[{"alternative_title":["LNCS"],"type":"conference","extern":1,"publist_id":"3478","abstract":[{"lang":"eng","text":"We introduce a new class of functions that can be minimized in polynomial time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥ f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree. Special cases include previously studied L-convex and bisubmodular functions, which can be obtained with particular choices of trees. We present a polynomial-time algorithm for minimizing functions in the new class. It combines Murota's steepest descent algorithm for L-convex functions with bisubmodular minimization algorithms. "}],"intvolume":" 6907","publisher":"Springer","publication_status":"published","title":"Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions","status":"public","_id":"3204","year":"2011","volume":6907,"date_created":"2018-12-11T12:02:00Z","date_updated":"2021-01-12T07:41:47Z","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"}],"day":"09","month":"08","page":"400 - 411","quality_controlled":0,"main_file_link":[{"open_access":"0","url":"http://arxiv.org/pdf/1007.1229v3"}],"citation":{"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.","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","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.","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","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.","short":"V. Kolmogorov, in:, Springer, 2011, pp. 400–411.","mla":"Kolmogorov, Vladimir. Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions. Vol. 6907, Springer, 2011, pp. 400–11, doi:10.1007/978-3-642-22993-0_37."},"doi":"10.1007/978-3-642-22993-0_37","date_published":"2011-08-09T00:00:00Z","conference":{"name":"MFCS: Mathematical Foundations of Computer Science"}},{"abstract":[{"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.","lang":"eng"}],"publist_id":"3476","extern":1,"type":"conference","author":[{"last_name":"Osokin","first_name":"Anton","full_name":"Osokin, Anton"},{"first_name":"Dmitry","last_name":"Vetrov","full_name":"Vetrov, Dmitry"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"}],"date_updated":"2021-01-12T07:41:47Z","date_created":"2018-12-11T12:02:00Z","year":"2011","_id":"3206","publication_status":"published","title":"Submodular decomposition framework for inference in associative Markov networks with global constraints","status":"public","publisher":"IEEE","day":"22","month":"08","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"date_published":"2011-08-22T00:00:00Z","doi":"10.1109/CVPR.2011.5995361","main_file_link":[{"url":"http://arxiv.org/pdf/1103.1077v1","open_access":"0"}],"citation":{"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","ieee":"A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework for inference in associative Markov networks with global constraints,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896.","ista":"Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework for inference in associative Markov networks with global constraints. CVPR: Computer Vision and Pattern Recognition, 1889–1896.","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","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.","short":"A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896.","mla":"Osokin, Anton, et al. Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints. IEEE, 2011, pp. 1889–96, doi:10.1109/CVPR.2011.5995361."},"quality_controlled":0,"page":"1889 - 1896"},{"type":"conference","abstract":[{"lang":"eng","text":"This paper proposes a novel Linear Programming (LP) based algorithm, called Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori (MAP) inference in probabilistic graphical models. Unlike traditional message passing algorithms, which operate uniformly on the whole factor graph, our method dynamically chooses regions of the factor graph on which to focus message-passing efforts. We propose two criteria for selecting regions, including an efficiently computable upper-bound on the increase in the objective possible by passing messages in any particular region. This bound is derived from the theory of primal-dual methods from combinatorial optimization, and the forest that maximizes the bounds can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental results show that our dynamic schedules significantly speed up state-of-the-art LP-based message-passing algorithms on a wide variety of real-world problems."}],"publist_id":"3475","extern":1,"_id":"3205","year":"2011","status":"public","publication_status":"published","title":"Dynamic tree block coordinate ascent","publisher":"Omnipress","author":[{"full_name":"Tarlow, Daniel","last_name":"Tarlow","first_name":"Daniel"},{"last_name":"Batra","first_name":"Druv","full_name":"Batra, Druv"},{"last_name":"Kohli","first_name":"Pushmeet","full_name":"Kohli, Pushmeet"},{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"}],"date_updated":"2021-01-12T07:41:47Z","date_created":"2018-12-11T12:02:00Z","day":"01","month":"01","citation":{"short":"D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120.","mla":"Tarlow, Daniel, et al. Dynamic Tree Block Coordinate Ascent. Omnipress, 2011, pp. 113–20.","chicago":"Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011.","ama":"Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent. In: Omnipress; 2011:113-120.","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.","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.","ista":"Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate ascent. ICML: International Conference on Machine Learning, 113–120."},"main_file_link":[{"url":"http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf","open_access":"0"}],"quality_controlled":0,"page":"113 - 120","conference":{"name":"ICML: International Conference on Machine Learning"},"date_published":"2011-01-01T00:00:00Z"},{"day":"22","month":"08","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"doi":"10.1109/CVPR.2011.5995530","date_published":"2011-08-22T00:00:00Z","quality_controlled":0,"page":"2217 - 2224","citation":{"short":"S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.","mla":"Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24, doi:10.1109/CVPR.2011.5995530.","chicago":"Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,” 2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530.","ama":"Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224. doi:10.1109/CVPR.2011.5995530","apa":"Vicente, S., Rother, C., & Kolmogorov, V. (2011). Object cosegmentation (pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2011.5995530","ieee":"S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.","ista":"Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer Vision and Pattern Recognition, 2217–2224."},"extern":1,"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."}],"publist_id":"3477","type":"conference","date_updated":"2021-01-12T07:41:48Z","date_created":"2018-12-11T12:02:01Z","author":[{"full_name":"Vicente, Sara","first_name":"Sara","last_name":"Vicente"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"}],"title":"Object cosegmentation","status":"public","publication_status":"published","publisher":"IEEE","year":"2011","_id":"3207"},{"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.","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","ieee":"B. Barak et al., “Leftover hash lemma revisited,” presented at the CRYPTO: International Cryptology Conference, 2011, vol. 6841, 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","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.","mla":"Barak, Boaz, et al. Leftover Hash Lemma Revisited. Vol. 6841, Springer, 2011, pp. 1–20, doi: 10.1007/978-3-642-22792-9_1.","short":"B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert, Y. Yu, in:, Springer, 2011, pp. 1–20."},"page":"1 - 20","quality_controlled":0,"doi":" 10.1007/978-3-642-22792-9_1","date_published":"2011-01-01T00:00:00Z","conference":{"name":"CRYPTO: International Cryptology Conference"},"day":"01","month":"01","year":"2011","_id":"3240","publisher":"Springer","intvolume":" 6841","title":"Leftover hash lemma revisited","publication_status":"published","status":"public","author":[{"full_name":"Barak, Boaz","first_name":"Boaz","last_name":"Barak"},{"full_name":"Dodis, Yevgeniy","last_name":"Dodis","first_name":"Yevgeniy"},{"first_name":"Hugo","last_name":"Krawczyk","full_name":"Krawczyk, Hugo"},{"first_name":"Olivier","last_name":"Pereira","full_name":"Pereira, Olivier"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak"},{"full_name":"Standaert, François-Xavier","last_name":"Standaert","first_name":"François"},{"full_name":"Yu, Yu","last_name":"Yu","first_name":"Yu"}],"volume":6841,"date_created":"2018-12-11T12:02:12Z","date_updated":"2021-01-12T07:42:03Z","type":"conference","alternative_title":["LNCS"],"publist_id":"3440","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."}],"extern":1},{"type":"conference","alternative_title":["LNCS"],"publist_id":"3383","ec_funded":1,"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."}],"year":"2011","_id":"3264","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","editor":[{"full_name":"Yang, Hongseok","first_name":"Hongseok","last_name":"Yang"}],"intvolume":" 7078","department":[{"_id":"ToHe"}],"publisher":"Springer","status":"public","title":"Solving recursion-free Horn clauses over LI+UIF","publication_status":"published","author":[{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","first_name":"Ashutosh"},{"full_name":"Popeea, Corneliu","last_name":"Popeea","first_name":"Corneliu"},{"first_name":"Andrey","last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey"}],"volume":7078,"oa_version":"None","date_created":"2018-12-11T12:02:20Z","date_updated":"2021-01-12T07:42:15Z","day":"05","month":"12","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.","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","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.","mla":"Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF. Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16.","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203."},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"page":"188 - 203","quality_controlled":"1","doi":"10.1007/978-3-642-25318-8_16","date_published":"2011-12-05T00:00:00Z","conference":{"start_date":"2011-12-05","location":"Kenting, Taiwan","end_date":"2011-12-07","name":"APLAS: Asian Symposium on Programming Languages and Systems"},"language":[{"iso":"eng"}]},{"_id":"3266","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems Foundation","intvolume":" 24","department":[{"_id":"HeEd"}],"publication_status":"published","status":"public","title":"Probabilistic joint image segmentation and labeling","author":[{"full_name":"Ion, Adrian","first_name":"Adrian","last_name":"Ion","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Carreira, Joao","last_name":"Carreira","first_name":"Joao"},{"full_name":"Sminchisescu, Cristian","last_name":"Sminchisescu","first_name":"Cristian"}],"volume":24,"oa_version":"None","date_created":"2018-12-11T12:02:21Z","date_updated":"2021-01-12T07:42:15Z","type":"conference","publist_id":"3381","abstract":[{"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.","lang":"eng"}],"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.","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.","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.","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.","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.","mla":"Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.” NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation, 2011, pp. 1827–35.","short":"A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835."},"publication":"NIPS Proceedings","page":"1827 - 1835","quality_controlled":"1","date_published":"2011-12-01T00:00:00Z","conference":{"start_date":"2011-12-12","location":"Granada, Spain","end_date":"2011-12-14","name":"NIPS: Neural Information Processing Systems"},"language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"12"},{"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf"}],"quality_controlled":"1","doi":"10.1111/j.1467-8659.2011.01985.x","language":[{"iso":"eng"}],"publist_id":"3377","year":"2011","department":[{"_id":"HeEd"}],"publisher":"Wiley-Blackwell","publication_status":"published","author":[{"full_name":"Sheng, Yu","first_name":"Yu","last_name":"Sheng"},{"full_name":"Cutler, Barbara","first_name":"Barbara","last_name":"Cutler"},{"first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"last_name":"Nasman","first_name":"Joshua","full_name":"Nasman, Joshua"}],"volume":30,"date_updated":"2021-01-12T07:42:16Z","date_created":"2018-12-11T12:02:22Z","scopus_import":1,"article_processing_charge":"No","day":"19","citation":{"ama":"Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 2011;30(4):1261-1268. doi:10.1111/j.1467-8659.2011.01985.x","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.","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","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.","mla":"Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” Computer Graphics Forum, vol. 30, no. 4, Wiley-Blackwell, 2011, pp. 1261–68, doi:10.1111/j.1467-8659.2011.01985.x.","short":"Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268.","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."},"publication":"Computer Graphics Forum","page":"1261 - 1268","article_type":"original","date_published":"2011-07-19T00:00:00Z","type":"journal_article","issue":"4","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3269","intvolume":" 30","status":"public","title":"Perceptual global illumination cancellation in complex projection environments","oa_version":"Published Version"},{"author":[{"last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"full_name":"Freedman, Daniel","last_name":"Freedman","first_name":"Daniel"}],"related_material":{"record":[{"id":"10909","relation":"earlier_version","status":"public"}]},"date_updated":"2023-02-21T16:07:10Z","date_created":"2018-12-11T12:02:21Z","volume":45,"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3267","year":"2011","status":"public","title":"Hardness results for homology localization","publication_status":"published","publisher":"Springer","intvolume":" 45","department":[{"_id":"HeEd"}],"abstract":[{"text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We 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.","lang":"eng"}],"publist_id":"3379","issue":"3","type":"journal_article","date_published":"2011-01-14T00:00:00Z","doi":"10.1007/s00454-010-9322-8","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","citation":{"short":"C. Chen, D. Freedman, Discrete & Computational Geometry 45 (2011) 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.","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.","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","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete & Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011.","ista":"Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete & Computational Geometry. 45(3), 425–448."},"quality_controlled":"1","page":"425 - 448","day":"14","month":"01","scopus_import":1},{"day":"30","month":"11","language":[{"iso":"eng"}],"date_published":"2011-11-30T00:00:00Z","page":"239 - 268","quality_controlled":"1","citation":{"ama":"Freedman D, Chen C. Algebraic topology for computer vision. In: Computer Vision. Nova Science Publishers; 2011:239-268.","ista":"Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer Vision. Computer Science, Technology and Applications, , 239–268.","ieee":"D. Freedman and C. Chen, “Algebraic topology for computer vision,” in Computer Vision, Nova Science Publishers, 2011, pp. 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.","short":"D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011, pp. 239–268.","chicago":"Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” In Computer Vision, 239–68. Nova Science Publishers, 2011."},"main_file_link":[{"url":"http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf"}],"publication":"Computer Vision","extern":"1","publist_id":"3378","abstract":[{"lang":"eng","text":"Algebraic topology is generally considered one of the purest subfield of mathematics. However, over the last decade two interesting new lines of research have emerged, one focusing on algorithms for algebraic topology, and the other on applications of algebraic topology in engineering and science. Amongst the new areas in which the techniques have been applied are computer vision and image processing. In this paper, we survey the results of these endeavours. Because algebraic topology is an area of mathematics with which most computer vision practitioners have no experience, we review the machinery behind the theories of homology and persistent homology; our review emphasizes intuitive explanations. In terms of applications to computer vision, we focus on four illustrative problems: shape signatures, natural image statistics, image denoising, and segmentation. Our hope is that this review will stimulate interest on the part of computer vision researchers to both use and extend the tools of this new field. "}],"alternative_title":["Computer Science, Technology and Applications"],"type":"book_chapter","oa_version":"None","date_created":"2018-12-11T12:02:22Z","date_updated":"2021-01-12T07:42:16Z","author":[{"first_name":"Daniel","last_name":"Freedman","full_name":"Freedman, Daniel"},{"full_name":"Chen, Chao","first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Nova Science Publishers","title":"Algebraic topology for computer vision","publication_status":"published","status":"public","year":"2011","_id":"3268","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6399","relation":"main_file","date_updated":"2020-07-14T12:46:06Z","date_created":"2019-05-10T10:51:43Z","checksum":"57a5eb11dd05241c48c44f492b3ec3ac","file_name":"2011_PLOS_Smutny.PDF","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1984567}],"intvolume":" 6","ddc":["570"],"title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens","status":"public","_id":"3288","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"22","date_published":"2011-07-22T00:00:00Z","citation":{"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.","mla":"Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458.","short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).","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).","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","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.","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"},"publication":"PLoS One","license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"3357","file_date_updated":"2020-07-14T12:46:06Z","volume":6,"date_created":"2018-12-11T12:02:28Z","date_updated":"2021-01-12T07:42:25Z","author":[{"orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","first_name":"Michael","full_name":"Smutny, Michael"},{"full_name":"Wu, Selwin","first_name":"Selwin","last_name":"Wu"},{"last_name":"Gomez","first_name":"Guillermo","full_name":"Gomez, Guillermo"},{"full_name":"Mangold, Sabine","first_name":"Sabine","last_name":"Mangold"},{"last_name":"Yap","first_name":"Alpha","full_name":"Yap, Alpha"},{"full_name":"Hamilton, Nicholas","first_name":"Nicholas","last_name":"Hamilton"}],"department":[{"_id":"CaHe"}],"publisher":"Public Library of Science","publication_status":"published","year":"2011","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.","month":"07","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0022458","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"abstract":[{"lang":"eng","text":"Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes by electrostatic interactions with negatively charged lipids. It turned out that for inhibition of microbial growth a high CAMP membrane concentration is required, which can be realized by the incorporation of hydrophobic groups within the peptide. Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial over eukaryotic host membranes, thereby causing the risk of detrimental side-effects. In this study we addressed how cationic amphipathic peptides—in particular a CAMP with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics of molecules in eukaryotic membranes. We found KLK to selectively inhibit the endocytosis of a subgroup of membrane proteins and lipids by electrostatically interacting with negatively charged sialic acid moieties. Ultrastructural characterization revealed the formation of membrane invaginations representing fission or fusion intermediates, in which the sialylated proteins and lipids were immobilized. Experiments on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively arrest sialylated membrane constituents."}],"issue":"10","publist_id":"3359","extern":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","author":[{"first_name":"Julian","last_name":"Weghuber","full_name":"Weghuber, Julian"},{"full_name":"Aichinger, Michael C.","first_name":"Michael","last_name":"Aichinger"},{"full_name":"Brameshuber, Mario","last_name":"Brameshuber","first_name":"Mario"},{"full_name":"Stefan Wieser","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","first_name":"Stefan"},{"first_name":"Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Verena Ruprecht"},{"first_name":"Birgit","last_name":"Plochberger","full_name":"Plochberger, Birgit"},{"first_name":"Josef","last_name":"Madl","full_name":"Madl, Josef"},{"first_name":"Andreas","last_name":"Horner","full_name":"Horner, Andreas"},{"first_name":"Siegfried","last_name":"Reipert","full_name":"Reipert, Siegfried"},{"last_name":"Lohner","first_name":"Karl","full_name":"Lohner, Karl"},{"first_name":"Tamas","last_name":"Henics","full_name":"Henics, Tamas"},{"full_name":"Schuetz, Gerhard J","last_name":"Schuetz","first_name":"Gerhard"}],"date_updated":"2021-01-12T07:42:24Z","date_created":"2018-12-11T12:02:28Z","volume":1808,"year":"2011","_id":"3286","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. ","status":"public","publication_status":"published","title":"Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells","publisher":"Elsevier","intvolume":" 1808","month":"10","day":"01","doi":"10.1016/j.bbamem.2011.06.007","date_published":"2011-10-01T00:00:00Z","publication":"Biochimica et Biophysica Acta (BBA) - Biomembranes","tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"ama":"Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590. doi:10.1016/j.bbamem.2011.06.007","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.","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.","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","mla":"Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011, pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007.","short":"J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger, J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.","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."},"quality_controlled":0,"page":"2581 - 2590"},{"month":"12","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.2174/138920311798841753","date_published":"2011-12-01T00:00:00Z","page":"714 - 724","quality_controlled":"1","citation":{"short":"V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide Science 12 (2011) 714–724.","mla":"Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753.","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.","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","ieee":"V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” Current Protein & Peptide Science, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.","ista":"Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724."},"publication":"Current Protein & Peptide Science","issue":"8","publist_id":"3358","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."}],"type":"journal_article","oa_version":"None","volume":12,"date_created":"2018-12-11T12:02:28Z","date_updated":"2021-01-12T07:42:24Z","author":[{"first_name":"Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena"},{"full_name":"Axmann, Markus","first_name":"Markus","last_name":"Axmann"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan"},{"last_name":"Schuetz","first_name":"Gerhard","full_name":"Schuetz, Gerhard"}],"department":[{"_id":"CaHe"},{"_id":"MiSi"}],"publisher":"Bentham Science Publishers","intvolume":" 12","publication_status":"published","title":"What can we learn from single molecule trajectories?","status":"public","_id":"3287","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011"},{"language":[{"iso":"eng"}],"date_published":"2011-06-08T00:00:00Z","doi":"10.1016/j.bpj.2011.04.035","page":"2839 - 2845","citation":{"mla":"Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035.","short":"V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011) 2839–2845.","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.","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","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.","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","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."},"publication":"Biophysical Journal","day":"08","month":"06","oa_version":"None","volume":100,"date_updated":"2021-01-12T07:42:23Z","date_created":"2018-12-11T12:02:27Z","author":[{"first_name":"Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena"},{"orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","first_name":"Stefan","full_name":"Wieser, Stefan"},{"last_name":"Marguet","first_name":"Didier","full_name":"Marguet, Didier"},{"full_name":"Schuetz, Gerhard","first_name":"Gerhard","last_name":"Schuetz"}],"publisher":"Biophysical Society","intvolume":" 100","title":"Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes","publication_status":"published","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3285","acknowledgement":"Y 250-B03/Austrian Science Fund FWF/Austria","year":"2011","extern":"1","publist_id":"3360","issue":"11","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"conference":{"start_date":"2011-06-14","end_date":"2011-06-15","name":"HotCloud: Workshop on Hot Topics in Cloud Computing"},"date_published":"2011-06-14T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 2011, pp. 1–6.","short":"T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6.","chicago":"Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey. “Static Scheduling in Clouds,” 1–6. USENIX, 2011.","ama":"Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds. In: USENIX; 2011:1-6.","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.","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.","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."},"oa":1,"quality_controlled":"1","page":"1 - 6","day":"14","month":"06","has_accepted_license":"1","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Anmol","last_name":"Singh","id":"72A86902-E99F-11E9-9F62-915534D1B916","full_name":"Singh, Anmol"},{"full_name":"Singh, Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu","last_name":"Singh"},{"full_name":"Wies, Thomas","first_name":"Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","first_name":"Damien","last_name":"Zufferey","full_name":"Zufferey, Damien"}],"pubrep_id":"90","date_updated":"2021-01-12T07:42:31Z","date_created":"2018-12-11T12:02:33Z","oa_version":"Submitted Version","file":[{"file_name":"IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf","access_level":"open_access","content_type":"application/pdf","file_size":232770,"creator":"system","relation":"main_file","file_id":"5333","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:18:14Z","checksum":"21a461ac004bb535c83320fe79b30375"}],"_id":"3302","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","005"],"publication_status":"published","title":"Static scheduling in clouds","status":"public","publisher":"USENIX","department":[{"_id":"ToHe"}],"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","publist_id":"3338","type":"conference"},{"author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Mateescu, Maria","first_name":"Maria","last_name":"Mateescu"}],"pubrep_id":"91","date_created":"2018-12-11T12:02:33Z","date_updated":"2021-01-12T07:42:30Z","file":[{"file_name":"IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":240820,"file_id":"5331","relation":"main_file","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:18:12Z","checksum":"aa4d7a832a5419e6c0090650ebff2b9a"}],"oa_version":"Submitted Version","_id":"3301","year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Tail approximation for the chemical master equation","ddc":["005","570"],"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Tampere International Center for Signal Processing","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."}],"file_date_updated":"2020-07-14T12:46:06Z","publist_id":"3339","type":"conference","conference":{"name":"WCSB: Workshop on Computational Systems Biology (TICSP)"},"date_published":"2011-01-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"chicago":"Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011.","mla":"Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical Master Equation. Tampere International Center for Signal Processing, 2011.","short":"T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal Processing, 2011.","ista":"Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP).","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.","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.","ama":"Henzinger TA, Mateescu M. Tail approximation for the chemical master equation. In: Tampere International Center for Signal Processing; 2011."},"quality_controlled":"1","month":"01","day":"01","has_accepted_license":"1"},{"file":[{"creator":"system","file_size":255780,"content_type":"application/pdf","file_name":"IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf","access_level":"open_access","date_created":"2018-12-12T10:07:50Z","date_updated":"2020-07-14T12:46:06Z","checksum":"7f5c65509db1a9fb049abedd9663ed06","file_id":"4649","relation":"main_file"}],"oa_version":"Submitted Version","pubrep_id":"92","title":"Propagation models for computing biochemical reaction networks","status":"public","ddc":["000","004"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3299","abstract":[{"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.","lang":"eng"}],"type":"conference","date_published":"2011-09-21T00:00:00Z","page":"1 - 3","citation":{"ama":"Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction networks. In: Springer; 2011:1-3. doi: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.","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.","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","mla":"Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510.","short":"T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.","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."},"day":"21","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T12:02:32Z","date_updated":"2021-01-12T07:42:29Z","author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Mateescu","first_name":"Maria","full_name":"Mateescu, Maria"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"year":"2011","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"3341","language":[{"iso":"eng"}],"conference":{"name":"CMSB: Computational Methods in Systems Biology","end_date":"2011-09-23","location":"Paris, France","start_date":"2011-09-21"},"doi":"10.1145/2037509.2037510","quality_controlled":"1","oa":1,"month":"09"},{"ec_funded":1,"publist_id":"3323","date_created":"2018-12-11T12:02:38Z","date_updated":"2021-01-12T07:42:36Z","author":[{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Greimel, Karin","first_name":"Karin","last_name":"Greimel"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","year":"2011","month":"07","language":[{"iso":"eng"}],"doi":"10.1109/SIES.2011.5953660","conference":{"location":"Vasteras, Sweden","start_date":"2011-06-15","end_date":"2011-06-17","name":" SIES: International Symposium on Industrial Embedded Systems"},"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse"}],"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."}],"type":"conference","oa_version":"Published Version","status":"public","title":"Specification-centered robustness","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3316","article_processing_charge":"No","day":"14","scopus_import":1,"date_published":"2011-07-14T00:00:00Z","page":"176 - 185","citation":{"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.","mla":"Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660.","short":"R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–185.","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.","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","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.","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"},"publication":"6th IEEE International Symposium on Industrial and Embedded Systems"},{"month":"12","day":"04","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2011-12-04T00:00:00Z","doi":"10.1038/nn.3002","page":"20 - 22","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/"}],"citation":{"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.","mla":"Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” Nature Neuroscience, vol. 15, Nature Publishing Group, 2011, pp. 20–22, doi:10.1038/nn.3002.","short":"E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22.","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.","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.","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"},"oa":1,"publication":"Nature Neuroscience","publist_id":"3321","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","volume":15,"date_created":"2018-12-11T12:02:38Z","date_updated":"2021-01-12T07:42:37Z","author":[{"first_name":"Emmanuel","last_name":"Eggermann","full_name":"Eggermann, Emmanuel"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"publisher":"Nature Publishing Group","intvolume":" 15","department":[{"_id":"PeJo"}],"title":"How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses","status":"public","publication_status":"published","_id":"3318","year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"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"}],"alternative_title":["LNCS"],"type":"book_chapter","oa_version":"Preprint","intvolume":" 6970","status":"public","title":"Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3335","day":"09","series_title":"Special Issue on Voronoi Diagrams and Delaunay Triangulation","scopus_import":1,"date_published":"2011-11-09T00:00:00Z","page":"60 - 101","citation":{"ama":"Van De Weygaert R, Vegter G, Edelsbrunner H, et al. Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In: Gavrilova M, Tan K, Mostafavi M, eds. Transactions on Computational Science XIV. Vol 6970. Special Issue on Voronoi Diagrams and Delaunay Triangulation. Springer; 2011:60-101. doi:10.1007/978-3-642-25249-5_3","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.","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.","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","mla":"Van De Weygaert, Rien, et al. “Alpha, Betti and the Megaparsec Universe: On the Topology of the Cosmic Web.” Transactions on Computational Science XIV, edited by Marina Gavrilova et al., vol. 6970, Springer, 2011, pp. 60–101, doi:10.1007/978-3-642-25249-5_3.","short":"R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park, W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi (Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101.","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."},"publication":"Transactions on Computational Science XIV","publist_id":"3295","volume":6970,"date_updated":"2021-01-12T07:42:44Z","date_created":"2018-12-11T12:02:44Z","author":[{"last_name":"Van De Weygaert","first_name":"Rien","full_name":"Van De Weygaert, Rien"},{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jones, Bernard","first_name":"Bernard","last_name":"Jones"},{"first_name":"Pratyush","last_name":"Pranav","full_name":"Pranav, Pratyush"},{"full_name":"Park, Changbom","first_name":"Changbom","last_name":"Park"},{"full_name":"Hellwing, Wojciech","last_name":"Hellwing","first_name":"Wojciech"},{"last_name":"Eldering","first_name":"Bob","full_name":"Eldering, Bob"},{"full_name":"Kruithof, Nico","first_name":"Nico","last_name":"Kruithof"},{"full_name":"Bos, Patrick","last_name":"Bos","first_name":"Patrick"},{"last_name":"Hidding","first_name":"Johan","full_name":"Hidding, Johan"},{"full_name":"Feldbrugge, Job","last_name":"Feldbrugge","first_name":"Job"},{"last_name":"Ten Have","first_name":"Eline","full_name":"Ten Have, Eline"},{"first_name":"Matti","last_name":"Van Engelen","full_name":"Van Engelen, Matti"},{"full_name":"Caroli, Manuel","first_name":"Manuel","last_name":"Caroli"},{"full_name":"Teillaud, Monique","first_name":"Monique","last_name":"Teillaud"}],"editor":[{"full_name":"Gavrilova, Marina","last_name":"Gavrilova","first_name":"Marina"},{"last_name":"Tan","first_name":"Kenneth","full_name":"Tan, Kenneth"},{"first_name":"Mir","last_name":"Mostafavi","full_name":"Mostafavi, Mir"}],"department":[{"_id":"HeEd"}],"publisher":"Springer","publication_status":"published","year":"2011","month":"11","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-25249-5_3","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1306.3640"]},"main_file_link":[{"url":"http://arxiv.org/abs/1306.3640","open_access":"1"}]}]