:00:00Z","doi":"10.4204/EPTCS.54.6","date_created":"2018-12-11T12:02:49Z"},{"_id":"335","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T07:42:51Z","citation":{"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.","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.","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","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","short":"M. Ibáñez, J. Fan, W. Li, D. Cadavid, R. Nafria, A. Carrete, A. Cabot, Chemistry of Materials 23 (2011) 3095–3104.","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.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Jiandong","last_name":"Fan","full_name":"Fan, Jiandong"},{"last_name":"Li","full_name":"Li, Wenhua","first_name":"Wenhua"},{"last_name":"Cadavid","full_name":"Cadavid, Doris","first_name":"Doris"},{"first_name":"Raquel","full_name":"Nafria, Raquel","last_name":"Nafria"},{"full_name":"Carrete, Alex","last_name":"Carrete","first_name":"Alex"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"publist_id":"7492","article_processing_charge":"No","title":"Means and limits of control of the shell parameters in hollow nanoparticles obtained by the Kirkendall effect","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. "}],"oa_version":"None","publisher":"American Chemical Society","quality_controlled":"1","month":"05","intvolume":" 23","publication_status":"published","year":"2011","day":"24","language":[{"iso":"eng"}],"publication":"Chemistry of Materials","page":"3095 - 3104","date_published":"2011-05-24T00:00:00Z","volume":23,"issue":"12","doi":"10.1021/cm2006633","date_created":"2018-12-11T11:45:53Z"},{"_id":"3352","type":"journal_article","status":"public","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_updated":"2021-01-12T07:42:52Z","citation":{"ista":"Fisher J, Harel D, Henzinger TA. 2011. Biology as reactivity. Communications of the ACM. 54(10), 72–82.","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.","apa":"Fisher, J., Harel, D., & Henzinger, T. A. (2011). Biology as reactivity. Communications of the ACM. ACM. https://doi.org/10.1145/2001269.2001289","ama":"Fisher J, Harel D, Henzinger TA. Biology as reactivity. Communications of the ACM. 2011;54(10):72-82. doi: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.","short":"J. Fisher, D. Harel, T.A. Henzinger, Communications of the ACM 54 (2011) 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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jasmin","last_name":"Fisher","full_name":"Fisher, Jasmin"},{"first_name":"David","full_name":"Harel, David","last_name":"Harel"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"publist_id":"3267","department":[{"_id":"ToHe"}],"title":"Biology as reactivity","abstract":[{"text":"Exploring the connection of biology with reactive systems to better understand living systems.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"ACM","intvolume":" 54","month":"10","year":"2011","publication_status":"published","publication":"Communications of the ACM","language":[{"iso":"eng"}],"day":"01","page":"72 - 82","date_created":"2018-12-11T12:02:50Z","ec_funded":1,"volume":54,"date_published":"2011-10-01T00:00:00Z","issue":"10","doi":"10.1145/2001269.2001289"},{"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"01","intvolume":" 6901","scopus_import":1,"alternative_title":["LNCS"],"file":[{"file_name":"2011_CONCUR_Fisher.pdf","date_created":"2020-05-19T16:17:48Z","file_size":337125,"date_updated":"2020-07-14T12:46:10Z","creator":"dernst","file_id":"7870","checksum":"6bf2453d8e52e979ddb58d17325bad26","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6901,"ec_funded":1,"_id":"3362","status":"public","type":"conference","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2011-09-06","location":"Aachen, Germany","end_date":"2011-09-09"},"ddc":["000"],"date_updated":"2021-01-12T07:42:57Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:10Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"day":"01","has_accepted_license":"1","year":"2011","doi":"10.1007/978-3-642-23217-6_27","date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T12:02:54Z","page":"404 - 418","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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.","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.","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."},"title":"Dynamic reactive modules","publist_id":"3253","author":[{"full_name":"Fisher, Jasmin","last_name":"Fisher","first_name":"Jasmin"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"last_name":"Piterman","full_name":"Piterman, Nir","first_name":"Nir"},{"last_name":"Singh","full_name":"Singh, Anmol","first_name":"Anmol"},{"first_name":"Moshe","last_name":"Vardi","full_name":"Vardi, Moshe"}],"article_processing_charge":"No"},{"status":"public","pubrep_id":"77","type":"conference","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2011-04-03","location":"Saarbrucken, Germany","start_date":"2011-03-26"},"_id":"3365","file_date_updated":"2020-07-14T12:46:10Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["000","005"],"date_updated":"2021-01-12T07:42:58Z","month":"09","intvolume":" 6605","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"volume":6605,"file":[{"file_name":"IST-2012-77-v1+1_QUASY-_quantitative_synthesis_tool.pdf","date_created":"2018-12-12T10:13:37Z","creator":"system","file_size":475661,"date_updated":"2020-07-14T12:46:10Z","checksum":"762e52eb296f6dbfbf2a75d98b8ebaee","file_id":"5022","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"QUASY: quantitative synthesis tool","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Barbara","last_name":"Jobstmann","full_name":"Jobstmann, Barbara"},{"first_name":"Rohit","last_name":"Singh","full_name":"Singh, Rohit"}],"publist_id":"3248","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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"},"publisher":"Springer","quality_controlled":"1","oa":1,"date_published":"2011-09-29T00:00:00Z","doi":"10.1007/978-3-642-19835-9_24","date_created":"2018-12-11T12:02:55Z","page":"267 - 271","day":"29","has_accepted_license":"1","year":"2011"},{"day":"13","language":[{"iso":"eng"}],"publication_status":"published","year":"2011","date_published":"2011-06-13T00:00:00Z","doi":"10.1145/1998196.1998228","related_material":{"record":[{"relation":"later_version","id":"2939","status":"public"}]},"date_created":"2018-12-11T12:02:56Z","page":"207 - 216","oa_version":"None","abstract":[{"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.","lang":"eng"}],"month":"06","scopus_import":1,"publisher":"ACM","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","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.","short":"C. Chen, M. Kerber, in:, ACM, 2011, pp. 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.","ista":"Chen C, Kerber M. 2011. An output sensitive algorithm for persistent homology. SoCG: Symposium on Computational Geometry, 207–216.","chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology,” 207–16. 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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.","lang":"eng"}],"month":"04","publisher":"ArXiv","main_file_link":[{"url":"https://arxiv.org/abs/1104.0127","open_access":"1"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Mathieu Tracol. “The Decidability Frontier for Probabilistic Automata on Infinite Words.” ArXiv, n.d.","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.","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.","ieee":"K. Chatterjee, T. A. Henzinger, and M. Tracol, “The decidability frontier for probabilistic automata on infinite words.” ArXiv.","short":"K. Chatterjee, T.A. Henzinger, M. Tracol, (n.d.)."},"date_updated":"2020-01-21T13:20:24Z","title":"The decidability frontier for probabilistic automata on infinite words","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Tracol","full_name":"Tracol, Mathieu","first_name":"Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3251","external_id":{"arxiv":["1104.0127"]},"_id":"3363","status":"public","project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"type":"preprint"},{"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:43:02Z","status":"public","type":"journal_article","_id":"3372","volume":471,"issue":"7339","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 471","month":"03","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/"}],"scopus_import":1,"pmid":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"title":"Inclusive fitness theory and eusociality","external_id":{"pmid":["21430721"]},"publist_id":"3237","author":[{"last_name":"Abbot","full_name":"Abbot, Patrick","first_name":"Patrick"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"last_name":"Alcock","full_name":"Alcock, John","first_name":"John"},{"full_name":"Alizon, Samuel","last_name":"Alizon","first_name":"Samuel"},{"first_name":"Joao","full_name":"Alpedrinha, Joao","last_name":"Alpedrinha"},{"first_name":"Malte","last_name":"Andersson","full_name":"Andersson, Malte"},{"first_name":"Jean","last_name":"Andre","full_name":"Andre, Jean"},{"full_name":"Van Baalen, Minus","last_name":"Van Baalen","first_name":"Minus"},{"first_name":"Francois","full_name":"Balloux, Francois","last_name":"Balloux"},{"last_name":"Balshine","full_name":"Balshine, Sigal","first_name":"Sigal"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas 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Sébastien","last_name":"Lion","first_name":"Sébastien"},{"last_name":"Lyon","full_name":"Lyon, Bruce","first_name":"Bruce"},{"first_name":"James","last_name":"Marshall","full_name":"Marshall, James"},{"first_name":"Richard","last_name":"Mcelreath","full_name":"Mcelreath, Richard"},{"first_name":"Yannis","last_name":"Michalakis","full_name":"Michalakis, Yannis"},{"last_name":"Michod","full_name":"Michod, Richard","first_name":"Richard"},{"full_name":"Mock, Douglas","last_name":"Mock","first_name":"Douglas"},{"full_name":"Monnin, Thibaud","last_name":"Monnin","first_name":"Thibaud"},{"full_name":"Montgomerie, Robert","last_name":"Montgomerie","first_name":"Robert"},{"last_name":"Moore","full_name":"Moore, Allen","first_name":"Allen"},{"full_name":"Mueller, Ulrich","last_name":"Mueller","first_name":"Ulrich"},{"full_name":"Noë, Ronald","last_name":"Noë","first_name":"Ronald"},{"first_name":"Samir","last_name":"Okasha","full_name":"Okasha, Samir"},{"first_name":"Pekka","full_name":"Pamilo, Pekka","last_name":"Pamilo"},{"first_name":"Geoff","last_name":"Parker","full_name":"Parker, Geoff"},{"last_name":"Pedersen","full_name":"Pedersen, Jes","first_name":"Jes"},{"last_name":"Pen","full_name":"Pen, Ido","first_name":"Ido"},{"full_name":"Pfennig, David","last_name":"Pfennig","first_name":"David"},{"first_name":"David","last_name":"Queller","full_name":"Queller, David"},{"last_name":"Rankin","full_name":"Rankin, Daniel","first_name":"Daniel"},{"first_name":"Sarah","last_name":"Reece","full_name":"Reece, Sarah"},{"last_name":"Reeve","full_name":"Reeve, Hudson","first_name":"Hudson"},{"full_name":"Reuter, Max","last_name":"Reuter","first_name":"Max"},{"last_name":"Roberts","full_name":"Roberts, Gilbert","first_name":"Gilbert"},{"first_name":"Simon","last_name":"Robson","full_name":"Robson, Simon"},{"full_name":"Roze, Denis","last_name":"Roze","first_name":"Denis"},{"full_name":"Rousset, Francois","last_name":"Rousset","first_name":"Francois"},{"full_name":"Rueppell, Olav","last_name":"Rueppell","first_name":"Olav"},{"full_name":"Sachs, Joel","last_name":"Sachs","first_name":"Joel"},{"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"},{"full_name":"Scott Phillips, Tom","last_name":"Scott Phillips","first_name":"Tom"},{"first_name":"Janet","full_name":"Shellmann Sherman, Janet","last_name":"Shellmann Sherman"},{"full_name":"Sherman, Paul","last_name":"Sherman","first_name":"Paul"},{"first_name":"David","full_name":"Shuker, David","last_name":"Shuker"},{"full_name":"Smith, Jeff","last_name":"Smith","first_name":"Jeff"},{"first_name":"Joseph","full_name":"Spagna, Joseph","last_name":"Spagna"},{"first_name":"Beverly","last_name":"Strassmann","full_name":"Strassmann, Beverly"},{"first_name":"Andrew","last_name":"Suarez","full_name":"Suarez, Andrew"},{"first_name":"Liselotte","last_name":"Sundström","full_name":"Sundström, Liselotte"},{"first_name":"Michael","last_name":"Taborsky","full_name":"Taborsky, Michael"},{"first_name":"Peter","last_name":"Taylor","full_name":"Taylor, Peter"},{"full_name":"Thompson, Graham","last_name":"Thompson","first_name":"Graham"},{"full_name":"Tooby, John","last_name":"Tooby","first_name":"John"},{"full_name":"Tsutsui, Neil","last_name":"Tsutsui","first_name":"Neil"},{"last_name":"Tsuji","full_name":"Tsuji, Kazuki","first_name":"Kazuki"},{"full_name":"Turillazzi, Stefano","last_name":"Turillazzi","first_name":"Stefano"},{"full_name":"Úbeda, Francisco","last_name":"Úbeda","first_name":"Francisco"},{"first_name":"Edward","last_name":"Vargo","full_name":"Vargo, Edward"},{"first_name":"Bernard","last_name":"Voelkl","full_name":"Voelkl, Bernard"},{"last_name":"Wenseleers","full_name":"Wenseleers, Tom","first_name":"Tom"},{"first_name":"Stuart","last_name":"West","full_name":"West, Stuart"},{"first_name":"Mary","last_name":"West Eberhard","full_name":"West Eberhard, Mary"},{"full_name":"Westneat, David","last_name":"Westneat","first_name":"David"},{"first_name":"Diane","last_name":"Wiernasz","full_name":"Wiernasz, Diane"},{"full_name":"Wild, Geoff","last_name":"Wild","first_name":"Geoff"},{"last_name":"Wrangham","full_name":"Wrangham, Richard","first_name":"Richard"},{"first_name":"Andrew","last_name":"Young","full_name":"Young, Andrew"},{"first_name":"David","last_name":"Zeh","full_name":"Zeh, David"},{"last_name":"Zeh","full_name":"Zeh, Jeanne","first_name":"Jeanne"},{"last_name":"Zink","full_name":"Zink, Andrew","first_name":"Andrew"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4.","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.","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.","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","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."},"date_created":"2018-12-11T12:02:57Z","doi":"10.1038/nature09831","date_published":"2011-03-23T00:00:00Z","page":"E1 - E4","publication":"Nature","day":"23","year":"2011","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group"},{"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","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.","short":"M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 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.","ista":"Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology and Evolution. 22(6), 724.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3238","author":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Parent","full_name":"Parent, Carole","first_name":"Carole"}],"title":"Cells on the move in Philadelphia","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","year":"2011","has_accepted_license":"1","publication":"Molecular Biology and Evolution","day":"15","page":"724","date_created":"2018-12-11T12:02:57Z","doi":"10.1091/mbc.E10-12-0958","date_published":"2011-03-15T00:00:00Z","_id":"3371","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","article_type":"original","pubrep_id":"373","status":"public","date_updated":"2021-01-12T07:43:01Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:46:11Z","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 22","month":"03","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:46:11Z","file_size":105421,"date_created":"2018-12-12T10:17:29Z","file_name":"IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5283","checksum":"3467986ab7a64e7694ffd1013b5d9da9"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","issue":"6","volume":22},{"date_created":"2018-12-11T12:02:58Z","volume":23,"date_published":"2011-04-01T00:00:00Z","doi":"10.1088/0953-8984/23/15/153102","issue":"15","publication_status":"published","year":"2011","language":[{"iso":"eng"}],"publication":"Journal of Physics: Condensed Matter","day":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1101.4240"}],"oa":1,"quality_controlled":"1","publisher":"IOP Publishing Ltd.","scopus_import":1,"intvolume":" 23","month":"04","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'."}],"oa_version":"Submitted Version","author":[{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Aleksandra","last_name":"Walczak","full_name":"Walczak, Aleksandra"}],"publist_id":"3233","title":"Information transmission in genetic regulatory networks a review","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T07:43:03Z","citation":{"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","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","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.","short":"G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).","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.","ista":"Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"3374","article_number":"153102"},{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024655"}],"scopus_import":1,"intvolume":" 108","month":"01","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"volume":108,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"3368","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T07:43:00Z","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","page":"E9 - E10","date_created":"2018-12-11T12:02:56Z","doi":"10.1073/pnas.1010767108","date_published":"2011-01-18T00:00:00Z","year":"2011","publication":"PNAS","day":"18","external_id":{"pmid":["21212360"]},"author":[{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"id":"260FD49C-E911-11E9-B5EA-D9538404589B","first_name":"Stephanie","last_name":"Möllmert","full_name":"Möllmert, Stephanie"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"publist_id":"3244","title":"Enveloping cell layer differentiation at the surface of zebrafish germ layer tissue explants","citation":{"short":"G. Krens, S. Möllmert, C.-P.J. Heisenberg, PNAS 108 (2011) E9–E10.","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.","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","status":"public","_id":"3370","publist_id":"3241","author":[{"last_name":"Kupczok","full_name":"Kupczok, Anne","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"}],"title":"Consequences of different null models on the tree shape bias of supertree methods","department":[{"_id":"JoBo"}],"date_updated":"2021-01-12T07:43:01Z","citation":{"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.","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","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.","short":"A. Kupczok, Systematic Biology 60 (2011) 218–225.","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.","ista":"Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"url":"http://eprints.cs.univie.ac.at/3226/","open_access":"1"}],"publisher":"Oxford University Press","quality_controlled":"1","intvolume":" 60","month":"03","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."}],"oa_version":"Submitted Version","page":"218 - 225","date_created":"2018-12-11T12:02:57Z","doi":"10.1093/sysbio/syq086","issue":"2","volume":60,"date_published":"2011-03-01T00:00:00Z","publication_status":"published","year":"2011","publication":"Systematic Biology","language":[{"iso":"eng"}],"day":"01"},{"month":"01","intvolume":" 69","publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","oa_version":"None","abstract":[{"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.","lang":"eng"}],"date_published":"2011-01-27T00:00:00Z","doi":"10.1016/j.neuron.2011.01.010","volume":69,"issue":"2","date_created":"2018-12-11T12:02:56Z","page":"185 - 187","day":"27","publication":"Neuron","language":[{"iso":"eng"}],"year":"2011","publication_status":"published","status":"public","type":"journal_article","_id":"3369","title":"The multiple faces of RIM","department":[{"_id":"PeJo"}],"author":[{"first_name":"Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87","full_name":"Pernia-Andrade, Alejandro","last_name":"Pernia-Andrade"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"publist_id":"3243","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:43:00Z","citation":{"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.","ieee":"A. Pernia-Andrade and P. M. Jonas, “The multiple faces of RIM,” Neuron, vol. 69, no. 2. Elsevier, pp. 185–187, 2011.","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 69 (2011) 185–187.","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.","ista":"Pernia-Andrade A, Jonas PM. 2011. The multiple faces of RIM. Neuron. 69(2), 185–187."}},{"type":"journal_article","article_type":"original","status":"public","_id":"3396","file_date_updated":"2020-07-14T12:46:12Z","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T07:43:11Z","ddc":["570"],"scopus_import":1,"intvolume":" 138","month":"09","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"}],"oa_version":"Published Version","volume":138,"issue":"21","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2019-10-07T14:19:42Z","file_name":"2011_Development_Stockinger.pdf","date_updated":"2020-07-14T12:46:12Z","file_size":4672439,"creator":"dernst","checksum":"ca12b79e01ef36c1ef1aea31cf7e7139","file_id":"6930","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"author":[{"id":"261CB030-E90D-11E9-B182-F697D44B663C","first_name":"Petra","full_name":"Stockinger, Petra","last_name":"Stockinger"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"}],"publist_id":"3210","title":"Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube","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","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.","short":"P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Company of Biologists","quality_controlled":"1","page":"4673 - 4683","date_created":"2018-12-11T12:03:06Z","date_published":"2011-09-28T00:00:00Z","doi":"10.1242/dev.071233","year":"2011","has_accepted_license":"1","publication":"Development","day":"28"},{"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"09","intvolume":" 189","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":189,"ec_funded":1,"_id":"3394","status":"public","type":"journal_article","date_updated":"2021-01-12T07:43:11Z","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"day":"01","publication":"Genetics","year":"2011","doi":"10.1534/genetics.111.129817","date_published":"2011-09-01T00:00:00Z","date_created":"2018-12-11T12:03:05Z","page":"227 - 235","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","short":"J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.","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."},"title":"Genetic drift widens the expected cline but narrows the expected cline width","publist_id":"3213","author":[{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}]},{"oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","year":"2011","publication":"Genetics","day":"01","page":"953 - 973","date_created":"2018-12-11T12:03:04Z","doi":"10.1534/genetics.111.127555","date_published":"2011-08-01T00:00:00Z","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Barton NH, Etheridge A. 2011. The relation between reproductive value and genetic contribution. Genetics. 188(4), 953–973.","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.","short":"N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.","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","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","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}],"publist_id":"3217","title":"The relation between reproductive value and genetic contribution","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/"}],"scopus_import":1,"intvolume":" 188","month":"08","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":188,"issue":"4","_id":"3390","type":"journal_article","status":"public","date_updated":"2021-01-12T07:43:09Z","department":[{"_id":"NiBa"}]},{"language":[{"iso":"eng"}],"publication_status":"published","volume":26,"issue":"8","ec_funded":1,"oa_version":"Submitted Version","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"}],"month":"08","intvolume":" 26","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.2854"}],"date_updated":"2021-01-12T07:43:10Z","department":[{"_id":"NiBa"}],"_id":"3391","status":"public","type":"journal_article","day":"01","publication":"Trends in Ecology and Evolution","year":"2011","date_published":"2011-08-01T00:00:00Z","doi":"10.1016/j.tree.2011.04.002","date_created":"2018-12-11T12:03:04Z","page":"424 - 432","quality_controlled":"1","publisher":"Cell Press","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.","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"},"title":"The contribution of statistical physics to evolutionary biology","publist_id":"3216","author":[{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}]},{"intvolume":" 23","month":"10","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188705/"}],"oa":1,"publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"oa_version":"Submitted Version","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."}],"date_created":"2018-12-11T12:03:06Z","issue":"5","date_published":"2011-10-01T00:00:00Z","volume":23,"doi":"10.1016/j.ceb.2011.07.004","page":"508 - 514","language":[{"iso":"eng"}],"publication":"Current Opinion in Cell Biology","day":"01","publication_status":"published","year":"2011","status":"public","type":"journal_article","_id":"3397","department":[{"_id":"CaHe"}],"title":"The role of adhesion energy in controlling cell-cell contacts","author":[{"id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon","orcid":"0000-0002-3688-1474","full_name":"Maître, Jean-Léon","last_name":"Maître"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"publist_id":"3211","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Opinion in Cell Biology 23 (2011) 508–514.","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.","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","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","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."},"date_updated":"2021-01-12T07:43:12Z"},{"department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:46:12Z","date_updated":"2021-01-12T07:43:15Z","ddc":["570","571"],"type":"journal_article","status":"public","pubrep_id":"832","_id":"3405","issue":"232","volume":2,"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:46:12Z","file_size":387654,"date_created":"2018-12-12T10:11:36Z","file_name":"IST-2017-832-v1+1_janovjak.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4891","checksum":"6b68d65aadd97c18d663eb117a0a9d35"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"03","intvolume":" 2","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."}],"oa_version":"Submitted Version","author":[{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"full_name":"Sandoz, Guillaume","last_name":"Sandoz","first_name":"Guillaume"},{"full_name":"Isacoff, Ehud","last_name":"Isacoff","first_name":"Ehud"}],"publist_id":"2997","title":"Modern ionotropic glutamate receptor with a K+ selectivity signature sequence","citation":{"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.","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","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","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.","short":"H.L. Janovjak, G. Sandoz, E. Isacoff, Nature Communications 2 (2011) 1–6.","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.","ista":"Janovjak HL, Sandoz G, Isacoff E. 2011. Modern ionotropic glutamate receptor with a K+ selectivity signature sequence. Nature Communications. 2(232), 1–6."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"1 - 6","date_published":"2011-03-08T00:00:00Z","doi":"10.1038/ncomms1231","date_created":"2018-12-11T12:03:09Z","has_accepted_license":"1","year":"2011","day":"08","publication":"Nature Communications","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1},{"article_processing_charge":"No","publist_id":"7491","author":[{"last_name":"Li","full_name":"Li, Wenhua","first_name":"Wenhua"},{"first_name":"Alexey","full_name":"Shavel, Alexey","last_name":"Shavel"},{"full_name":"Guzman, Roger","last_name":"Guzman","first_name":"Roger"},{"last_name":"Rubio Garcia","full_name":"Rubio Garcia, Javier","first_name":"Javier"},{"first_name":"Cristina","full_name":"Flox, Cristina","last_name":"Flox"},{"last_name":"Fan","full_name":"Fan, Jiandong","first_name":"Jiandong"},{"last_name":"Cadavid","full_name":"Cadavid, Doris","first_name":"Doris"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Joan","last_name":"Morante","full_name":"Morante, Joan"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"title":"Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons","date_updated":"2021-01-12T07:43:17Z","citation":{"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.","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.","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.","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"341","page":"10332 - 10334","date_created":"2018-12-11T11:45:55Z","volume":47,"doi":"10.1039/c1cc13803k","date_published":"2011-10-07T00:00:00Z","issue":"37","year":"2011","publication_status":"published","publication":"Chemical Communications","language":[{"iso":"eng"}],"day":"07","quality_controlled":"1","publisher":"Royal Society of Chemistry (RSC) ","intvolume":" 47","month":"10","abstract":[{"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.","lang":"eng"}],"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.","oa_version":"None"},{"scopus_import":1,"publisher":"Nature Publishing Group","intvolume":" 13","month":"01","abstract":[{"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.","lang":"eng"}],"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.","oa_version":"None","page":"117 - 123","date_created":"2018-12-11T12:03:17Z","doi":"10.1038/ncb2154","date_published":"2011-01-23T00:00:00Z","issue":"2","volume":13,"year":"2011","publication_status":"published","publication":"Nature Cell Biology","language":[{"iso":"eng"}],"day":"23","type":"journal_article","status":"public","_id":"3429","publist_id":"2971","author":[{"first_name":"Nicolas","last_name":"Plachta","full_name":"Plachta, Nicolas"},{"first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"},{"first_name":"Shirley","full_name":"Pease, Shirley","last_name":"Pease"},{"first_name":"Scott","last_name":"Fraser","full_name":"Fraser, Scott"},{"first_name":"Periklis","full_name":"Pantazis, Periklis","last_name":"Pantazis"}],"department":[{"_id":"ToBo"}],"title":"Oct4 kinetics predict cell lineage patterning in the early mammalian embryo","date_updated":"2021-01-12T07:43:24Z","citation":{"short":"N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell Biology 13 (2011) 117–123.","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.","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","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"volume":769,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf","open_access":"1"}],"alternative_title":["Methods in Molecular Biology"],"intvolume":" 769","month":"05","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T07:43:55Z","type":"journal_article","article_type":"original","status":"public","_id":"3505","page":"149 - 165","date_created":"2018-12-11T12:03:41Z","date_published":"2011-05-17T00:00:00Z","doi":"10.1007/978-1-61779-207-6_11","year":"2011","publication":"Cell Migration","day":"17","oa":1,"publisher":"Springer","quality_controlled":"1","article_processing_charge":"No","publist_id":"2882","author":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Tim","full_name":"Lämmermann, Tim","last_name":"Lämmermann"}],"title":"In vitro analysis of chemotactic leukocyte migration in 3D environments","citation":{"ista":"Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 769, 149–165.","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.","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","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","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.","short":"M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492.","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","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."},"title":"Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description","author":[{"last_name":"Palero","full_name":"Palero, Ferran","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","first_name":"Ferran"},{"full_name":"Guerao, Guillermo","last_name":"Guerao","first_name":"Guillermo"},{"last_name":"Clark","full_name":"Clark, Paul","first_name":"Paul"},{"first_name":"Pere","last_name":"Abello","full_name":"Abello, Pere"}],"publist_id":"2443","article_processing_charge":"No","day":"01","publication":"Journal of the Marine Biological Association of the United Kingdom","year":"2011","date_published":"2011-03-01T00:00:00Z","doi":"10.1017/S0025315410000287","date_created":"2018-12-11T12:05:09Z","page":"485 - 492","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"date_updated":"2021-01-12T07:52:10Z","department":[{"_id":"NiBa"}],"_id":"3784","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"2","volume":91,"oa_version":"Published Version","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."}],"month":"03","intvolume":" 91","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf"}]},{"oa_version":"None","acknowledgement":"Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.","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."}],"month":"01","intvolume":" 77","publisher":"Szegedi Tudományegyetem","quality_controlled":"1","day":"01","publication":"Acta Sci. Math. (Szeged)","language":[{"iso":"eng"}],"year":"2011","publication_status":"published","issue":"1-2","volume":77,"date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T12:05:08Z","page":"359 - 367","_id":"3781","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:52:09Z","citation":{"chicago":"Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta Sci. Math. (Szeged). Szegedi Tudományegyetem, 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.","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.","short":"B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367.","apa":"Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Sci. Math. (Szeged). Szegedi Tudományegyetem.","ama":"Fasy BT. The difference in length of curves in R^n. Acta Sci Math (Szeged). 2011;77(1-2):359-367."},"department":[{"_id":"HeEd"}],"title":"The difference in length of curves in R^n","publist_id":"2446","author":[{"full_name":"Fasy, Brittany Terese","last_name":"Fasy","first_name":"Brittany Terese","id":"F65D502E-E68D-11E9-9252-C644099818F6"}]},{"file":[{"creator":"system","date_updated":"2020-07-14T12:46:16Z","file_size":436875,"date_created":"2018-12-12T10:07:42Z","file_name":"IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4640","checksum":"aaf22b4d7bd4277ffe8db532119cf474"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6570,"oa_version":"Submitted Version","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."}],"month":"05","intvolume":" 6570","alternative_title":["LNCS"],"ddc":["000"],"date_updated":"2021-01-12T07:52:15Z","file_date_updated":"2020-07-14T12:46:16Z","department":[{"_id":"HeEd"}],"_id":"3796","series_title":"Dedicated to Hermann Maurer on the Occasion of His 70th Birthday","status":"public","pubrep_id":"539","type":"book_chapter","day":"03","publication":"Rainbow of Computer Science","has_accepted_license":"1","year":"2011","date_published":"2011-05-03T00:00:00Z","doi":"10.1007/978-3-642-19391-0_2","date_created":"2018-12-11T12:05:13Z","page":"20 - 35","publisher":"Springer","quality_controlled":"1","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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."},"title":"Covering and packing with spheres by diagonal distortion in R^n","editor":[{"first_name":"Cristian","full_name":"Calude, Cristian","last_name":"Calude"},{"full_name":"Rozenberg, Grzegorz","last_name":"Rozenberg","first_name":"Grzegorz"},{"last_name":"Salomaa","full_name":"Salomaa, Arto","first_name":"Arto"}],"publist_id":"2427","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"}]},{"issue":"4","related_material":{"record":[{"relation":"earlier_version","id":"3841","status":"public"}]},"volume":22,"publication_status":"published","file":[{"date_created":"2018-12-12T10:08:45Z","file_name":"IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf","date_updated":"2020-07-14T12:46:11Z","file_size":222840,"creator":"system","file_id":"4707","checksum":"df88431872586c773fbcfea37d7b36a2","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"06","intvolume":" 22","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:46:11Z","department":[{"_id":"ToHe"}],"date_updated":"2023-02-23T11:45:03Z","ddc":["000"],"type":"journal_article","status":"public","pubrep_id":"628","_id":"3381","page":"823 - 841","date_published":"2011-06-01T00:00:00Z","doi":"10.1142/S0129054111008441","date_created":"2018-12-11T12:03:00Z","has_accepted_license":"1","year":"2011","day":"01","publication":"IJFCS: International Journal of Foundations of Computer Science","quality_controlled":"1","publisher":"World Scientific Publishing","oa":1,"publist_id":"3226","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Barbara","last_name":"Jobstmann","full_name":"Jobstmann, Barbara"},{"first_name":"Verena","last_name":"Wolf","full_name":"Wolf, Verena"}],"title":"Formalisms for specifying Markovian population models","citation":{"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.","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.","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.","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","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"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"external_id":{"arxiv":["1003.2233"]},"article_processing_charge":"No","author":[{"full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek"},{"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"},{"last_name":"Kapitulnik","full_name":"Kapitulnik, A","first_name":"A"}],"publist_id":"7443","title":"STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3","citation":{"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).","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.","short":"Z. Alpichshev, J.G. Analytis, J.H. Chu, I.R. Fisher, A. Kapitulnik, Physical Review B - Condensed Matter and Materials Physics 84 (2011).","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2018-12-11T11:46:10Z","date_published":"2011-07-21T00:00:00Z","doi":"10.1103/PhysRevB.84.041104","year":"2011","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"21","type":"journal_article","article_type":"original","status":"public","_id":"386","date_updated":"2021-01-12T07:52:44Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1003.2233"}],"intvolume":" 84","month":"07","abstract":[{"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. ","lang":"eng"}],"oa_version":"Preprint","volume":84,"issue":"4","publication_status":"published","language":[{"iso":"eng"}]},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"12","intvolume":" 7","publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"3480e1594bbef25ff7462fa93a8a814e","file_id":"5231","creator":"system","date_updated":"2020-07-14T12:46:07Z","file_size":588863,"date_created":"2018-12-12T10:16:42Z","file_name":"IST-2016-86-v2+1_1011.0688_3_.pdf"}],"language":[{"iso":"eng"}],"volume":7,"issue":"4","related_material":{"record":[{"id":"3876","status":"public","relation":"earlier_version"}]},"license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"_id":"3315","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"status":"public","pubrep_id":"506","date_updated":"2023-02-23T11:46:35Z","ddc":["000","005"],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:07Z","publisher":"International Federation of Computational Logic","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2011","day":"14","publication":"Logical Methods in Computer Science","date_published":"2011-12-14T00:00:00Z","doi":"10.2168/LMCS-7(4:8)2011","date_created":"2018-12-11T12:02:37Z","project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"}],"citation":{"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.","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","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science 7 (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.","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.","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 7(4)."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"publist_id":"3324","title":"Timed parity games: Complexity and robustness"},{"author":[{"first_name":"Bei","full_name":"Wang, Bei","last_name":"Wang"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"full_name":"Morozov, Dmitriy","last_name":"Morozov","first_name":"Dmitriy"}],"publist_id":"2161","department":[{"_id":"HeEd"}],"title":"Computing elevation maxima by searching the Gauss sphere","date_updated":"2021-01-12T07:53:31Z","citation":{"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","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","short":"B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics 16 (2011) 1–13.","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.","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"3965","page":"1 - 13","date_created":"2018-12-11T12:06:09Z","volume":16,"issue":"2.2","date_published":"2011-05-01T00:00:00Z","doi":"10.1145/1963190.1970375","publication_status":"published","year":"2011","publication":"Journal of Experimental Algorithmics","language":[{"iso":"eng"}],"day":"01","publisher":"ACM","quality_controlled":"1","scopus_import":1,"intvolume":" 16","month":"05","abstract":[{"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.","lang":"eng"}],"oa_version":"None"},{"_id":"3086","type":"journal_article","status":"public","date_updated":"2021-01-12T07:40:57Z","citation":{"short":"M. Furutani, N. Sakamoto, S. Yoshida, T. Kajiwara, H. Robert, J. Friml, M. Tasaka, Development 138 (2011) 2069–2078.","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.","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","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","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.","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.","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."},"extern":1,"author":[{"first_name":"Masahiko","full_name":"Furutani, Masahiko","last_name":"Furutani"},{"first_name":"Norihito","last_name":"Sakamoto","full_name":"Sakamoto, Norihito"},{"full_name":"Yoshida, Shuhei","last_name":"Yoshida","first_name":"Shuhei"},{"full_name":"Kajiwara, Takahito","last_name":"Kajiwara","first_name":"Takahito"},{"last_name":"Robert","full_name":"Robert, Hélène S","first_name":"Hélène"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"},{"first_name":"Masao","last_name":"Tasaka","full_name":"Tasaka, Masao"}],"publist_id":"3615","title":"Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers","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."}],"publisher":"Company of Biologists","quality_controlled":0,"intvolume":" 138","month":"05","year":"2011","publication_status":"published","publication":"Development","day":"01","page":"2069 - 2078","date_created":"2018-12-11T12:01:17Z","volume":138,"issue":"10","doi":"10.1242/dev.057745","date_published":"2011-05-01T00:00:00Z"},{"date_published":"2011-05-01T00:00:00Z","volume":23,"issue":"5","doi":"10.1105/tpc.111.083030","date_created":"2018-12-11T12:01:18Z","page":"1920 - 1931","day":"01","publication":"Plant Cell","publication_status":"published","year":"2011","month":"05","intvolume":" 23","publisher":"American Society of Plant Biologists","quality_controlled":0,"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."}],"title":"Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis","publist_id":"3614","author":[{"full_name":"Kitakura, Saeko","last_name":"Kitakura","first_name":"Saeko"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"first_name":"Christian","last_name":"Löfke","full_name":"Löfke, Christian"},{"full_name":"Teichmann, Thomas","last_name":"Teichmann","first_name":"Thomas"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"extern":1,"date_updated":"2021-01-12T07:40:57Z","citation":{"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","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","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.","short":"S. Kitakura, S. Vanneste, S. Robert, C. Löfke, T. Teichmann, H. Tanaka, J. Friml, Plant Cell 23 (2011) 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.","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.","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."},"status":"public","type":"journal_article","_id":"3087"},{"_id":"3085","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T07:40:57Z","citation":{"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.","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.","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.","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.","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"},"title":"Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis","author":[{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"},{"first_name":"Carlos","full_name":"Galván-Ampudia, Carlos S","last_name":"Galván Ampudia"},{"last_name":"Demarsy","full_name":"Demarsy, Emilie","first_name":"Emilie"},{"full_name":"Łangowski, Łukasz","last_name":"Łangowski","first_name":"Łukasz"},{"last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen"},{"last_name":"Fan","full_name":"Fan, Yuanwei","first_name":"Yuanwei"},{"full_name":"Morita, Miyo T","last_name":"Morita","first_name":"Miyo"},{"first_name":"Masao","full_name":"Tasaka, Masao","last_name":"Tasaka"},{"first_name":"Christian","full_name":"Fankhauser, Christian","last_name":"Fankhauser"},{"full_name":"Offringa, Remko","last_name":"Offringa","first_name":"Remko"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"3616","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."}],"intvolume":" 13","month":"04","publisher":"Nature Publishing Group","quality_controlled":0,"publication":"Nature Cell Biology","day":"01","year":"2011","publication_status":"published","date_created":"2018-12-11T12:01:17Z","doi":"10.1038/ncb2208","volume":13,"issue":"4","date_published":"2011-04-01T00:00:00Z","page":"447 - 453"},{"type":"journal_article","status":"public","_id":"3084","author":[{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"last_name":"Feraru","full_name":"Feraru, Mugurel I","first_name":"Mugurel"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"first_name":"Alexandre","last_name":"Martinière","full_name":"Martinière, Alexandre"},{"full_name":"Mouille, Grégory","last_name":"Mouille","first_name":"Grégory"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Vernhettes","full_name":"Vernhettes, Samantha","first_name":"Samantha"},{"full_name":"Runions, John","last_name":"Runions","first_name":"John"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"}],"publist_id":"3618","title":"PIN polarity maintenance by the cell wall in Arabidopsis","date_updated":"2021-01-12T07:40:56Z","citation":{"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.","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.","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","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.","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.","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."},"extern":1,"quality_controlled":0,"publisher":"Cell Press","month":"02","intvolume":" 21","abstract":[{"lang":"eng","text":"\nA 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."}],"page":"338 - 343","issue":"4","volume":21,"doi":"10.1016/j.cub.2011.01.036","date_published":"2011-02-22T00:00:00Z","date_created":"2018-12-11T12:01:17Z","publication_status":"published","year":"2011","day":"22","publication":"Current Biology"},{"publist_id":"3619","author":[{"full_name":"Balla, Jozef","last_name":"Balla","first_name":"Jozef"},{"first_name":"Petr","last_name":"Kalousek","full_name":"Kalousek, Petr"},{"last_name":"Reinöhl","full_name":"Reinöhl, Vilém","first_name":"Vilém"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Stanislav","last_name":"Procházka","full_name":"Procházka, Stanislav"}],"title":"Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth","date_updated":"2021-01-12T07:40:56Z","citation":{"short":"J. Balla, P. Kalousek, V. Reinöhl, J. Friml, S. Procházka, Plant Journal 65 (2011) 571–577.","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.","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","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.","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.","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."},"extern":1,"type":"journal_article","status":"public","_id":"3082","page":"571 - 577","date_created":"2018-12-11T12:01:16Z","volume":65,"date_published":"2011-02-01T00:00:00Z","issue":"4","doi":"10.1111/j.1365-313X.2010.04443.x","year":"2011","publication_status":"published","publication":"Plant Journal","day":"01","quality_controlled":0,"publisher":"Wiley-Blackwell","intvolume":" 65","month":"02","abstract":[{"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.","lang":"eng"}]},{"citation":{"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.","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.","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","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.","short":"D. Robinson, D. Scheuring, S. Naramoto, J. Friml, Plant Cell 23 (2011) 846–849."},"date_updated":"2021-01-12T07:40:56Z","extern":1,"author":[{"last_name":"Robinson","full_name":"Robinson, David G","first_name":"David"},{"first_name":"David","full_name":"Scheuring, David","last_name":"Scheuring"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3617","title":"ARF1 localizes to the golgi and the trans Golgi network","_id":"3083","type":"journal_article","status":"public","publication_status":"published","year":"2011","publication":"Plant Cell","day":"01","page":"846 - 849","date_created":"2018-12-11T12:01:16Z","doi":"10.1105/tpc.110.082099","issue":"3","date_published":"2011-03-01T00:00:00Z","volume":23,"publisher":"American Society of Plant Biologists","quality_controlled":0,"intvolume":" 23","month":"03"},{"day":"01","publication":"Cell Research","year":"2011","publication_status":"published","doi":"10.1038/cr.2011.99","volume":21,"date_published":"2011-01-01T00:00:00Z","issue":"12","date_created":"2018-12-11T12:01:23Z","page":"1711 - 1722","abstract":[{"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","lang":"eng"}],"month":"01","intvolume":" 21","publisher":"Nature Publishing Group","quality_controlled":0,"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357998/","open_access":"1"}],"extern":1,"citation":{"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.","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.","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","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.","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_updated":"2021-01-12T07:41:04Z","title":"The AP 3 adaptor complex is required for vacuolar function in Arabidopsis","publist_id":"3597","author":[{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"first_name":"Barbara","last_name":"Möller","full_name":"Möller, Barbara"},{"full_name":"Hwang, Inhwan","last_name":"Hwang","first_name":"Inhwan"},{"full_name":"Feraru, Mugurel I","last_name":"Feraru","first_name":"Mugurel"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"_id":"3101","status":"public","type":"journal_article"},{"abstract":[{"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.","lang":"eng"}],"quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 7","month":"10","publication_status":"published","year":"2011","publication":"Molecular Systems Biology","day":"25","date_created":"2018-12-11T12:01:22Z","date_published":"2011-10-25T00:00:00Z","doi":"10.1038/msb.2011.72","volume":7,"_id":"3098","type":"journal_article","status":"public","date_updated":"2021-01-12T07:41:02Z","citation":{"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.","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.","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).","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","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."},"extern":1,"author":[{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"orcid":"0000-0001-7263-0560","full_name":"Krzysztof Wabnik","last_name":"Wabnik","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexandre","full_name":"Martinière, Alexandre","last_name":"Martinière"},{"first_name":"Łukasz","full_name":"Łangowski, Łukasz","last_name":"Łangowski"},{"full_name":"Willig, Katrin","last_name":"Willig","first_name":"Katrin"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"first_name":"Johannes","last_name":"Leitner","full_name":"Leitner, Johannes"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"full_name":"Jakobs, Stefan","last_name":"Jakobs","first_name":"Stefan"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"first_name":"Willy","last_name":"Govaerts","full_name":"Govaerts, Willy J"},{"first_name":"Stefan","full_name":"Hell, Stefan W","last_name":"Hell"},{"last_name":"Runions","full_name":"Runions, John","first_name":"John"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3601","title":"Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane"},{"_id":"3100","type":"journal_article","status":"public","date_updated":"2021-01-12T07:41:04Z","citation":{"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.","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.","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.","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.","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","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."},"extern":1,"publist_id":"3600","author":[{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Frederik","full_name":"Coppens, Frederik","last_name":"Coppens"},{"last_name":"Lee","full_name":"Lee, EunKyoung","first_name":"Eunkyoung"},{"first_name":"Tyler","full_name":"Donner, Tyler J","last_name":"Donner"},{"full_name":"Xie, Zidian","last_name":"Xie","first_name":"Zidian"},{"first_name":"Gert","last_name":"Van Isterdael","full_name":"Van Isterdael, Gert"},{"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","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"first_name":"Marnik","last_name":"Vuylsteke","full_name":"Vuylsteke, Marnik"},{"full_name":"De Veylder, Lieven","last_name":"De Veylder","first_name":"Lieven"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Inzé","full_name":"Inzé, Dirk","first_name":"Dirk"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"full_name":"Scarpella, Enrico","last_name":"Scarpella","first_name":"Enrico"},{"last_name":"Sack","full_name":"Sack, Fred","first_name":"Fred"},{"first_name":"Gerrit","full_name":"Beemster, Gerrit T","last_name":"Beemster"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"}],"title":"Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ","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."}],"quality_controlled":0,"publisher":"Wiley-Blackwell","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160660/"}],"oa":1,"month":"08","intvolume":" 30","publication_status":"published","year":"2011","day":"17","publication":"EMBO Journal","page":"3430 - 3441","date_published":"2011-08-17T00:00:00Z","volume":30,"issue":"16","doi":"10.1038/emboj.2011.240","date_created":"2018-12-11T12:01:23Z"},{"intvolume":" 108","month":"10","quality_controlled":0,"publisher":"National Academy of Sciences","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T12:01:23Z","date_published":"2011-10-25T00:00:00Z","doi":"10.1073/pnas.1108581108","issue":"43","volume":108,"page":"17850 - 17855","publication":"PNAS","day":"25","year":"2011","publication_status":"published","status":"public","type":"journal_article","_id":"3099","title":"Clusters of bioactive compounds target dynamic endomembrane networks in vivo","author":[{"first_name":"Georgia","full_name":"Drakakaki, Georgia","last_name":"Drakakaki"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"last_name":"Szatmári","full_name":"Szatmári, Anna-Maria","first_name":"Anna"},{"last_name":"Brown","full_name":"Brown, Michelle Q","first_name":"Michelle"},{"first_name":"Shingo","full_name":"Nagawa, Shingo","last_name":"Nagawa"},{"first_name":"Daniël","full_name":"Van Damme, Daniël","last_name":"Van Damme"},{"last_name":"Leonard","full_name":"Leonard, Marylin","first_name":"Marylin"},{"full_name":"Yang, Zhenbiao","last_name":"Yang","first_name":"Zhenbiao"},{"first_name":"Thomas","last_name":"Girke","full_name":"Girke, Thomas"},{"first_name":"Sandra","last_name":"Schmid","full_name":"Schmid, Sandra L"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"},{"last_name":"Raikhel","full_name":"Raikhel, Natasha V","first_name":"Natasha"},{"first_name":"Glen","full_name":"Hicks, Glen R","last_name":"Hicks"}],"publist_id":"3602","extern":1,"citation":{"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.","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.","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.","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","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","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."},"date_updated":"2021-01-12T07:41:02Z"},{"date_created":"2018-12-11T12:01:21Z","volume":191,"issue":"4","date_published":"2011-01-01T00:00:00Z","doi":" 10.1111/j.1469-8137.2011.03757.x","page":"970 - 983","publication":"New Phytologist","day":"01","year":"2011","publication_status":"published","intvolume":" 191","month":"01","quality_controlled":0,"publisher":"Wiley-Blackwell","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."}],"title":"Auxin minimum defines a developmental window for lateral root initiation","author":[{"first_name":"Joseph","full_name":"Dubrovsky, Joseph G","last_name":"Dubrovsky"},{"first_name":"Selene","last_name":"Napsucialy Mendivil","full_name":"Napsucialy-Mendivil, Selene"},{"full_name":"Duclercq, Jérôme","last_name":"Duclercq","first_name":"Jérôme"},{"first_name":"Yan","full_name":"Cheng, Yan","last_name":"Cheng"},{"first_name":"Svetlana","last_name":"Shishkova","full_name":"Shishkova, Svetlana O"},{"full_name":"Ivanchenko, Maria G","last_name":"Ivanchenko","first_name":"Maria"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"},{"first_name":"Angus","full_name":"Murphy, Angus S","last_name":"Murphy"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Eva Benková"}],"publist_id":"3605","extern":1,"citation":{"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.","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.","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","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.","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_updated":"2021-01-12T07:41:01Z","status":"public","type":"journal_article","_id":"3095"},{"_id":"3097","type":"journal_article","status":"public","date_updated":"2021-01-12T07:41:02Z","citation":{"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.","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","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","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.","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.","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.","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."},"extern":1,"publist_id":"3603","author":[{"full_name":"Peter Marhavy","orcid":"0000-0001-5227-5741","last_name":"Marhavy","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"full_name":"Abas, Lindy","last_name":"Abas","first_name":"Lindy"},{"last_name":"Abuzeineh","full_name":"Abuzeineh, Anas","first_name":"Anas"},{"last_name":"Duclercq","full_name":"Duclercq, Jérôme","first_name":"Jérôme"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"last_name":"Pařezová","full_name":"Pařezová, Markéta","first_name":"Markéta"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Eva Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis","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."}],"publisher":"Cell Press","quality_controlled":0,"intvolume":" 21","month":"10","year":"2011","publication_status":"published","publication":"Developmental Cell","day":"18","page":"796 - 804","date_created":"2018-12-11T12:01:22Z","date_published":"2011-10-18T00:00:00Z","doi":"10.1016/j.devcel.2011.08.014","volume":21,"issue":"4"},{"doi":"10.1016/j.tplants.2011.05.002","date_published":"2011-09-01T00:00:00Z","volume":16,"issue":"9","date_created":"2018-12-11T12:01:21Z","page":"468 - 475","day":"01","language":[{"iso":"eng"}],"publication":"Trends in Plant Science","year":"2011","publication_status":"published","month":"09","intvolume":" 16","quality_controlled":"1","publisher":"Cell Press","oa_version":"None","abstract":[{"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.","lang":"eng"}],"title":"Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization","author":[{"last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"full_name":"Govaerts, Willy","last_name":"Govaerts","first_name":"Willy"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"3604","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:41:01Z","citation":{"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.","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.","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","short":"K.T. Wabnik, J. Kleine Vehn, W. Govaerts, J. Friml, Trends in Plant Science 16 (2011) 468–475.","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.","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."},"status":"public","type":"journal_article","_id":"3096"},{"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."}],"month":"06","intvolume":" 31","quality_controlled":0,"publisher":"Society for Neuroscience","day":"08","publication":"Journal of Neuroscience","year":"2011","publication_status":"published","volume":31,"issue":"23","date_published":"2011-06-08T00:00:00Z","doi":"10.1523/JNEUROSCI.0294-11.2011","date_created":"2018-12-11T12:01:36Z","page":"8605 - 8616","_id":"3138","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T07:41:19Z","citation":{"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.","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.","short":"D. Sullivan, J.L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, G. Buzsáki, Journal of Neuroscience 31 (2011) 8605–8616.","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.","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","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."},"title":"Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity","author":[{"first_name":"David","last_name":"Sullivan","full_name":"Sullivan, David W"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036"},{"full_name":"Mizuseki, Kenji","last_name":"Mizuseki","first_name":"Kenji"},{"last_name":"Montgomery","full_name":"Montgomery, Sean M","first_name":"Sean"},{"first_name":"Kamran","last_name":"Diba","full_name":"Diba, Kamran"},{"last_name":"Buzsáki","full_name":"Buzsáki, György","first_name":"György"}],"publist_id":"3559"},{"publisher":"National Academy of Sciences","quality_controlled":0,"month":"05","intvolume":" 108","abstract":[{"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.","lang":"eng"}],"page":"7902 - 7907","volume":108,"date_published":"2011-05-10T00:00:00Z","issue":"19","doi":"10.1073/pnas.1019507108","date_created":"2018-12-11T12:01:39Z","year":"2011","publication_status":"published","day":"10","publication":"PNAS","type":"journal_article","status":"public","_id":"3145","publist_id":"3549","author":[{"first_name":"Bosiljka","last_name":"Tasic","full_name":"Tasic, Bosiljka"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Simon Hippenmeyer","last_name":"Hippenmeyer"},{"last_name":"Wang","full_name":"Wang, Charlene","first_name":"Charlene"},{"first_name":"Matthew","last_name":"Gamboa","full_name":"Gamboa, Matthew"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"last_name":"Chen Tsai","full_name":"Chen-Tsai, Yanru","first_name":"Yanru"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"}],"title":"Site specific integrase mediated transgenesis in mice via pronuclear injection","citation":{"short":"B. Tasic, S. Hippenmeyer, C. Wang, M. Gamboa, H. Zong, Y. Chen Tsai, L. Luo, PNAS 108 (2011) 7902–7907.","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.","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","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","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.","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.","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."},"date_updated":"2021-01-12T07:41:22Z","extern":1},{"extern":1,"date_updated":"2021-01-12T07:41:26Z","citation":{"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.","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.","short":"M. Degennaro, T. Hurd, D.E. Siekhaus, B. Biteau, H. Jasper, R. Lehmann, Developmental Cell 20 (2011) 233–243.","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","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","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.","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."},"title":"Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion","publist_id":"3541","author":[{"first_name":"Matthew","last_name":"Degennaro","full_name":"DeGennaro, Matthew"},{"full_name":"Hurd, Thomas R","last_name":"Hurd","first_name":"Thomas"},{"last_name":"Siekhaus","full_name":"Daria Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benoit","last_name":"Biteau","full_name":"Biteau, Benoit"},{"full_name":"Jasper, Heinrich","last_name":"Jasper","first_name":"Heinrich"},{"first_name":"Ruth","last_name":"Lehmann","full_name":"Lehmann, Ruth"}],"_id":"3154","status":"public","type":"journal_article","publication":"Developmental Cell","day":"15","year":"2011","publication_status":"published","date_created":"2018-12-11T12:01:42Z","doi":"10.1016/j.devcel.2010.12.007","volume":20,"date_published":"2011-02-15T00:00:00Z","issue":"2","page":"233 - 243","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."}],"intvolume":" 20","month":"02","publisher":"Cell Press","quality_controlled":0},{"publication_status":"published","year":"2011","day":"01","page":"391 - 402","date_created":"2018-12-11T12:02:12Z","date_published":"2011-01-01T00:00:00Z","volume":"6755 ","issue":"Part 1","doi":"10.1007/978-3-642-22006-7_33","abstract":[{"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.","lang":"eng"}],"alternative_title":["LNCS"],"quality_controlled":0,"publisher":"Springer","month":"01","citation":{"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.","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.","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.","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."},"date_updated":"2021-01-12T07:42:02Z","extern":1,"publist_id":"3441","author":[{"first_name":"Sebastian","full_name":"Faust, Sebastian","last_name":"Faust"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak"},{"first_name":"Daniele","last_name":"Venturi","full_name":"Venturi, Daniele"}],"title":"Tamper proof circuits How to trade leakage for tamper resilience","_id":"3239","conference":{"name":"ICALP: Automata, Languages and Programming"},"type":"conference","status":"public"},{"year":"2011","publication_status":"published","day":"01","page":"58 - 69","doi":"10.1007/978-3-642-19571-6_5","volume":"6597 ","date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T12:02:11Z","abstract":[{"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.","lang":"eng"}],"quality_controlled":0,"alternative_title":["LNCS"],"publisher":"Springer","month":"01","citation":{"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.","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","short":"A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.","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.","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.","ista":"Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69."},"date_updated":"2021-01-12T07:42:00Z","extern":1,"publist_id":"3443","author":[{"first_name":"Abhishek","last_name":"Jain","full_name":"Jain, Abhishek"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"}],"title":"Parallel repetition for leakage resilience amplification revisited","_id":"3236","type":"conference","conference":{"name":"TCC: Theory of Cryptography Conference"},"status":"public"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"381","status":"public","_id":"3276","publist_id":"3370","author":[{"full_name":"Prentice, Jason S","last_name":"Prentice","first_name":"Jason"},{"last_name":"Homann","full_name":"Homann, Jan","first_name":"Jan"},{"first_name":"Kristina","last_name":"Simmons","full_name":"Simmons, Kristina D"},{"full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay","first_name":"Vijay"},{"full_name":"Nelson, Philip C","last_name":"Nelson","first_name":"Philip"}],"title":"Fast, scalable, Bayesian spike identification for multi-electrode arrays","file_date_updated":"2020-07-14T12:46:06Z","date_updated":"2021-01-12T07:42:19Z","citation":{"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).","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.","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","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","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.","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)."},"extern":1,"oa":1,"publisher":"Public Library of Science","quality_controlled":0,"intvolume":" 6","month":"07","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.\n\nMichael 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.\n\n","date_created":"2018-12-11T12:02:24Z","issue":"7","date_published":"2011-07-20T00:00:00Z","volume":6,"doi":"10.1371/journal.pone.0019884","publication_status":"published","year":"2011","publication":"PLoS One","day":"20","file":[{"file_name":"IST-2015-381-v1+1_journal.pone.0019884.pdf","date_created":"2018-12-12T10:11:38Z","file_size":885464,"date_updated":"2020-07-14T12:46:06Z","creator":"system","file_id":"4894","checksum":"654464e99683b55a699734213d5356f1","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}]},{"status":"public","type":"book_chapter","_id":"3271","title":"Efficient computation of persistent homology for cubical data","editor":[{"last_name":"Peikert","full_name":"Peikert, Ronald","first_name":"Ronald"},{"full_name":"Hauser, Helwig","last_name":"Hauser","first_name":"Helwig"},{"last_name":"Carr","full_name":"Carr, Hamish","first_name":"Hamish"},{"first_name":"Raphael","last_name":"Fuchs","full_name":"Fuchs, Raphael"}],"department":[{"_id":"HeEd"}],"publist_id":"3375","author":[{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert"},{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen"},{"full_name":"Vuçini, Erald","last_name":"Vuçini","first_name":"Erald"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:18Z","citation":{"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","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","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.","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.","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.","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.","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."},"month":"11","quality_controlled":"1","publisher":"Springer","scopus_import":1,"alternative_title":["Theory, Algorithms, and Applications"],"oa_version":"None","abstract":[{"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.","lang":"eng"}],"date_published":"2011-11-14T00:00:00Z","doi":"10.1007/978-3-642-23175-9_7","date_created":"2018-12-11T12:02:23Z","page":"91 - 106","day":"14","publication":"Topological Methods in Data Analysis and Visualization II","language":[{"iso":"eng"}],"year":"2011","publication_status":"published"},{"date_updated":"2021-01-12T07:42:20Z","citation":{"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.","short":"R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution 61 (2011) 237–243.","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","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.","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.","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."},"extern":1,"publist_id":"3368","author":[{"first_name":"Roger","full_name":"Vila, Roger","last_name":"Vila"},{"full_name":"Pierce, Naomi E","last_name":"Pierce","first_name":"Naomi"},{"first_name":"David","full_name":"Nash, David R","last_name":"Nash"},{"orcid":"0000-0003-1832-8883","full_name":"Line Ugelvig","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"}],"title":"A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade","_id":"3278","type":"journal_article","status":"public","publication_status":"published","year":"2011","publication":"Molecular Phylogenetics and Evolution","day":"01","page":"237 - 243","date_created":"2018-12-11T12:02:25Z","volume":61,"issue":"1","doi":"10.1016/j.ympev.2011.05.016","date_published":"2011-10-01T00:00:00Z","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.\nWe 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."}],"quality_controlled":0,"publisher":"Elsevier","intvolume":" 61","month":"10"},{"publication_status":"published","year":"2011","language":[{"iso":"eng"}],"day":"01","page":"197 - 200","date_created":"2018-12-11T12:02:22Z","date_published":"2011-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions."}],"oa_version":"None","quality_controlled":"1","publisher":"TU Dortmund","month":"01","citation":{"mla":"Chen, Chao, and Michael Kerber. Persistent Homology Computation with a Twist. TU Dortmund, 2011, pp. 197–200.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200.","apa":"Chen, C., & Kerber, M. (2011). Persistent homology computation with a twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland: TU Dortmund.","short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.","ieee":"C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland, 2011, pp. 197–200.","chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200."},"date_updated":"2021-01-12T07:42:17Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chen","full_name":"Chen, Chao","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"}],"publist_id":"3376","department":[{"_id":"HeEd"}],"title":"Persistent homology computation with a twist","_id":"3270","conference":{"end_date":"2011-03-30","location":"Morschach, Switzerland","start_date":"2011-03-28","name":"EuroCG: European Workshop on Computational Geometry"},"type":"conference","status":"public"},{"page":"33 - 42","doi":"10.1145/2019406.2019411","date_published":"2011-08-05T00:00:00Z","date_created":"2018-12-11T12:02:32Z","has_accepted_license":"1","year":"2011","day":"05","publisher":"ACM","quality_controlled":"1","oa":1,"author":[{"last_name":"Raveendran","full_name":"Raveendran, Karthik","first_name":"Karthik"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"},{"first_name":"Greg","full_name":"Turk, Greg","last_name":"Turk"}],"publist_id":"3343","title":"Hybrid smoothed particle hydrodynamics","editor":[{"first_name":"Stephen","last_name":"Spencer","full_name":"Spencer, Stephen"}],"citation":{"mla":"Raveendran, Karthik, et al. Hybrid Smoothed Particle Hydrodynamics. Edited by Stephen Spencer, ACM, 2011, pp. 33–42, doi:10.1145/2019406.2019411.","short":"K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp. 33–42.","ieee":"K. Raveendran, C. Wojtan, and G. Turk, “Hybrid smoothed particle hydrodynamics,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada, 2011, pp. 33–42.","apa":"Raveendran, K., Wojtan, C., & Turk, G. (2011). Hybrid smoothed particle hydrodynamics. In S. Spencer (Ed.) (pp. 33–42). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada: ACM. https://doi.org/10.1145/2019406.2019411","ama":"Raveendran K, Wojtan C, Turk G. Hybrid smoothed particle hydrodynamics. In: Spencer S, ed. ACM; 2011:33-42. doi:10.1145/2019406.2019411","chicago":"Raveendran, Karthik, Chris Wojtan, and Greg Turk. “Hybrid Smoothed Particle Hydrodynamics.” edited by Stephen Spencer, 33–42. ACM, 2011. https://doi.org/10.1145/2019406.2019411.","ista":"Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file":[{"file_name":"IST-2016-598-v1+1_HybridSPH_Preprint.pdf","date_created":"2018-12-12T10:09:44Z","file_size":2536216,"date_updated":"2020-07-14T12:46:06Z","creator":"system","checksum":"6579d27709946e0eefbfa60a456b4913","file_id":"4769","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"08","abstract":[{"lang":"eng","text":"We present a new algorithm for enforcing incompressibility for Smoothed Particle Hydrodynamics (SPH) by preserving uniform density across the domain. We propose a hybrid method that uses a Poisson solve on a coarse grid to enforce a divergence free velocity field, followed by a local density correction of the particles. This avoids typical grid artifacts and maintains the Lagrangian nature of SPH by directly transferring pressures onto particles. Our method can be easily integrated with existing SPH techniques such as the incompressible PCISPH method as well as weakly compressible SPH by adding an additional force term. We show that this hybrid method accelerates convergence towards uniform density and permits a significantly larger time step compared to earlier approaches while producing similar results. We demonstrate our approach in a variety of scenarios with significant pressure gradients such as splashing liquids."}],"oa_version":"Submitted Version","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:46:06Z","date_updated":"2023-02-23T11:21:05Z","ddc":["000"],"type":"conference","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2011-08-05","end_date":"2011-08-07","location":"Vancouver, Canada"},"status":"public","pubrep_id":"598","_id":"3298"},{"publisher":"ACM","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2011","day":"07","date_published":"2011-08-07T00:00:00Z","doi":"10.1145/2037636.2037644","date_created":"2018-12-11T12:02:31Z","article_number":"8","citation":{"chicago":"Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation with Mesh-Based Surface Tracking.” ACM, 2011. https://doi.org/10.1145/2037636.2037644.","ista":"Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 8.","mla":"Wojtan, Chris, et al. Liquid Simulation with Mesh-Based Surface Tracking. 8, ACM, 2011, doi:10.1145/2037636.2037644.","ama":"Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface tracking. In: ACM; 2011. doi:10.1145/2037636.2037644","apa":"Wojtan, C., Müller Fischer, M., & Brochu, T. (2011). Liquid simulation with mesh-based surface tracking. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada: ACM. https://doi.org/10.1145/2037636.2037644","short":"C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.","ieee":"C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3344","author":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"last_name":"Müller Fischer","full_name":"Müller Fischer, Matthias","first_name":"Matthias"},{"last_name":"Brochu","full_name":"Brochu, Tyson","first_name":"Tyson"}],"title":"Liquid simulation with mesh-based surface tracking","abstract":[{"text":"Animating detailed liquid surfaces has always been a challenge for computer graphics researchers and visual effects artists. Over the past few years, researchers in this field have focused on mesh-based surface tracking to synthesize extremely detailed liquid surfaces as efficiently as possible. This course provides a solid understanding of the steps required to create a fluid simulator with a mesh-based liquid surface.\r\n\r\nThe course begins with an overview of several existing liquid-surface-tracking techniques and the pros and cons of each method. Then it explains how to embed a triangle mesh into a finite-difference-based fluid simulator and describes several methods for allowing the liquid surface to merge together or break apart. The final section showcases the benefits and further applications of a mesh-based liquid surface, highlighting state-of-the-art methods for tracking colors and textures, maintaining liquid volume, preserving small surface features, and simulating realistic surface-tension waves.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"08","publication_status":"published","file":[{"date_updated":"2020-07-14T12:46:06Z","file_size":34672096,"creator":"system","date_created":"2018-12-12T10:13:34Z","file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8d508ad7c82f50978acbaa4170ee0a75","file_id":"5018"}],"language":[{"iso":"eng"}],"_id":"3297","type":"conference","conference":{"end_date":"2011-08-11","location":"Vancouver, BC, Canada","start_date":"2011-08-07","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"status":"public","pubrep_id":"599","date_updated":"2023-02-23T11:21:02Z","ddc":["000"],"file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"ChWo"}]},{"day":"01","publication":"Genetics","year":"2011","date_published":"2011-11-01T00:00:00Z","doi":"10.1534/genetics.111.129569","date_created":"2018-12-11T12:02:29Z","page":"977 - 987","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129569","ama":"Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569","short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","ieee":"K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011.","mla":"Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:10.1534/genetics.111.129569.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987.","chicago":"Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129569."},"title":"A general method for calculating likelihoods under the coalescent process","publist_id":"3355","author":[{"last_name":"Lohse","full_name":"Lohse, Konrad","first_name":"Konrad"},{"first_name":"Richard","full_name":"Harrison, Richard","last_name":"Harrison"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":189,"issue":"3","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small."}],"month":"11","intvolume":" 189","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/"}],"date_updated":"2021-01-12T07:42:26Z","department":[{"_id":"NiBa"}],"_id":"3290","status":"public","type":"journal_article"},{"year":"2011","has_accepted_license":"1","publication":"Proceedings of the IEEE International Conference on Computer Vision","day":"31","date_created":"2018-12-11T12:02:36Z","date_published":"2011-12-31T00:00:00Z","doi":"10.1109/ICCV.2011.6126475","acknowledgement":"This research is supported by the National Science Foundation (NSF) under grant DBI-0820624.","oa":1,"quality_controlled":"1","publisher":"IEEE","citation":{"apa":"Zheng, Y., Gu, S., Edelsbrunner, H., Tomasi, C., & Benfey, P. (2011). Detailed reconstruction of 3D plant root shape. Proceedings of the IEEE International Conference on Computer Vision. Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126475","ama":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. Detailed Reconstruction of 3D Plant Root Shape. IEEE; 2011. doi:10.1109/ICCV.2011.6126475","ieee":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey, Detailed reconstruction of 3D plant root shape. IEEE, 2011.","short":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, P. Benfey, Detailed Reconstruction of 3D Plant Root Shape, IEEE, 2011.","mla":"Zheng, Ying, et al. “Detailed Reconstruction of 3D Plant Root Shape.” Proceedings of the IEEE International Conference on Computer Vision, 6126475, IEEE, 2011, doi:10.1109/ICCV.2011.6126475.","ista":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction of 3D plant root shape, IEEE,p.","chicago":"Zheng, Ying, Steve Gu, Herbert Edelsbrunner, Carlo Tomasi, and Philip Benfey. Detailed Reconstruction of 3D Plant Root Shape. Proceedings of the IEEE International Conference on Computer Vision. IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126475."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"3328","author":[{"last_name":"Zheng","full_name":"Zheng, Ying","first_name":"Ying"},{"last_name":"Gu","full_name":"Gu, Steve","first_name":"Steve"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tomasi, Carlo","last_name":"Tomasi","first_name":"Carlo"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"}],"title":"Detailed reconstruction of 3D plant root shape","article_number":"6126475","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4727","checksum":"30a33564b7b45a7ee31610898267fd0e","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:09:04Z","file_name":"IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf","creator":"system","date_updated":"2020-07-14T12:46:07Z","file_size":5622728}],"abstract":[{"lang":"eng","text":"We study the 3D reconstruction of plant roots from multiple 2D images. To meet the challenge caused by the delicate nature of thin branches, we make three innovations to cope with the sensitivity to image quality and calibration. First, we model the background as a harmonic function to improve the segmentation of the root in each 2D image. Second, we develop the concept of the regularized visual hull which reduces the effect of jittering and refraction by ensuring consistency with one 2D image. Third, we guarantee connectedness through adjustments to the 3D reconstruction that minimize global error. Our software is part of a biological phenotype/genotype study of agricultural root systems. It has been tested on more than 40 plant roots and results are promising in terms of reconstruction quality and efficiency."}],"oa_version":"Submitted Version","month":"12","date_updated":"2020-07-14T23:03:43Z","ddc":["000"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:07Z","_id":"3312","conference":{"name":"ICCV: International Conference on Computer Vision","location":"Barcelona, Spain","end_date":"2011-11-13","start_date":"2011-11-06"},"type":"conference_poster","pubrep_id":"541","status":"public"},{"month":"11","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Interpreting an image as a function on a compact sub- set of the Euclidean plane, we get its scale-space by diffu- sion, spreading the image over the entire plane. This gener- ates a 1-parameter family of functions alternatively defined as convolutions with a progressively wider Gaussian ker- nel. We prove that the corresponding 1-parameter family of persistence diagrams have norms that go rapidly to zero as time goes to infinity. This result rationalizes experimental observations about scale-space. We hope this will lead to targeted improvements of related computer vision methods."}],"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":614050,"date_updated":"2020-07-14T12:46:07Z","file_name":"IST-2016-540-v1+1_2011-P-08-RunEmpty.pdf","date_created":"2018-12-12T10:17:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5282","checksum":"6984684081ba123808b344f9f2e64a8f"}],"publication_status":"published","pubrep_id":"540","status":"public","conference":{"name":"ICCV: International Conference on Computer Vision","location":"Barcelona, Spain","end_date":"2011-11-13","start_date":"2011-11-06"},"type":"conference","_id":"3313","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:07Z","ddc":["000"],"date_updated":"2021-01-12T07:42:35Z","oa":1,"quality_controlled":"1","publisher":"IEEE","date_created":"2018-12-11T12:02:37Z","doi":"10.1109/ICCV.2011.6126271","date_published":"2011-11-06T00:00:00Z","publication":"Proceedings of the IEEE International Conference on Computer Vision","day":"06","year":"2011","has_accepted_license":"1","article_number":"6126271","title":"Diffusion runs low on persistence fast","publist_id":"3327","author":[{"full_name":"Chen, Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.” In Proceedings of the IEEE International Conference on Computer Vision. IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126271.","ista":"Chen C, Edelsbrunner H. 2011. Diffusion runs low on persistence fast. Proceedings of the IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision, 6126271.","mla":"Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.” Proceedings of the IEEE International Conference on Computer Vision, 6126271, IEEE, 2011, doi:10.1109/ICCV.2011.6126271.","ama":"Chen C, Edelsbrunner H. Diffusion runs low on persistence fast. In: Proceedings of the IEEE International Conference on Computer Vision. IEEE; 2011. doi:10.1109/ICCV.2011.6126271","apa":"Chen, C., & Edelsbrunner, H. (2011). Diffusion runs low on persistence fast. In Proceedings of the IEEE International Conference on Computer Vision. Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126271","short":"C. Chen, H. Edelsbrunner, in:, Proceedings of the IEEE International Conference on Computer Vision, IEEE, 2011.","ieee":"C. Chen and H. Edelsbrunner, “Diffusion runs low on persistence fast,” in Proceedings of the IEEE International Conference on Computer Vision, Barcelona, Spain, 2011."}},{"citation":{"chicago":"Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” In Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, edited by R van de Weygaert, G Vegter, J Ritzerveld, and V Icke. Springer, n.d.","ista":"Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. .","mla":"Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, edited by R van de Weygaert et al., Springer.","ama":"Edelsbrunner H. Alpha shapes - a survey. In: van de Weygaert R, Vegter G, Ritzerveld J, Icke V, eds. Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. Springer.","apa":"Edelsbrunner, H. (n.d.). Alpha shapes - a survey. In R. van de Weygaert, G. Vegter, J. Ritzerveld, & V. Icke (Eds.), Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. Springer.","short":"H. Edelsbrunner, in:, R. van de Weygaert, G. Vegter, J. Ritzerveld, V. Icke (Eds.), Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, Springer, n.d.","ieee":"H. Edelsbrunner, “Alpha shapes - a survey,” in Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, R. van de Weygaert, G. Vegter, J. Ritzerveld, and V. Icke, Eds. Springer."},"date_updated":"2022-05-24T07:56:30Z","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"3329","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2022-05-24T07:55:05Z","department":[{"_id":"HeEd"}],"title":"Alpha shapes - a survey","editor":[{"last_name":"van de Weygaert","full_name":"van de Weygaert, R","first_name":"R"},{"first_name":"G","last_name":"Vegter","full_name":"Vegter, G"},{"last_name":"Ritzerveld","full_name":"Ritzerveld, J","first_name":"J"},{"first_name":"V","last_name":"Icke","full_name":"Icke, V"}],"_id":"3311","type":"book_chapter","status":"public","year":"2011","publication_status":"inpress","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings","file":[{"date_updated":"2022-05-24T07:55:05Z","file_size":475254,"creator":"dernst","date_created":"2022-05-24T07:55:05Z","file_name":"2010_AlphaShapes.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a592ea438351e7280eea993a7713ab8f","file_id":"11408","success":1}],"day":"31","date_created":"2018-12-11T12:02:36Z","date_published":"2011-12-31T00:00:00Z","abstract":[{"text":"Alpha shapes have been conceived in 1981 as an attempt to define the shape of a finite set of point in the plane. Since then, connections to diverse areas in the sciences and engineering have developed, including to pattern recognition, digital shape sampling and processing, and structural molecular biology. This survey begins with a historical account and discusses geometric, algorithmic, topological, and combinatorial aspects of alpha shapes in this sequence.","lang":"eng"}],"oa_version":"Submitted Version","oa":1,"publisher":"Springer","quality_controlled":"1","month":"12"},{"oa_version":"Submitted Version","abstract":[{"text":"Weighted automata map input words to numerical values. Ap- plications of weighted automata include formal verification of quantitative properties, as well as text, speech, and image processing. A weighted au- tomaton is defined with respect to a semiring. For the tropical semiring, the weight of a run is the sum of the weights of the transitions taken along the run, and the value of a word is the minimal weight of an accepting run on it. In the 90’s, Krob studied the decidability of problems on rational series defined with respect to the tropical semiring. Rational series are strongly related to weighted automata, and Krob’s results apply to them. In par- ticular, it follows from Krob’s results that the universality problem (that is, deciding whether the values of all words are below some threshold) is decidable for weighted automata defined with respect to the tropical semir- ing with domain ∪ {∞}, and that the equality problem is undecidable when the domain is ∪ {∞}. In this paper we continue the study of the borders of decidability in weighted automata, describe alternative and direct proofs of the above results, and tighten them further. Unlike the proofs of Krob, which are algebraic in their nature, our proofs stay in the terrain of state machines, and the reduction is from the halting problem of a two-counter machine. This enables us to significantly simplify Krob’s reasoning, make the un- decidability result accessible to the automata-theoretic community, and strengthen it to apply already to a very simple class of automata: all the states are accepting, there are no initial nor final weights, and all the weights on the transitions are from the set {−1, 0, 1}. The fact we work directly with the automata enables us to tighten also the decidability re- sults and to show that the universality problem for weighted automata defined with respect to the tropical semiring with domain ∪ {∞}, and in fact even with domain ≥0 ∪ {∞}, is PSPACE-complete. Our results thus draw a sharper picture about the decidability of decision problems for weighted automata, in both the front of containment vs. universality and the front of the ∪ {∞} vs. the ∪ {∞} domains.","lang":"eng"}],"month":"10","intvolume":" 6996","alternative_title":["LNCS"],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a7ca08a2cb1b6925f4c18a3034ae5659","file_id":"7868","date_updated":"2020-07-14T12:46:07Z","file_size":182309,"creator":"dernst","date_created":"2020-05-19T16:08:32Z","file_name":"2011_LNCS_Almagor.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6996,"_id":"3326","status":"public","type":"conference","conference":{"location":"Taipei, Taiwan","end_date":"2011-10-14","start_date":"2011-10-11","name":"ATVA: Automated Technology for Verification and Analysis"},"ddc":["000"],"date_updated":"2021-01-12T07:42:40Z","file_date_updated":"2020-07-14T12:46:07Z","department":[{"_id":"ToHe"}],"quality_controlled":"1","publisher":"Springer","oa":1,"day":"14","has_accepted_license":"1","year":"2011","doi":"10.1007/978-3-642-24372-1_37","date_published":"2011-10-14T00:00:00Z","date_created":"2018-12-11T12:02:41Z","page":"482 - 491","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Almagor, S., Boker, U., & Kupferman, O. (2011). What’s decidable about weighted automata (Vol. 6996, pp. 482–491). Presented at the ATVA: Automated Technology for Verification and Analysis, Taipei, Taiwan: Springer. https://doi.org/10.1007/978-3-642-24372-1_37","ama":"Almagor S, Boker U, Kupferman O. What’s decidable about weighted automata . In: Vol 6996. Springer; 2011:482-491. doi:10.1007/978-3-642-24372-1_37","short":"S. Almagor, U. Boker, O. Kupferman, in:, Springer, 2011, pp. 482–491.","ieee":"S. Almagor, U. Boker, and O. Kupferman, “What’s decidable about weighted automata ,” presented at the ATVA: Automated Technology for Verification and Analysis, Taipei, Taiwan, 2011, vol. 6996, pp. 482–491.","mla":"Almagor, Shaull, et al. What’s Decidable about Weighted Automata . Vol. 6996, Springer, 2011, pp. 482–91, doi:10.1007/978-3-642-24372-1_37.","ista":"Almagor S, Boker U, Kupferman O. 2011. What’s decidable about weighted automata . ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 6996, 482–491.","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “What’s Decidable about Weighted Automata ,” 6996:482–91. Springer, 2011. https://doi.org/10.1007/978-3-642-24372-1_37."},"title":"What’s decidable about weighted automata ","publist_id":"3309","author":[{"first_name":"Shaull","full_name":"Almagor, Shaull","last_name":"Almagor"},{"last_name":"Boker","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"article_processing_charge":"No"},{"department":[{"_id":"ToHe"}],"title":"Streaming transducers for algorithmic verification of single pass list processing programs","article_processing_charge":"No","author":[{"first_name":"Rajeev","full_name":"Alur, Rajeev","last_name":"Alur"},{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"}],"publist_id":"3310","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Alur, Rajeev, and Pavol Cerny. Streaming Transducers for Algorithmic Verification of Single Pass List Processing Programs. Vol. 46, no. 1, ACM, 2011, pp. 599–610, doi:10.1145/1926385.1926454.","short":"R. Alur, P. Cerny, in:, ACM, 2011, pp. 599–610.","ieee":"R. Alur and P. Cerny, “Streaming transducers for algorithmic verification of single pass list processing programs,” presented at the POPL: Principles of Programming Languages, Texas, USA, 2011, vol. 46, no. 1, pp. 599–610.","apa":"Alur, R., & Cerny, P. (2011). Streaming transducers for algorithmic verification of single pass list processing programs (Vol. 46, pp. 599–610). Presented at the POPL: Principles of Programming Languages, Texas, USA: ACM. https://doi.org/10.1145/1926385.1926454","ama":"Alur R, Cerny P. Streaming transducers for algorithmic verification of single pass list processing programs. In: Vol 46. ACM; 2011:599-610. doi:10.1145/1926385.1926454","chicago":"Alur, Rajeev, and Pavol Cerny. “Streaming Transducers for Algorithmic Verification of Single Pass List Processing Programs,” 46:599–610. ACM, 2011. https://doi.org/10.1145/1926385.1926454.","ista":"Alur R, Cerny P. 2011. Streaming transducers for algorithmic verification of single pass list processing programs. POPL: Principles of Programming Languages vol. 46, 599–610."},"date_updated":"2022-03-21T08:12:51Z","status":"public","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2011-01-28","location":"Texas, USA","start_date":"2011-01-26"},"type":"conference","_id":"3325","date_created":"2018-12-11T12:02:41Z","volume":46,"doi":"10.1145/1926385.1926454","date_published":"2011-01-26T00:00:00Z","issue":"1","page":"599 - 610","language":[{"iso":"eng"}],"day":"26","publication_status":"published","year":"2011","intvolume":" 46","month":"01","scopus_import":"1","publisher":"ACM","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"We introduce streaming data string transducers that map input data strings to output data strings in a single left-to-right pass in linear time. Data strings are (unbounded) sequences of data values, tagged with symbols from a finite set, over a potentially infinite data do- main that supports only the operations of equality and ordering. The transducer uses a finite set of states, a finite set of variables ranging over the data domain, and a finite set of variables ranging over data strings. At every step, it can make decisions based on the next in- put symbol, updating its state, remembering the input data value in its data variables, and updating data-string variables by concatenat- ing data-string variables and new symbols formed from data vari- ables, while avoiding duplication. We establish that the problems of checking functional equivalence of two streaming transducers, and of checking whether a streaming transducer satisfies pre/post verification conditions specified by streaming acceptors over in- put/output data-strings, are in PSPACE. We identify a class of imperative and a class of functional pro- grams, manipulating lists of data items, which can be effectively translated to streaming data-string transducers. The imperative pro- grams dynamically modify a singly-linked heap by changing next- pointers of heap-nodes and by adding new nodes. The main re- striction specifies how the next-pointers can be used for traversal. We also identify an expressively equivalent fragment of functional programs that traverse a list using syntactically restricted recursive calls. Our results lead to algorithms for assertion checking and for checking functional equivalence of two programs, written possibly in different programming styles, for commonly used routines such as insert, delete, and reverse."}]},{"_id":"3324","conference":{"location":"Texas, USA","end_date":"2011-01-25","start_date":"2011-01-23","name":"VMCAI: Verification Model Checking and Abstract Interpretation"},"type":"conference","status":"public","date_updated":"2021-01-12T07:42:39Z","department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Automated termination provers often use the following schema to prove that a program terminates: construct a relational abstraction of the program's transition relation and then show that the relational abstraction is well-founded. The focus of current tools has been on developing sophisticated techniques for constructing the abstractions while relying on known decidable logics (such as linear arithmetic) to express them. We believe we can significantly increase the class of programs that are amenable to automated termination proofs by identifying more expressive decidable logics for reasoning about well-founded relations. We therefore present a new decision procedure for reasoning about multiset orderings, which are among the most powerful orderings used to prove termination. We show that, using our decision procedure, one can automatically prove termination of natural abstractions of programs."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://infoscience.epfl.ch/record/170697/","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 6538","month":"01","publication_status":"published","language":[{"iso":"eng"}],"volume":6538,"citation":{"mla":"Piskac, Ruzica, and Thomas Wies. Decision Procedures for Automating Termination Proofs. Edited by Ranjit Jhala and David Schmidt, vol. 6538, Springer, 2011, pp. 371–86, doi:10.1007/978-3-642-18275-4_26.","short":"R. Piskac, T. Wies, in:, R. Jhala, D. Schmidt (Eds.), Springer, 2011, pp. 371–386.","ieee":"R. Piskac and T. Wies, “Decision procedures for automating termination proofs,” presented at the VMCAI: Verification Model Checking and Abstract Interpretation, Texas, USA, 2011, vol. 6538, pp. 371–386.","apa":"Piskac, R., & Wies, T. (2011). Decision procedures for automating termination proofs. In R. Jhala & D. Schmidt (Eds.) (Vol. 6538, pp. 371–386). Presented at the VMCAI: Verification Model Checking and Abstract Interpretation, Texas, USA: Springer. https://doi.org/10.1007/978-3-642-18275-4_26","ama":"Piskac R, Wies T. Decision procedures for automating termination proofs. In: Jhala R, Schmidt D, eds. Vol 6538. Springer; 2011:371-386. doi:10.1007/978-3-642-18275-4_26","chicago":"Piskac, Ruzica, and Thomas Wies. “Decision Procedures for Automating Termination Proofs.” edited by Ranjit Jhala and David Schmidt, 6538:371–86. Springer, 2011. https://doi.org/10.1007/978-3-642-18275-4_26.","ista":"Piskac R, Wies T. 2011. Decision procedures for automating termination proofs. VMCAI: Verification Model Checking and Abstract Interpretation, LNCS, vol. 6538, 371–386."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ruzica","last_name":"Piskac","full_name":"Piskac, Ruzica"},{"full_name":"Wies, Thomas","last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3311","title":"Decision procedures for automating termination proofs","editor":[{"full_name":"Jhala, Ranjit","last_name":"Jhala","first_name":"Ranjit"},{"first_name":"David","last_name":"Schmidt","full_name":"Schmidt, David"}],"oa":1,"quality_controlled":"1","publisher":"Springer","year":"2011","day":"01","page":"371 - 386","date_created":"2018-12-11T12:02:40Z","date_published":"2011-01-01T00:00:00Z","doi":"10.1007/978-3-642-18275-4_26"},{"alternative_title":["LNCS"],"publisher":"Springer","quality_controlled":"1","month":"03","intvolume":" 6604","abstract":[{"lang":"eng","text":"We solve the open problems of translating, when possible, all common classes of nondeterministic word automata to deterministic and nondeterministic co-Büchi word automata. The handled classes include Büchi, parity, Rabin, Streett and Muller automata. The translations follow a unified approach and are all asymptotically tight. The problem of translating Büchi automata to equivalent co-Büchi automata was solved in [2], leaving open the problems of translating automata with richer acceptance conditions. For these classes, one cannot easily extend or use the construction in [2]. In particular, going via an intermediate Büchi automaton is not optimal and might involve a blow-up exponentially higher than the known lower bound. Other known translations are also not optimal and involve a doubly exponential blow-up. We describe direct, simple, and asymptotically tight constructions, involving a 2Θ(n) blow-up. The constructions are variants of the subset construction, and allow for symbolic implementations. Beyond the theoretical importance of the results, the new constructions have various applications, among which is an improved algorithm for translating, when possible, LTL formulas to deterministic Büchi word automata."}],"oa_version":"None","page":"184 - 198","doi":"10.1007/978-3-642-19805-2_13","date_published":"2011-03-29T00:00:00Z","volume":6604,"date_created":"2018-12-11T12:02:41Z","publication_status":"published","year":"2011","day":"29","language":[{"iso":"eng"}],"type":"conference","conference":{"location":"Saarbrücken, Germany","end_date":"2011-04-03","start_date":"2011-03-26","name":"FoSSaCS: Foundations of Software Science and Computation Structures"},"status":"public","_id":"3327","publist_id":"3308","author":[{"last_name":"Boker","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"title":"Co-Büching them all","editor":[{"full_name":"Hofmann, Martin","last_name":"Hofmann","first_name":"Martin"}],"citation":{"mla":"Boker, Udi, and Orna Kupferman. Co-Büching Them All. Edited by Martin Hofmann, vol. 6604, Springer, 2011, pp. 184–98, doi:10.1007/978-3-642-19805-2_13.","ieee":"U. Boker and O. Kupferman, “Co-Büching them all,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Saarbrücken, Germany, 2011, vol. 6604, pp. 184–198.","short":"U. Boker, O. Kupferman, in:, M. Hofmann (Ed.), Springer, 2011, pp. 184–198.","ama":"Boker U, Kupferman O. Co-Büching them all. In: Hofmann M, ed. Vol 6604. Springer; 2011:184-198. doi:10.1007/978-3-642-19805-2_13","apa":"Boker, U., & Kupferman, O. (2011). Co-Büching them all. In M. Hofmann (Ed.) (Vol. 6604, pp. 184–198). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Saarbrücken, Germany: Springer. https://doi.org/10.1007/978-3-642-19805-2_13","chicago":"Boker, Udi, and Orna Kupferman. “Co-Büching Them All.” edited by Martin Hofmann, 6604:184–98. Springer, 2011. https://doi.org/10.1007/978-3-642-19805-2_13.","ista":"Boker U, Kupferman O. 2011. Co-Büching them all. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 6604, 184–198."},"date_updated":"2021-01-12T07:42:41Z","extern":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"ChLa"}],"title":"Learning anticipation policies for robot table tennis","publist_id":"3293","author":[{"last_name":"Wang","full_name":"Wang, Zhikun","first_name":"Zhikun"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"},{"full_name":"Mülling, Katharina","last_name":"Mülling","first_name":"Katharina"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wang Z, Lampert C, Mülling K, Schölkopf B, Peters J. 2011. Learning anticipation policies for robot table tennis. IROS: RSJ International Conference on Intelligent Robots and Systems, 332–337.","chicago":"Wang, Zhikun, Christoph Lampert, Katharina Mülling, Bernhard Schölkopf, and Jan Peters. “Learning Anticipation Policies for Robot Table Tennis,” 332–37. IEEE, 2011. https://doi.org/10.1109/IROS.2011.6094892.","ama":"Wang Z, Lampert C, Mülling K, Schölkopf B, Peters J. Learning anticipation policies for robot table tennis. In: IEEE; 2011:332-337. doi:10.1109/IROS.2011.6094892","apa":"Wang, Z., Lampert, C., Mülling, K., Schölkopf, B., & Peters, J. (2011). Learning anticipation policies for robot table tennis (pp. 332–337). Presented at the IROS: RSJ International Conference on Intelligent Robots and Systems, San Francisco, USA: IEEE. https://doi.org/10.1109/IROS.2011.6094892","short":"Z. Wang, C. Lampert, K. Mülling, B. Schölkopf, J. Peters, in:, IEEE, 2011, pp. 332–337.","ieee":"Z. Wang, C. Lampert, K. Mülling, B. Schölkopf, and J. Peters, “Learning anticipation policies for robot table tennis,” presented at the IROS: RSJ International Conference on Intelligent Robots and Systems, San Francisco, USA, 2011, pp. 332–337.","mla":"Wang, Zhikun, et al. Learning Anticipation Policies for Robot Table Tennis. IEEE, 2011, pp. 332–37, doi:10.1109/IROS.2011.6094892."},"date_updated":"2021-01-12T07:42:45Z","status":"public","type":"conference","conference":{"start_date":"2011-09-25","end_date":"2011-09-30","location":"San Francisco, USA","name":"IROS: RSJ International Conference on Intelligent Robots and Systems"},"_id":"3337","doi":"10.1109/IROS.2011.6094892","date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T12:02:45Z","page":"332 - 337","day":"01","language":[{"iso":"eng"}],"year":"2011","publication_status":"published","month":"01","scopus_import":1,"publisher":"IEEE","quality_controlled":"1","oa_version":"None","abstract":[{"text":"Playing table tennis is a difficult task for robots, especially due to their limitations of acceleration. A key bottleneck is the amount of time needed to reach the desired hitting position and velocity of the racket for returning the incoming ball. Here, it often does not suffice to simply extrapolate the ball's trajectory after the opponent returns it but more information is needed. Humans are able to predict the ball's trajectory based on the opponent's moves and, thus, have a considerable advantage. Hence, we propose to incorporate an anticipation system into robot table tennis players, which enables the robot to react earlier while the opponent is performing the striking movement. Based on visual observation of the opponent's racket movement, the robot can predict the aim of the opponent and adjust its movement generation accordingly. The policies for deciding how and when to react are obtained by reinforcement learning. We conduct experiments with an existing robot player to show that the learned reaction policy can significantly improve the performance of the overall system.","lang":"eng"}]},{"title":"Magnifying lens abstraction for stochastic games with discounted and long-run average objectives","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Luca","full_name":"De Alfaro, Luca","last_name":"De Alfaro"},{"first_name":"Roy","full_name":"Pritam, Roy","last_name":"Pritam"}],"publist_id":"3286","external_id":{"arxiv":["1107.2132"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, De Alfaro L, Pritam R. 2011. Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv, .","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Roy Pritam. “Magnifying Lens Abstraction for Stochastic Games with Discounted and Long-Run Average Objectives.” ArXiv. ArXiv, 2011.","short":"K. Chatterjee, L. De Alfaro, R. Pritam, ArXiv (2011).","ieee":"K. Chatterjee, L. De Alfaro, and R. Pritam, “Magnifying lens abstraction for stochastic games with discounted and long-run average objectives,” arXiv. ArXiv, 2011.","ama":"Chatterjee K, De Alfaro L, Pritam R. Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv. 2011.","apa":"Chatterjee, K., De Alfaro, L., & Pritam, R. (2011). Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv. ArXiv.","mla":"Chatterjee, Krishnendu, et al. “Magnifying Lens Abstraction for Stochastic Games with Discounted and Long-Run Average Objectives.” ArXiv, ArXiv, 2011."},"date_updated":"2021-01-12T07:42:46Z","status":"public","type":"preprint","_id":"3339","date_published":"2011-07-11T00:00:00Z","date_created":"2018-12-11T12:02:46Z","page":"17","day":"11","language":[{"iso":"eng"}],"publication":"arXiv","year":"2011","publication_status":"published","month":"07","publisher":"ArXiv","main_file_link":[{"url":"http://arxiv.org/abs/1107.2132","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Turn-based stochastic games and its important subclass Markov decision processes (MDPs) provide models for systems with both probabilistic and nondeterministic behaviors. We consider turn-based stochastic games with two classical quantitative objectives: discounted-sum and long-run average objectives. The game models and the quantitative objectives are widely used in probabilistic verification, planning, optimal inventory control, network protocol and performance analysis. Games and MDPs that model realistic systems often have very large state spaces, and probabilistic abstraction techniques are necessary to handle the state-space explosion. The commonly used full-abstraction techniques do not yield space-savings for systems that have many states with similar value, but does not necessarily have similar transition structure. A semi-abstraction technique, namely Magnifying-lens abstractions (MLA), that clusters states based on value only, disregarding differences in their transition relation was proposed for qualitative objectives (reachability and safety objectives). In this paper we extend the MLA technique to solve stochastic games with discounted-sum and long-run average objectives. We present the MLA technique based abstraction-refinement algorithm for stochastic games and MDPs with discounted-sum objectives. For long-run average objectives, our solution works for all MDPs and a sub-class of stochastic games where every state has the same value. "}]},{"abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with ω-regular specifications given as parity objectives. We consider the problem of computing the set of almost-sure winning states from where the objective can be ensured with probability 1. The algorithms for the computation of the almost-sure winning set for parity objectives iteratively use the solutions for the almost-sure winning set for Büchi objectives (a special case of parity objectives). Our contributions are as follows: First, we present the first subquadratic symbolic algorithm to compute the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes O(nm) symbolic steps as compared to the previous known algorithm that takes O(n 2) symbolic steps, where n is the number of states and m is the number of edges of the MDP. In practice MDPs often have constant out-degree, and then our symbolic algorithm takes O(nn) symbolic steps, as compared to the previous known O(n 2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose algorithm, with the following two properties: (a) the algorithm iteratively computes subsets of the almost-sure winning set and its complement, as compared to all previous algorithms that discover the almost-sure winning set upon termination; and (b) requires O(nK) symbolic steps, where K is the maximal number of edges of strongly connected components (scc’s) of the MDP. The win-lose algorithm requires symbolic computation of scc’s. Third, we improve the algorithm for symbolic scc computation; the previous known algorithm takes linear symbolic steps, and our new algorithm improves the constants associated with the linear number of steps. In the worst case the previous known algorithm takes 5·n symbolic steps, whereas our new algorithm takes 4 ·n symbolic steps."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.3348"}],"alternative_title":["LNCS"],"intvolume":" 6806","month":"08","publication_status":"published","language":[{"iso":"eng"}],"volume":6806,"related_material":{"record":[{"id":"2831","status":"public","relation":"later_version"}]},"_id":"3342","conference":{"name":"CAV: Computer Aided Verification","location":"Snowbird, USA","end_date":"2011-07-20","start_date":"2011-07-14"},"type":"conference","status":"public","date_updated":"2023-02-23T11:00:13Z","department":[{"_id":"KrCh"}],"oa":1,"quality_controlled":"1","publisher":"Springer","year":"2011","day":"11","page":"260 - 276","date_created":"2018-12-11T12:02:47Z","doi":"10.1007/978-3-642-22110-1_21","date_published":"2011-08-11T00:00:00Z","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"citation":{"short":"K. Chatterjee, M.H. Henzinger, M. Joglekar, S. Nisarg, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 260–276.","ieee":"K. Chatterjee, M. H. Henzinger, M. Joglekar, and S. Nisarg, “Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives,” presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806, pp. 260–276.","apa":"Chatterjee, K., Henzinger, M. H., Joglekar, M., & Nisarg, S. (2011). Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. In G. Gopalakrishnan & S. Qadeer (Eds.) (Vol. 6806, pp. 260–276). Presented at the CAV: Computer Aided Verification, Snowbird, USA: Springer. https://doi.org/10.1007/978-3-642-22110-1_21","ama":"Chatterjee K, Henzinger MH, Joglekar M, Nisarg S. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. In: Gopalakrishnan G, Qadeer S, eds. Vol 6806. Springer; 2011:260-276. doi:10.1007/978-3-642-22110-1_21","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives. Edited by Ganesh Gopalakrishnan and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 260–76, doi:10.1007/978-3-642-22110-1_21.","ista":"Chatterjee K, Henzinger MH, Joglekar M, Nisarg S. 2011. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. CAV: Computer Aided Verification, LNCS, vol. 6806, 260–276.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Manas Joglekar, and Shah Nisarg. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:260–76. Springer, 2011. https://doi.org/10.1007/978-3-642-22110-1_21."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_processing_charge":"No","external_id":{"arxiv":["1104.3348"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"last_name":"Joglekar","full_name":"Joglekar, Manas","first_name":"Manas"},{"full_name":"Nisarg, Shah","last_name":"Nisarg","first_name":"Shah"}],"publist_id":"3282","title":"Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives","editor":[{"first_name":"Ganesh","last_name":"Gopalakrishnan","full_name":"Gopalakrishnan, Ganesh"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"}]},{"day":"16","year":"2011","doi":"10.1007/978-3-642-21254-3_16","date_published":"2011-06-16T00:00:00Z","date_created":"2018-12-11T12:02:48Z","page":"216 - 226","quality_controlled":"1","publisher":"Springer","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. Finitary Languages. Vol. 6638, Springer, 2011, pp. 216–26, doi:10.1007/978-3-642-21254-3_16.","short":"K. Chatterjee, N. Fijalkow, in:, Springer, 2011, pp. 216–226.","ieee":"K. Chatterjee and N. Fijalkow, “Finitary languages,” presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain, 2011, vol. 6638, pp. 216–226.","apa":"Chatterjee, K., & Fijalkow, N. (2011). Finitary languages (Vol. 6638, pp. 216–226). Presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain: Springer. https://doi.org/10.1007/978-3-642-21254-3_16","ama":"Chatterjee K, Fijalkow N. Finitary languages. In: Vol 6638. Springer; 2011:216-226. doi:10.1007/978-3-642-21254-3_16","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Finitary Languages,” 6638:216–26. Springer, 2011. https://doi.org/10.1007/978-3-642-21254-3_16.","ista":"Chatterjee K, Fijalkow N. 2011. Finitary languages. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 216–226."},"title":"Finitary languages","publist_id":"3274","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"A1B5DD72-E997-11E9-8398-E808B6C6ADC0","first_name":"Nathanaël","last_name":"Fijalkow","full_name":"Fijalkow, Nathanaël"}],"external_id":{"arxiv":["1101.1727"]},"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6638,"oa_version":"Preprint","abstract":[{"text":"The class of omega-regular languages provides a robust specification language in verification. Every omega-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens "eventually". Finitary liveness was proposed by Alur and Henzinger as a stronger formulation of liveness. It requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider automata with finitary acceptance conditions defined by finitary Buchi, parity and Streett languages. We study languages expressible by such automata: we give their topological complexity and present a regular-expression characterization. We compare the expressive power of finitary automata and give optimal algorithms for classical decisions questions. We show that the finitary languages are Sigma 2-complete; we present a complete picture of the expressive power of various classes of automata with finitary and infinitary acceptance conditions; we show that the languages defined by finitary parity automata exactly characterize the star-free fragment of omega B-regular languages; and we show that emptiness is NLOGSPACE-complete and universality as well as language inclusion are PSPACE-complete for finitary parity and Streett automata.","lang":"eng"}],"month":"06","intvolume":" 6638","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1101.1727"}],"date_updated":"2021-01-12T07:42:50Z","department":[{"_id":"KrCh"}],"_id":"3347","status":"public","type":"conference","conference":{"start_date":"2011-05-26","location":"Tarragona, Spain","end_date":"2011-05-31","name":"LATA: Language and Automata Theory and Applications"}},{"month":"06","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1104.3489","open_access":"1"}],"quality_controlled":"1","scopus_import":1,"publisher":"IEEE","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with k reward functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the single-objective case, both randomization and memory are necessary for strategies, and that finite-memory randomized strategies are sufficient. Under the satisfaction objective, in contrast to the single-objective case, infinite memory is necessary for strategies, and that randomized memoryless strategies are sufficient for epsilon-approximation, for all epsilon>;0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be epsilon-approximated in time polynomial in the size of the MDP and 1/epsilon, and exponential in the number of reward functions, for all epsilon>;0. Our results also reveal flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, correct the flaws and obtain improved results."}],"ec_funded":1,"date_created":"2018-12-11T12:02:48Z","date_published":"2011-06-21T00:00:00Z","doi":"10.1109/LICS.2011.10","language":[{"iso":"eng"}],"day":"21","year":"2011","publication_status":"published","status":"public","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"LICS: Logic in Computer Science","start_date":"2011-06-21","end_date":"2011-06-24","location":"Toronto, Canada"},"type":"conference","article_number":"5970225","_id":"3346","department":[{"_id":"KrCh"}],"title":"Two views on multiple mean payoff objectives in Markov Decision Processes","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Brožek","full_name":"Brožek, Václav","first_name":"Václav"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"last_name":"Kučera","full_name":"Kučera, Antonín","first_name":"Antonín"}],"publist_id":"3275","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2011. Two views on multiple mean payoff objectives in Markov Decision Processes. LICS: Logic in Computer Science, 5970225.","chicago":"Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Two Views on Multiple Mean Payoff Objectives in Markov Decision Processes.” IEEE, 2011. https://doi.org/10.1109/LICS.2011.10.","short":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, in:, IEEE, 2011.","ieee":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Two views on multiple mean payoff objectives in Markov Decision Processes,” presented at the LICS: Logic in Computer Science, Toronto, Canada, 2011.","ama":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Two views on multiple mean payoff objectives in Markov Decision Processes. In: IEEE; 2011. doi:10.1109/LICS.2011.10","apa":"Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., & Kučera, A. (2011). Two views on multiple mean payoff objectives in Markov Decision Processes. Presented at the LICS: Logic in Computer Science, Toronto, Canada: IEEE. https://doi.org/10.1109/LICS.2011.10","mla":"Brázdil, Tomáš, et al. Two Views on Multiple Mean Payoff Objectives in Markov Decision Processes. 5970225, IEEE, 2011, doi:10.1109/LICS.2011.10."},"date_updated":"2021-01-12T07:42:49Z"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:50Z","citation":{"ista":"Chatterjee K, Prabhu V. 2011. Synthesis of memory efficient real time controllers for safety objectives. HSCC: Hybrid Systems - Computation and Control, 221–230.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory Efficient Real Time Controllers for Safety Objectives,” 221–30. Springer, 2011. https://doi.org/10.1145/1967701.1967734.","ieee":"K. Chatterjee and V. Prabhu, “Synthesis of memory efficient real time controllers for safety objectives,” presented at the HSCC: Hybrid Systems - Computation and Control, Chicago, USA, 2011, pp. 221–230.","short":"K. Chatterjee, V. Prabhu, in:, Springer, 2011, pp. 221–230.","apa":"Chatterjee, K., & Prabhu, V. (2011). Synthesis of memory efficient real time controllers for safety objectives (pp. 221–230). Presented at the HSCC: Hybrid Systems - Computation and Control, Chicago, USA: Springer. https://doi.org/10.1145/1967701.1967734","ama":"Chatterjee K, Prabhu V. Synthesis of memory efficient real time controllers for safety objectives. In: Springer; 2011:221-230. doi:10.1145/1967701.1967734","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. Synthesis of Memory Efficient Real Time Controllers for Safety Objectives. Springer, 2011, pp. 221–30, doi:10.1145/1967701.1967734."},"title":"Synthesis of memory efficient real time controllers for safety objectives","department":[{"_id":"KrCh"}],"publist_id":"3273","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Prabhu","full_name":"Prabhu, Vinayak","first_name":"Vinayak"}],"_id":"3348","status":"public","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"type":"conference","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2011-04-12","end_date":"2011-04-14","location":"Chicago, USA"},"day":"31","language":[{"iso":"eng"}],"year":"2011","publication_status":"published","date_published":"2011-01-31T00:00:00Z","doi":"10.1145/1967701.1967734","date_created":"2018-12-11T12:02:49Z","page":"221 - 230","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two-player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a linear (in the number of clocks) number of memory bits. Precisely, we show that for safety objectives, a memory of size (3 · |C|+lg(|C|+1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential bound. We also settle the open question of whether winning region controller strategies require memory for safety objectives by showing with an example the necessity of memory for region strategies to win for safety objectives."}],"month":"01","publisher":"Springer","quality_controlled":"1","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1101.5842","open_access":"1"}]},{"date_created":"2018-12-11T12:02:47Z","doi":"10.1007/978-3-642-24288-5_1","date_published":"2011-10-15T00:00:00Z","volume":6945,"page":"1 - 1","language":[{"iso":"eng"}],"day":"15","year":"2011","publication_status":"published","intvolume":" 6945","month":"10","quality_controlled":"1","alternative_title":["LNCS"],"publisher":"Springer","oa_version":"None","abstract":[{"lang":"eng","text":"Games played on graphs provide the mathematical framework to analyze several important problems in computer science as well as mathematics, such as the synthesis problem of Church, model checking of open reactive systems and many others. On the basis of mode of interaction of the players these games can be classified as follows: (a) turn-based (players make moves in turns); and (b) concurrent (players make moves simultaneously). On the basis of the information available to the players these games can be classified as follows: (a) perfect-information (players have perfect view of the game); and (b) partial-information (players have partial view of the game). In this talk we will consider all these classes of games with reachability objectives, where the goal of one player is to reach a set of target vertices of the graph, and the goal of the opponent player is to prevent the player from reaching the target. We will survey the results for various classes of games, and the results range from linear time decision algorithms to EXPTIME-complete problems to undecidable problems."}],"editor":[{"last_name":"Delzanno","full_name":"Delzanno, Giorgo","first_name":"Giorgo"},{"full_name":"Potapov, Igor","last_name":"Potapov","first_name":"Igor"}],"department":[{"_id":"KrCh"}],"title":"Graph games with reachability objectives","publist_id":"3277","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:48Z","citation":{"ista":"Chatterjee K. 2011. Graph games with reachability objectives. RP: Reachability Problems, LNCS, vol. 6945, 1–1.","chicago":"Chatterjee, Krishnendu. “Graph Games with Reachability Objectives.” edited by Giorgo Delzanno and Igor Potapov, 6945:1–1. Springer, 2011. https://doi.org/10.1007/978-3-642-24288-5_1.","ieee":"K. Chatterjee, “Graph games with reachability objectives,” presented at the RP: Reachability Problems, Genoa, Italy, 2011, vol. 6945, pp. 1–1.","short":"K. Chatterjee, in:, G. Delzanno, I. Potapov (Eds.), Springer, 2011, pp. 1–1.","apa":"Chatterjee, K. (2011). Graph games with reachability objectives. In G. Delzanno & I. Potapov (Eds.) (Vol. 6945, pp. 1–1). Presented at the RP: Reachability Problems, Genoa, Italy: Springer. https://doi.org/10.1007/978-3-642-24288-5_1","ama":"Chatterjee K. Graph games with reachability objectives. In: Delzanno G, Potapov I, eds. Vol 6945. Springer; 2011:1-1. doi:10.1007/978-3-642-24288-5_1","mla":"Chatterjee, Krishnendu. Graph Games with Reachability Objectives. Edited by Giorgo Delzanno and Igor Potapov, vol. 6945, Springer, 2011, pp. 1–1, doi:10.1007/978-3-642-24288-5_1."},"status":"public","conference":{"name":"RP: Reachability Problems","start_date":"2011-09-28","end_date":"2011-09-30","location":"Genoa, Italy"},"type":"conference","_id":"3344"},{"date_created":"2018-12-11T12:02:47Z","doi":"10.1137/1.9781611973082.101","date_published":"2011-01-01T00:00:00Z","page":"1318 - 1336","language":[{"iso":"eng"}],"day":"01","year":"2011","publication_status":"published","month":"01","main_file_link":[{"url":"https://eprints.cs.univie.ac.at/21/","open_access":"1"}],"oa":1,"scopus_import":"1","quality_controlled":"1","publisher":"SIAM","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present faster and dynamic algorithms for the following problems arising in probabilistic verification: Computation of the maximal end-component (mec) decomposition of Markov decision processes (MDPs), and of the almost sure winning set for reachability and parity objectives in MDPs. We achieve the following running time for static algorithms in MDPs with graphs of n vertices and m edges: (1) O(m · min{ √m, n2/3 }) for the mec decomposition, improving the longstanding O(m·n) bound; (2) O(m·n2/3) for reachability objectives, improving the previous O(m · √m) bound for m > n4/3; and (3) O(m · min{ √m, n2/3 } · log(d)) for parity objectives with d priorities, improving the previous O(m · √m · d) bound. We also give incremental and decremental algorithms in linear time for mec decomposition and reachability objectives and O(m · log d) time for parity ob jectives."}],"title":"Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification","department":[{"_id":"KrCh"}],"article_processing_charge":"No","publist_id":"3278","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. “Faster and Dynamic Algorithms for Maximal End-Component Decomposition and Related Graph Problems in Probabilistic Verification,” 1318–36. SIAM, 2011. https://doi.org/10.1137/1.9781611973082.101.","ista":"Chatterjee K, Henzinger MH. 2011. Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification. SODA: Symposium on Discrete Algorithms, 1318–1336.","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. Faster and Dynamic Algorithms for Maximal End-Component Decomposition and Related Graph Problems in Probabilistic Verification. SIAM, 2011, pp. 1318–36, doi:10.1137/1.9781611973082.101.","ama":"Chatterjee K, Henzinger MH. Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification. In: SIAM; 2011:1318-1336. doi:10.1137/1.9781611973082.101","apa":"Chatterjee, K., & Henzinger, M. H. (2011). Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification (pp. 1318–1336). Presented at the SODA: Symposium on Discrete Algorithms, San Francisco, SA, United States: SIAM. https://doi.org/10.1137/1.9781611973082.101","ieee":"K. Chatterjee and M. H. Henzinger, “Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification,” presented at the SODA: Symposium on Discrete Algorithms, San Francisco, SA, United States, 2011, pp. 1318–1336.","short":"K. Chatterjee, M.H. Henzinger, in:, SIAM, 2011, pp. 1318–1336."},"date_updated":"2023-02-14T10:36:10Z","status":"public","conference":{"start_date":"2011-01-23","location":"San Francisco, SA, United States","end_date":"2011-01-25","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","_id":"3343"},{"page":"82 - 96","date_created":"2018-12-11T12:02:53Z","date_published":"2011-08-31T00:00:00Z","doi":"10.4230/LIPIcs.CSL.2011.82","year":"2011","has_accepted_license":"1","day":"31","oa":1,"publisher":"Springer","quality_controlled":"1","author":[{"first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","last_name":"Boker"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3255","title":"Determinizing discounted-sum automata","citation":{"ama":"Boker U, Henzinger TA. Determinizing discounted-sum automata. In: Vol 12. Springer; 2011:82-96. doi:10.4230/LIPIcs.CSL.2011.82","apa":"Boker, U., & Henzinger, T. A. (2011). Determinizing discounted-sum automata (Vol. 12, pp. 82–96). Presented at the CSL: Computer Science Logic, Bergen, Norway: Springer. https://doi.org/10.4230/LIPIcs.CSL.2011.82","ieee":"U. Boker and T. A. Henzinger, “Determinizing discounted-sum automata,” presented at the CSL: Computer Science Logic, Bergen, Norway, 2011, vol. 12, pp. 82–96.","short":"U. Boker, T.A. Henzinger, in:, Springer, 2011, pp. 82–96.","mla":"Boker, Udi, and Thomas A. Henzinger. Determinizing Discounted-Sum Automata. Vol. 12, Springer, 2011, pp. 82–96, doi:10.4230/LIPIcs.CSL.2011.82.","ista":"Boker U, Henzinger TA. 2011. Determinizing discounted-sum automata. CSL: Computer Science Logic, LIPIcs, vol. 12, 82–96.","chicago":"Boker, Udi, and Thomas A Henzinger. “Determinizing Discounted-Sum Automata,” 12:82–96. Springer, 2011. https://doi.org/10.4230/LIPIcs.CSL.2011.82."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"volume":12,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2012-82-v1+1_Determinizing_discounted-sum_automata.pdf","date_created":"2018-12-12T10:10:17Z","file_size":504270,"date_updated":"2020-07-14T12:46:10Z","creator":"system","file_id":"4803","checksum":"250603c6be8ccad4fbd4d7b24221f0ee","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 12","month":"08","abstract":[{"lang":"eng","text":"A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, which values a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by lambda^i, where the discount factor lambda is a fixed rational number greater than 1. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, which reflects the assumption that earlier weights are more important than later weights. Determinizing automata is often essential, for example, in formal verification, where there are polynomial algorithms for comparing two deterministic NDAs, while the equivalence problem for NDAs is not known to be decidable. Unfortunately, however, discounted-sum automata are, in general, not determinizable: it is currently known that for every rational discount factor 1 < lambda < 2, there is an NDA with lambda (denoted lambda-NDA) that cannot be determinized. We provide positive news, showing that every NDA with an integral factor is determinizable. We also complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: we show that for every non-integral rational factor lambda, there is a nondeterminizable lambda-NDA. Finally, we prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. This shows that for integral discount factors, the class of NDAs forms an attractive specification formalism in quantitative formal verification. All our results hold equally for automata over finite words and for automata over infinite words. "}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:10Z","date_updated":"2021-01-12T07:42:56Z","ddc":["004"],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"conference":{"location":"Bergen, Norway","end_date":"2011-09-15","start_date":"2011-09-12","name":"CSL: Computer Science Logic"},"type":"conference","pubrep_id":"82","status":"public","_id":"3360"}]