[{"doi":"10.1007/978-3-319-58771-4_19","year":"2017","publication_status":"published","editor":[{"first_name":"François","full_name":"Lauze, François","last_name":"Lauze"},{"last_name":"Dong","first_name":"Yiqiu","full_name":"Dong, Yiqiu"},{"full_name":"Bjorholm Dahl, Anders","first_name":"Anders","last_name":"Bjorholm Dahl"}],"oa_version":"Submitted Version","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"date_published":"2017-06-01T00:00:00Z","conference":{"start_date":"2017-06-04","end_date":"2017-06-08","location":"Kolding, Denmark","name":"SSVM: Scale Space and Variational Methods in Computer Vision"},"month":"06","intvolume":"     10302","author":[{"last_name":"Kuske","full_name":"Kuske, Jan","first_name":"Jan"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul"},{"first_name":"Stefanie","full_name":"Petra, Stefanie","last_name":"Petra"}],"quality_controlled":"1","publist_id":"7132","type":"conference","page":"235 - 246","publication_identifier":{"isbn":["978-331958770-7"]},"title":"A novel convex relaxation for non binary discrete tomography","scopus_import":1,"status":"public","ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:47:41Z","abstract":[{"lang":"eng","text":"We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations."}],"volume":10302,"main_file_link":[{"url":"https://arxiv.org/abs/1703.03769","open_access":"1"}],"date_updated":"2021-01-12T08:07:34Z","oa":1,"citation":{"chicago":"Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">https://doi.org/10.1007/978-3-319-58771-4_19</a>.","mla":"Kuske, Jan, et al. <i>A Novel Convex Relaxation for Non Binary Discrete Tomography</i>. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:<a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">10.1007/978-3-319-58771-4_19</a>.","ista":"Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 235–246.","ieee":"J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary discrete tomography,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.","short":"J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246.","apa":"Kuske, J., Swoboda, P., &#38; Petra, S. (2017). A novel convex relaxation for non binary discrete tomography. In F. Lauze, Y. Dong, &#38; A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. <a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">https://doi.org/10.1007/978-3-319-58771-4_19</a>","ama":"Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246. doi:<a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">10.1007/978-3-319-58771-4_19</a>"},"_id":"646","publisher":"Springer","day":"01","department":[{"_id":"VlKo"}],"alternative_title":["LNCS"]},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6894"}]},"ddc":["005"],"doi":"10.1007/978-3-319-65765-3_7","has_accepted_license":"1","file":[{"relation":"main_file","file_id":"4956","date_updated":"2020-07-14T12:47:31Z","content_type":"application/pdf","file_name":"IST-2017-831-v1+1_main.pdf","date_created":"2018-12-12T10:12:38Z","creator":"system","access_level":"open_access","file_size":3806864,"checksum":"faf546914ba29bcf9974ee36b6b16750"}],"year":"2017","publication_status":"published","project":[{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"oa_version":"Submitted Version","date_published":"2017-09-01T00:00:00Z","conference":{"end_date":"2017-09-07","start_date":"2017-09-05","name":"FORMATS: Formal Modelling and Analysis of Timed Systems","location":"Berlin, Germany"},"author":[{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov"},{"first_name":"Mirco","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","first_name":"Hui"}],"month":"09","quality_controlled":"1","publist_id":"7129","type":"conference","page":"116 - 132","scopus_import":1,"title":"Conic abstractions for hybrid systems","status":"public","publication_identifier":{"isbn":["978-331965764-6"]},"file_date_updated":"2020-07-14T12:47:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:47:41Z","abstract":[{"lang":"eng","text":"Despite researchers’ efforts in the last couple of decades, reachability analysis is still a challenging problem even for linear hybrid systems. Among the existing approaches, the most practical ones are mainly based on bounded-time reachable set over-approximations. For the purpose of unbounded-time analysis, one important strategy is to abstract the original system and find an invariant for the abstraction. In this paper, we propose an approach to constructing a new kind of abstraction called conic abstraction for affine hybrid systems, and to computing reachable sets based on this abstraction. The essential feature of a conic abstraction is that it partitions the state space of a system into a set of convex polyhedral cones which is derived from a uniform conic partition of the derivative space. Such a set of polyhedral cones is able to cut all trajectories of the system into almost straight segments so that every segment of a reach pipe in a polyhedral cone tends to be straight as well, and hence can be over-approximated tightly by polyhedra using similar techniques as HyTech or PHAVer. In particular, for diagonalizable affine systems, our approach can guarantee to find an invariant for unbounded reachable sets, which is beyond the capability of bounded-time reachability analysis tools. We implemented the approach in a tool and experiments on benchmarks show that our approach is more powerful than SpaceEx and PHAVer in dealing with diagonalizable systems."}],"volume":"10419 ","date_updated":"2023-09-07T12:53:00Z","oa":1,"citation":{"ieee":"S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.","mla":"Bogomolov, Sergiy, et al. <i>Conic Abstractions for Hybrid Systems</i>. Vol. 10419, Springer, 2017, pp. 116–32, doi:<a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">10.1007/978-3-319-65765-3_7</a>.","chicago":"Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">https://doi.org/10.1007/978-3-319-65765-3_7</a>.","ista":"Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 116–132.","ama":"Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid systems. In: Vol 10419. Springer; 2017:116-132. doi:<a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">10.1007/978-3-319-65765-3_7</a>","apa":"Bogomolov, S., Giacobbe, M., Henzinger, T. A., &#38; Kong, H. (2017). Conic abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">https://doi.org/10.1007/978-3-319-65765-3_7</a>","short":"S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132."},"_id":"647","publisher":"Springer","pubrep_id":"831","day":"01","alternative_title":["LNCS"],"department":[{"_id":"ToHe"}]},{"publist_id":"7125","type":"conference","publication_identifier":{"isbn":["978-331955910-0"]},"scopus_import":1,"title":"On the complexity of breaking pseudoentropy","status":"public","page":"600 - 613","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://eprint.iacr.org/2016/1186.pdf","open_access":"1"}],"date_updated":"2021-01-12T08:07:39Z","oa":1,"language":[{"iso":"eng"}],"volume":10185,"date_created":"2018-12-11T11:47:42Z","abstract":[{"lang":"eng","text":"Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method."}],"department":[{"_id":"KrPi"}],"alternative_title":["LNCS"],"citation":{"short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","ama":"Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:600-613. doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">10.1007/978-3-319-55911-7_43</a>","apa":"Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger &#38; S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">https://doi.org/10.1007/978-3-319-55911-7_43</a>","ieee":"M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613.","mla":"Skórski, Maciej. <i>On the Complexity of Breaking Pseudoentropy</i>. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">10.1007/978-3-319-55911-7_43</a>.","ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613.","chicago":"Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">https://doi.org/10.1007/978-3-319-55911-7_43</a>."},"day":"01","publisher":"Springer","_id":"648","doi":"10.1007/978-3-319-55911-7_43","year":"2017","oa_version":"Submitted Version","editor":[{"last_name":"Jäger","first_name":"Gerhard","full_name":"Jäger, Gerhard"},{"full_name":"Steila, Silvia","first_name":"Silvia","last_name":"Steila"}],"publication_status":"published","conference":{"end_date":"2017-04-22","start_date":"2017-04-20","name":"TAMC: Theory and Applications of Models of Computation","location":"Bern, Switzerland"},"date_published":"2017-04-01T00:00:00Z","quality_controlled":"1","intvolume":"     10185","month":"04","author":[{"full_name":"Skórski, Maciej","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","publist_id":"7119","status":"public","title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","scopus_import":1,"publication_identifier":{"issn":["03029743"]},"page":"586 - 599","citation":{"ama":"Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599. doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">10.1007/978-3-319-55911-7_42</a>","apa":"Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In G. Jäger &#38; S. Steila (Eds.) (Vol. 10185, pp. 586–599). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">https://doi.org/10.1007/978-3-319-55911-7_42</a>","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599.","ieee":"M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.","ista":"Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 586–599.","mla":"Skórski, Maciej. <i>A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds</i>. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">10.1007/978-3-319-55911-7_42</a>.","chicago":"Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">https://doi.org/10.1007/978-3-319-55911-7_42</a>."},"day":"01","_id":"650","publisher":"Springer","department":[{"_id":"KrPi"}],"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy."}],"volume":10185,"date_created":"2018-12-11T11:47:42Z","main_file_link":[{"url":"https://eprint.iacr.org/2016/965.pdf","open_access":"1"}],"date_updated":"2021-01-12T08:07:46Z","oa":1,"publication_status":"published","editor":[{"first_name":"Gerhard","full_name":"Jäger, Gerhard","last_name":"Jäger"},{"last_name":"Steila","full_name":"Steila, Silvia","first_name":"Silvia"}],"oa_version":"Submitted Version","doi":"10.1007/978-3-319-55911-7_42","year":"2017","intvolume":"     10185","author":[{"first_name":"Maciej","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski"}],"month":"01","quality_controlled":"1","conference":{"name":"TAMC: Theory and Applications of Models of Computation","location":"Bern, Switzerland","start_date":"2017-04-20","end_date":"2017-04-22"},"date_published":"2017-01-01T00:00:00Z"},{"date_published":"2017-12-01T00:00:00Z","conference":{"end_date":"2017-12-22","start_date":"2017-12-09","location":"Phuket, Thailand","name":"ISAAC: International Symposium on Algorithms and Computation"},"author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"}],"month":"12","intvolume":"        92","article_number":"34","quality_controlled":"1","ddc":["510"],"year":"2017","doi":"10.4230/LIPICS.ISAAC.2017.34","file":[{"relation":"main_file","file_id":"6518","date_updated":"2020-07-14T12:47:33Z","content_type":"application/pdf","date_created":"2019-06-04T12:20:35Z","file_name":"2017_LIPIcs-Fulek.pdf","creator":"kschuh","access_level":"open_access","file_size":588982,"checksum":"fc7a643e29621c8bbe49d36b39081f31"}],"has_accepted_license":"1","publication_status":"published","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"},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","abstract":[{"text":"A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle.","lang":"eng"}],"date_created":"2019-06-04T12:11:52Z","volume":92,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2021-01-12T08:07:51Z","_id":"6517","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"01","citation":{"ama":"Fulek R. Embedding graphs into embedded graphs. In: Vol 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">10.4230/LIPICS.ISAAC.2017.34</a>","apa":"Fulek, R. (2017). Embedding graphs into embedded graphs (Vol. 92). Presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">https://doi.org/10.4230/LIPICS.ISAAC.2017.34</a>","short":"R. Fulek, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand, 2017, vol. 92.","mla":"Fulek, Radoslav. <i>Embedding Graphs into Embedded Graphs</i>. Vol. 92, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">10.4230/LIPICS.ISAAC.2017.34</a>.","chicago":"Fulek, Radoslav. “Embedding Graphs into Embedded Graphs,” Vol. 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">https://doi.org/10.4230/LIPICS.ISAAC.2017.34</a>.","ista":"Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International Symposium on Algorithms and Computation vol. 92, 34."},"department":[{"_id":"UlWa"}],"scopus_import":1,"status":"public","title":"Embedding graphs into embedded graphs","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","license":"https://creativecommons.org/licenses/by/4.0/"},{"license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","status":"public","title":"Improved set-based symbolic algorithms for parity games","scopus_import":"1","department":[{"_id":"KrCh"}],"citation":{"ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Improved set-based symbolic algorithms for parity games,” presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden, 2017, vol. 82.","mla":"Chatterjee, Krishnendu, et al. <i>Improved Set-Based Symbolic Algorithms for Parity Games</i>. Vol. 82, 18, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">10.4230/LIPICS.CSL.2017.18</a>.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2017. Improved set-based symbolic algorithms for parity games. CSL: Conference on Computer Science Logic vol. 82, 18.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Set-Based Symbolic Algorithms for Parity Games,” Vol. 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">https://doi.org/10.4230/LIPICS.CSL.2017.18</a>.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Improved set-based symbolic algorithms for parity games. In: Vol 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">10.4230/LIPICS.CSL.2017.18</a>","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., &#38; Loitzenbauer, V. (2017). Improved set-based symbolic algorithms for parity games (Vol. 82). Presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">https://doi.org/10.4230/LIPICS.CSL.2017.18</a>"},"day":"01","_id":"6519","publisher":"Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik","date_updated":"2025-06-02T08:53:46Z","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Graph games with omega-regular winning conditions provide a mathematical framework to analyze a wide range of problems in the analysis of reactive systems and programs (such as the synthesis of reactive systems, program repair, and the verification of branching time properties). Parity conditions are canonical forms to specify omega-regular winning conditions. Graph games with parity conditions are equivalent to mu-calculus model checking, and thus a very important algorithmic problem. Symbolic algorithms are of great significance because they provide scalable algorithms for the analysis of large finite-state systems, as well as algorithms for the analysis of infinite-state systems with finite quotient. A set-based symbolic algorithm uses the basic set operations and the one-step predecessor operators. We consider graph games with n vertices and parity conditions with c priorities (equivalently, a mu-calculus formula with c alternations of least and greatest fixed points). While many explicit algorithms exist for graph games with parity conditions, for set-based symbolic algorithms there are only two algorithms (notice that we use space to refer to the number of sets stored by a symbolic algorithm): (a) the basic algorithm that requires O(n^c) symbolic operations and linear space; and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two set-based symbolic algorithms for parity games: (a) our first algorithm requires O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic operations and only linear space. We also present the first linear space set-based symbolic algorithm for parity games that requires at most a sub-exponential number of symbolic operations. "}],"volume":82,"date_created":"2019-06-04T12:42:43Z","oa_version":"Published Version","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"publication_status":"published","has_accepted_license":"1","file":[{"file_size":710185,"checksum":"7c2c9d09970af79026d7e37d9b632ef8","relation":"main_file","file_id":"6520","content_type":"application/pdf","date_updated":"2020-07-14T12:47:33Z","creator":"kschuh","date_created":"2019-06-04T12:56:52Z","file_name":"2017_LIPIcs-Chatterjee.pdf","access_level":"open_access"}],"doi":"10.4230/LIPICS.CSL.2017.18","year":"2017","ddc":["004"],"quality_controlled":"1","article_number":"18","intvolume":"        82","month":"08","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Dvorák","full_name":"Dvorák, Wolfgang","first_name":"Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"}],"conference":{"start_date":"2017-08-20","end_date":"2017-08-24","name":"CSL: Conference on Computer Science Logic","location":"Stockholm, Sweden"},"date_published":"2017-08-01T00:00:00Z"},{"ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","scopus_import":1,"title":"On the complexity of estimating Rènyi divergences","status":"public","publication_identifier":{"isbn":["9781509040964"]},"department":[{"_id":"KrPi"}],"citation":{"ista":"Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.","mla":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>, 8006529, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/isit.2017.8006529\">10.1109/isit.2017.8006529</a>.","chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/isit.2017.8006529\">https://doi.org/10.1109/isit.2017.8006529</a>.","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>, Aachen, Germany, 2017.","apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>. Aachen, Germany: IEEE. <a href=\"https://doi.org/10.1109/isit.2017.8006529\">https://doi.org/10.1109/isit.2017.8006529</a>","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>. IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/isit.2017.8006529\">10.1109/isit.2017.8006529</a>","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017."},"day":"09","_id":"6526","publisher":"IEEE","date_updated":"2021-01-12T08:07:53Z","main_file_link":[{"url":"https://arxiv.org/abs/1702.01666","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"date_created":"2019-06-06T12:53:09Z","abstract":[{"text":"This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity.","lang":"eng"}],"oa_version":"Preprint","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","doi":"10.1109/isit.2017.8006529","year":"2017","quality_controlled":"1","article_number":"8006529","month":"08","author":[{"full_name":"Skórski, Maciej","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski"}],"external_id":{"arxiv":["1702.01666"]},"publication":"2017 IEEE International Symposium on Information Theory (ISIT)","conference":{"location":"Aachen, Germany","name":"ISIT: International Symposium on Information Theory","end_date":"2017-06-30","start_date":"2017-06-25"},"date_published":"2017-08-09T00:00:00Z","arxiv":1},{"oa":1,"date_published":"2017-10-30T00:00:00Z","conference":{"location":"Dallas, TX, USA","name":"CCS: Conference on Computer and Communications Security","start_date":"2017-10-30","end_date":"2017-11-03"},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/443"}],"date_updated":"2021-01-12T08:07:53Z","publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","abstract":[{"lang":"eng","text":"A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n"}],"date_created":"2019-06-06T13:21:29Z","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"quality_controlled":"1","publisher":"ACM Press","_id":"6527","day":"30","citation":{"mla":"Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>, ACM Press, 2017, pp. 1001–17, doi:<a href=\"https://doi.org/10.1145/3133956.3134031\">10.1145/3133956.3134031</a>.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>, 1001–17. ACM Press, 2017. <a href=\"https://doi.org/10.1145/3133956.3134031\">https://doi.org/10.1145/3133956.3134031</a>.","ista":"Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017.","ieee":"J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>, Dallas, TX, USA, 2017, pp. 1001–1017.","apa":"Alwen, J. F., Blocki, J., &#38; Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i> (pp. 1001–1017). Dallas, TX, USA: ACM Press. <a href=\"https://doi.org/10.1145/3133956.3134031\">https://doi.org/10.1145/3133956.3134031</a>","ama":"Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>. ACM Press; 2017:1001-1017. doi:<a href=\"https://doi.org/10.1145/3133956.3134031\">10.1145/3133956.3134031</a>","short":"J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017."},"author":[{"last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F","first_name":"Joel F"},{"last_name":"Blocki","full_name":"Blocki, Jeremiah","first_name":"Jeremiah"},{"full_name":"Harsha, Ben","first_name":"Ben","last_name":"Harsha"}],"month":"10","page":"1001-1017","title":"Practical graphs for optimal side-channel resistant memory-hard functions","year":"2017","scopus_import":1,"publication_identifier":{"isbn":["9781450349468"]},"status":"public","doi":"10.1145/3133956.3134031","type":"conference","oa_version":"Submitted Version","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1},{"month":"03","intvolume":"        49","author":[{"last_name":"Makohon Moore","full_name":"Makohon Moore, Alvin","first_name":"Alvin"},{"full_name":"Zhang, Ming","first_name":"Ming","last_name":"Zhang"},{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter"},{"first_name":"Ivana","full_name":"Božić, Ivana","last_name":"Božić"},{"first_name":"Benjamin","full_name":"Allen, Benjamin","last_name":"Allen"},{"id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45","last_name":"Kundu","full_name":"Kundu, Deepanjan","first_name":"Deepanjan"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fay","full_name":"Wong, Fay","last_name":"Wong"},{"full_name":"Jiao, Yuchen","first_name":"Yuchen","last_name":"Jiao"},{"last_name":"Kohutek","full_name":"Kohutek, Zachary","first_name":"Zachary"},{"first_name":"Jungeui","full_name":"Hong, Jungeui","last_name":"Hong"},{"last_name":"Attiyeh","full_name":"Attiyeh, Marc","first_name":"Marc"},{"full_name":"Javier, Breanna","first_name":"Breanna","last_name":"Javier"},{"last_name":"Wood","full_name":"Wood, Laura","first_name":"Laura"},{"full_name":"Hruban, Ralph","first_name":"Ralph","last_name":"Hruban"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"first_name":"Nickolas","full_name":"Papadopoulos, Nickolas","last_name":"Papadopoulos"},{"last_name":"Kinzler","full_name":"Kinzler, Kenneth","first_name":"Kenneth"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"},{"full_name":"Iacobuzio Donahue, Christine","first_name":"Christine","last_name":"Iacobuzio Donahue"}],"quality_controlled":"1","pmid":1,"acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","external_id":{"pmid":["28092682"]},"publication":"Nature Genetics","date_published":"2017-03-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","ddc":["000"],"doi":"10.1038/ng.3764","has_accepted_license":"1","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"7050","date_updated":"2020-07-14T12:47:33Z","creator":"dernst","date_created":"2019-11-19T08:13:50Z","file_name":"2017_NatureGenetics_Makohon.pdf","access_level":"open_access","file_size":908099,"checksum":"e442dc3b7420a36ec805e9bb45cc1a2e"}],"year":"2017","citation":{"short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. <i>Nature Genetics</i>. 2017;49(3):358-366. doi:<a href=\"https://doi.org/10.1038/ng.3764\">10.1038/ng.3764</a>","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng.3764\">https://doi.org/10.1038/ng.3764</a>","ieee":"A. Makohon Moore <i>et al.</i>, “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” <i>Nature Genetics</i>, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017.","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” <i>Nature Genetics</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ng.3764\">https://doi.org/10.1038/ng.3764</a>.","mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” <i>Nature Genetics</i>, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:<a href=\"https://doi.org/10.1038/ng.3764\">10.1038/ng.3764</a>."},"_id":"653","publisher":"Nature Publishing Group","day":"01","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease."}],"volume":49,"date_created":"2018-12-11T11:47:43Z","article_type":"original","date_updated":"2022-06-10T09:55:08Z","oa":1,"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","publist_id":"7092","type":"journal_article","page":"358 - 366","scopus_import":"1","status":"public","title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","publication_identifier":{"issn":["10614036"]}},{"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"oa_version":"Submitted Version","publication_status":"published","doi":"10.1242/dev.144915","has_accepted_license":"1","file":[{"checksum":"eef22a0f42a55b232cb2d1188a2322cb","file_size":228206,"date_created":"2018-12-12T10:15:20Z","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","creator":"system","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5139","date_updated":"2020-07-14T12:47:33Z"}],"year":"2017","ddc":["571"],"quality_controlled":"1","intvolume":"       144","author":[{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna"},{"first_name":"Nicolas","full_name":"Rivron, Nicolas","last_name":"Rivron"}],"month":"03","publication":"Development","date_published":"2017-03-01T00:00:00Z","issue":"5","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publist_id":"7089","page":"733 - 736","publication_identifier":{"issn":["09501991"]},"status":"public","scopus_import":1,"title":"Creating to understand – developmental biology meets engineering in Paris","department":[{"_id":"AnKi"}],"citation":{"apa":"Kicheva, A., &#38; Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144915\">https://doi.org/10.1242/dev.144915</a>","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. <i>Development</i>. 2017;144(5):733-736. doi:<a href=\"https://doi.org/10.1242/dev.144915\">10.1242/dev.144915</a>","short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144915\">https://doi.org/10.1242/dev.144915</a>.","mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” <i>Development</i>, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:<a href=\"https://doi.org/10.1242/dev.144915\">10.1242/dev.144915</a>.","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” <i>Development</i>, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017."},"pubrep_id":"987","_id":"654","publisher":"Company of Biologists","day":"01","date_updated":"2021-01-12T08:07:54Z","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations."}],"volume":144,"date_created":"2018-12-11T11:47:44Z"},{"abstract":[{"lang":"eng","text":"The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell."}],"volume":6,"date_created":"2018-12-11T11:47:44Z","language":[{"iso":"eng"}],"oa":1,"date_updated":"2021-01-12T08:07:55Z","publisher":"eLife Sciences Publications","_id":"655","pubrep_id":"904","day":"06","citation":{"ista":"Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136.","mla":"Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” <i>ELife</i>, vol. 6, e23136, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.23136\">10.7554/eLife.23136</a>.","chicago":"Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.23136\">https://doi.org/10.7554/eLife.23136</a>.","ieee":"T. Renault <i>et al.</i>, “Bacterial flagella grow through an injection diffusion mechanism,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","apa":"Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.23136\">https://doi.org/10.7554/eLife.23136</a>","ama":"Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.23136\">10.7554/eLife.23136</a>","short":"T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017)."},"department":[{"_id":"CaGu"}],"title":"Bacterial flagella grow through an injection diffusion mechanism","scopus_import":1,"status":"public","publication_identifier":{"issn":["2050084X"]},"type":"journal_article","publist_id":"7082","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:33Z","date_published":"2017-03-06T00:00:00Z","publication":"eLife","intvolume":"         6","author":[{"full_name":"Renault, Thibaud","first_name":"Thibaud","last_name":"Renault"},{"first_name":"Anthony","full_name":"Abraham, Anthony","last_name":"Abraham"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guillaume","full_name":"Paradis, Guillaume","last_name":"Paradis"},{"first_name":"Simon","full_name":"Rainville, Simon","last_name":"Rainville"},{"full_name":"Charpentier, Emmanuelle","first_name":"Emmanuelle","last_name":"Charpentier"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"first_name":"Yuhai","full_name":"Tu, Yuhai","last_name":"Tu"},{"full_name":"Namba, Keiichi","first_name":"Keiichi","last_name":"Namba"},{"last_name":"Keener","full_name":"Keener, James","first_name":"James"},{"first_name":"Tohru","full_name":"Minamino, Tohru","last_name":"Minamino"},{"last_name":"Erhardt","full_name":"Erhardt, Marc","first_name":"Marc"}],"month":"03","article_number":"e23136","quality_controlled":"1","ddc":["579"],"year":"2017","doi":"10.7554/eLife.23136","has_accepted_license":"1","file":[{"relation":"main_file","date_updated":"2020-07-14T12:47:33Z","file_id":"4716","content_type":"application/pdf","creator":"system","file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","date_created":"2018-12-12T10:08:53Z","access_level":"open_access","checksum":"39e1c3e82ddac83a30422fa72fa1a383","file_size":5520359},{"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:08:54Z","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:33Z","file_id":"4717","relation":"main_file","checksum":"a6d542253028f52e00aa29739ddffe8f","file_size":11242920}],"publication_status":"published","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"},"oa_version":"Published Version"},{"issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["00278424"]},"scopus_import":1,"title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","status":"public","page":"E2533 - E2539","type":"journal_article","publist_id":"7076","department":[{"_id":"JiFr"}],"day":"21","_id":"657","publisher":"National Academy of Sciences","citation":{"ieee":"B. Möller <i>et al.</i>, “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” <i>PNAS</i>, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” <i>PNAS</i>, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:<a href=\"https://doi.org/10.1073/pnas.1616493114\">10.1073/pnas.1616493114</a>.","chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1616493114\">https://doi.org/10.1073/pnas.1616493114</a>.","ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. <i>PNAS</i>. 2017;114(12):E2533-E2539. doi:<a href=\"https://doi.org/10.1073/pnas.1616493114\">10.1073/pnas.1616493114</a>","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1616493114\">https://doi.org/10.1073/pnas.1616493114</a>","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539."},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/","open_access":"1"}],"date_updated":"2021-01-12T08:08:02Z","date_created":"2018-12-11T11:47:45Z","volume":114,"abstract":[{"text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.","lang":"eng"}],"language":[{"iso":"eng"}],"oa_version":"Submitted Version","publication_status":"published","year":"2017","doi":"10.1073/pnas.1616493114","quality_controlled":"1","intvolume":"       114","month":"03","author":[{"last_name":"Möller","full_name":"Möller, Barbara","first_name":"Barbara"},{"last_name":"Ten Hove","first_name":"Colette","full_name":"Ten Hove, Colette"},{"last_name":"Xiang","full_name":"Xiang, Daoquan","first_name":"Daoquan"},{"full_name":"Williams, Nerys","first_name":"Nerys","last_name":"Williams"},{"first_name":"Lorena","full_name":"López, Lorena","last_name":"López"},{"last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","full_name":"Yoshida, Saiko"},{"last_name":"Smit","full_name":"Smit, Margot","first_name":"Margot"},{"last_name":"Datla","first_name":"Raju","full_name":"Datla, Raju"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"}],"date_published":"2017-03-21T00:00:00Z","publication":"PNAS","external_id":{"pmid":["28265057"]},"pmid":1},{"quality_controlled":"1","article_number":"00008","month":"03","intvolume":"        11","author":[{"last_name":"Der","full_name":"Der, Ralf","first_name":"Ralf"},{"full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"publication":"Frontiers in Neurorobotics","date_published":"2017-03-16T00:00:00Z","oa_version":"Published Version","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_processing_charge":"Yes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","has_accepted_license":"1","file":[{"checksum":"b1bc43f96d1df3313c03032c2a46388d","file_size":8439566,"access_level":"open_access","date_created":"2018-12-12T10:18:49Z","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:47:33Z","file_id":"5371","relation":"main_file"}],"doi":"10.3389/fnbot.2017.00008","year":"2017","ddc":["006"],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"citation":{"ieee":"R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” <i>Frontiers in Neurorobotics</i>, vol. 11, no. MAR. Frontiers Research Foundation, 2017.","mla":"Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” <i>Frontiers in Neurorobotics</i>, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:<a href=\"https://doi.org/10.3389/fnbot.2017.00008\">10.3389/fnbot.2017.00008</a>.","chicago":"Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” <i>Frontiers in Neurorobotics</i>. Frontiers Research Foundation, 2017. <a href=\"https://doi.org/10.3389/fnbot.2017.00008\">https://doi.org/10.3389/fnbot.2017.00008</a>.","ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. <i>Frontiers in Neurorobotics</i>. 2017;11(MAR). doi:<a href=\"https://doi.org/10.3389/fnbot.2017.00008\">10.3389/fnbot.2017.00008</a>","apa":"Der, R., &#38; Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. <i>Frontiers in Neurorobotics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnbot.2017.00008\">https://doi.org/10.3389/fnbot.2017.00008</a>"},"day":"16","_id":"658","pubrep_id":"903","publisher":"Frontiers Research Foundation","date_updated":"2021-01-12T08:08:04Z","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors &quot;waiting&quot; to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics."}],"volume":11,"date_created":"2018-12-11T11:47:45Z","issue":"MAR","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publist_id":"7078","publication_identifier":{"issn":["16625218"]},"title":"Self organized behavior generation for musculoskeletal robots","scopus_import":1,"status":"public"},{"quality_controlled":"1","article_number":"14832","month":"03","author":[{"last_name":"Kage","full_name":"Kage, Frieda","first_name":"Frieda"},{"first_name":"Moritz","full_name":"Winterhoff, Moritz","last_name":"Winterhoff"},{"last_name":"Dimchev","full_name":"Dimchev, Vanessa","first_name":"Vanessa"},{"last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","full_name":"Müller, Jan"},{"last_name":"Thalheim","full_name":"Thalheim, Tobias","first_name":"Tobias"},{"last_name":"Freise","first_name":"Anika","full_name":"Freise, Anika"},{"first_name":"Stefan","full_name":"Brühmann, Stefan","last_name":"Brühmann"},{"last_name":"Kollasser","first_name":"Jana","full_name":"Kollasser, Jana"},{"last_name":"Block","full_name":"Block, Jennifer","first_name":"Jennifer"},{"first_name":"Georgi A","full_name":"Dimchev, Georgi A","last_name":"Dimchev"},{"last_name":"Geyer","full_name":"Geyer, Matthias","first_name":"Matthias"},{"last_name":"Schnittler","full_name":"Schnittler, Hams","first_name":"Hams"},{"last_name":"Brakebusch","full_name":"Brakebusch, Cord","first_name":"Cord"},{"last_name":"Stradal","first_name":"Theresia","full_name":"Stradal, Theresia"},{"last_name":"Carlier","first_name":"Marie","full_name":"Carlier, Marie"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Käs","first_name":"Josef","full_name":"Käs, Josef"},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"}],"intvolume":"         8","publication":"Nature Communications","date_published":"2017-03-22T00:00:00Z","oa_version":"Published Version","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","file":[{"access_level":"open_access","date_created":"2018-12-12T10:14:21Z","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","creator":"system","date_updated":"2020-07-14T12:47:34Z","content_type":"application/pdf","file_id":"5072","relation":"main_file","file_size":9523746,"checksum":"dae30190291c3630e8102d8714a8d23e"}],"has_accepted_license":"1","doi":"10.1038/ncomms14832","year":"2017","ddc":["570"],"department":[{"_id":"MiSi"}],"citation":{"ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832.","mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” <i>Nature Communications</i>, vol. 8, 14832, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14832\">10.1038/ncomms14832</a>.","chicago":"Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14832\">https://doi.org/10.1038/ncomms14832</a>.","ieee":"F. Kage <i>et al.</i>, “FMNL formins boost lamellipodial force generation,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14832\">https://doi.org/10.1038/ncomms14832</a>","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14832\">10.1038/ncomms14832</a>","short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017)."},"day":"22","_id":"659","publisher":"Nature Publishing Group","pubrep_id":"902","date_updated":"2021-01-12T08:08:06Z","oa":1,"language":[{"iso":"eng"}],"volume":8,"date_created":"2018-12-11T11:47:46Z","abstract":[{"lang":"eng","text":"Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching."}],"file_date_updated":"2020-07-14T12:47:34Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7075","type":"journal_article","status":"public","title":"FMNL formins boost lamellipodial force generation","scopus_import":1,"publication_identifier":{"issn":["20411723"]}},{"year":"2017","doi":"10.1073/pnas.1620274114","oa_version":"Submitted Version","publication_status":"published","date_published":"2017-03-28T00:00:00Z","publication":"PNAS","external_id":{"pmid":["28280102"]},"acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","pmid":1,"quality_controlled":"1","intvolume":"       114","month":"03","author":[{"last_name":"Rickman","first_name":"Jamie","full_name":"Rickman, Jamie"},{"last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748","first_name":"Christian F","full_name":"Düllberg, Christian F"},{"last_name":"Cade","first_name":"Nicholas","full_name":"Cade, Nicholas"},{"last_name":"Griffin","first_name":"Lewis","full_name":"Griffin, Lewis"},{"first_name":"Thomas","full_name":"Surrey, Thomas","last_name":"Surrey"}],"page":"3427 - 3432","scopus_import":1,"publication_identifier":{"issn":["00278424"]},"status":"public","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","type":"journal_article","publist_id":"7073","issue":"13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"date_updated":"2021-01-12T08:08:09Z","date_created":"2018-12-11T11:47:46Z","volume":114,"abstract":[{"lang":"eng","text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth."}],"language":[{"iso":"eng"}],"department":[{"_id":"MaLo"}],"publisher":"National Academy of Sciences","_id":"660","day":"28","citation":{"mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” <i>PNAS</i>, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:<a href=\"https://doi.org/10.1073/pnas.1620274114\">10.1073/pnas.1620274114</a>.","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1620274114\">https://doi.org/10.1073/pnas.1620274114</a>.","ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” <i>PNAS</i>, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., &#38; Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1620274114\">https://doi.org/10.1073/pnas.1620274114</a>","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. <i>PNAS</i>. 2017;114(13):3427-3432. doi:<a href=\"https://doi.org/10.1073/pnas.1620274114\">10.1073/pnas.1620274114</a>","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432."}},{"intvolume":"        19","month":"03","author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","first_name":"Michael","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090"},{"first_name":"Zsuzsa","full_name":"Ákos, Zsuzsa","last_name":"Ákos"},{"full_name":"Grigolon, Silvia","first_name":"Silvia","last_name":"Grigolon"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan"},{"last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena"},{"orcid":"0000-0001-5199-9940","first_name":"Daniel","full_name":"Capek, Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin","full_name":"Behrndt, Martin"},{"first_name":"Ekaterina","full_name":"Papusheva, Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tada","full_name":"Tada, Masazumi","first_name":"Masazumi"},{"first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"},{"first_name":"Tamás","full_name":"Vicsek, Tamás","last_name":"Vicsek"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"quality_controlled":"1","pmid":1,"publication":"Nature Cell Biology","external_id":{"pmid":["28346437"]},"date_published":"2017-03-27T00:00:00Z","publication_status":"published","oa_version":"Submitted Version","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"},{"call_identifier":"FWF","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","grant_number":"I 930-B20"}],"related_material":{"record":[{"id":"50","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8350"}]},"doi":"10.1038/ncb3492","year":"2017","citation":{"ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>.","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>.","ieee":"M. Smutny <i>et al.</i>, “Friction forces position the neural anlage,” <i>Nature Cell Biology</i>, vol. 19. Nature Publishing Group, pp. 306–317, 2017.","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. <i>Nature Cell Biology</i>. 2017;19:306-317. doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317."},"_id":"661","publisher":"Nature Publishing Group","day":"27","department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"abstract":[{"text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.","lang":"eng"}],"date_created":"2018-12-11T11:47:46Z","volume":19,"date_updated":"2024-03-25T23:30:21Z","main_file_link":[{"open_access":"1","url":"https://europepmc.org/articles/pmc5635970"}],"oa":1,"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"SSU"}],"publist_id":"7074","type":"journal_article","page":"306 - 317","publication_identifier":{"issn":["14657392"]},"status":"public","title":"Friction forces position the neural anlage","scopus_import":1},{"year":"2017","doi":"10.1063/1.4981525","oa_version":"Submitted Version","project":[{"_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963  TP A8","name":"Astrophysical instability of currents and turbulences"}],"publication_status":"published","date_published":"2017-04-01T00:00:00Z","publication":"Physics of Fluids","article_number":"044107","quality_controlled":"1","month":"04","intvolume":"        29","author":[{"first_name":"Liang","full_name":"Shi, Liang","last_name":"Shi"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"publication_identifier":{"issn":["10706631"]},"title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","status":"public","scopus_import":1,"type":"journal_article","publist_id":"7072","issue":"4","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"date_updated":"2021-01-12T08:08:15Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01714"}],"abstract":[{"lang":"eng","text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays."}],"date_created":"2018-12-11T11:47:47Z","volume":29,"language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"day":"01","publisher":"American Institute of Physics","_id":"662","citation":{"short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","ama":"Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. <i>Physics of Fluids</i>. 2017;29(4). doi:<a href=\"https://doi.org/10.1063/1.4981525\">10.1063/1.4981525</a>","apa":"Shi, L., Hof, B., Rampp, M., &#38; Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. <i>Physics of Fluids</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>","ieee":"L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” <i>Physics of Fluids</i>, vol. 29, no. 4. American Institute of Physics, 2017.","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” <i>Physics of Fluids</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>.","mla":"Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” <i>Physics of Fluids</i>, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1063/1.4981525\">10.1063/1.4981525</a>."}},{"year":"2017","file":[{"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:11:20Z","file_name":"IST-2017-817-v1+1_p163-kong.pdf","file_id":"4873","date_updated":"2020-07-14T12:47:34Z","content_type":"application/pdf","relation":"main_file","file_size":1650530,"checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63"}],"has_accepted_license":"1","doi":"10.1145/3049797.3049814","ddc":["000"],"oa_version":"Submitted Version","publication_status":"published","conference":{"start_date":"2017-04-18","end_date":"2017-04-20","name":"HSCC: Hybrid Systems Computation and Control ","location":"Pittsburgh, PA, United States"},"date_published":"2017-04-01T00:00:00Z","publication":"Proceedings of the 20th International Conference on Hybrid Systems","quality_controlled":"1","author":[{"full_name":"Kong, Hui","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong"},{"first_name":"Sergiy","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov"},{"last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"},{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"month":"04","scopus_import":1,"status":"public","title":"Safety verification of nonlinear hybrid systems based on invariant clusters","publication_identifier":{"isbn":["978-145034590-3"]},"page":"163 - 172","type":"conference","publist_id":"7067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:34Z","oa":1,"date_updated":"2021-01-12T08:08:17Z","date_created":"2018-12-11T11:47:47Z","abstract":[{"lang":"eng","text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. "}],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"day":"01","publisher":"ACM","_id":"663","pubrep_id":"817","citation":{"short":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.","ama":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: <i>Proceedings of the 20th International Conference on Hybrid Systems</i>. ACM; 2017:163-172. doi:<a href=\"https://doi.org/10.1145/3049797.3049814\">10.1145/3049797.3049814</a>","apa":"Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., &#38; Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In <i>Proceedings of the 20th International Conference on Hybrid Systems</i> (pp. 163–172). Pittsburgh, PA, United States: ACM. <a href=\"https://doi.org/10.1145/3049797.3049814\">https://doi.org/10.1145/3049797.3049814</a>","ieee":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, Pittsburgh, PA, United States, 2017, pp. 163–172.","ista":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.","chicago":"Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, 163–72. ACM, 2017. <a href=\"https://doi.org/10.1145/3049797.3049814\">https://doi.org/10.1145/3049797.3049814</a>.","mla":"Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, ACM, 2017, pp. 163–72, doi:<a href=\"https://doi.org/10.1145/3049797.3049814\">10.1145/3049797.3049814</a>."}},{"publication":"Cell Systems","date_published":"2017-04-26T00:00:00Z","month":"04","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","full_name":"Mitosch, Karin","first_name":"Karin"},{"id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","last_name":"Rieckh","first_name":"Georg","full_name":"Rieckh, Georg"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach"}],"intvolume":"         4","quality_controlled":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"818"}]},"ddc":["576","610"],"doi":"10.1016/j.cels.2017.03.001","has_accepted_license":"1","file":[{"file_size":2438660,"checksum":"04ff20011c3d9a601c514aa999a5fe1a","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","date_created":"2018-12-12T10:13:54Z","creator":"system","access_level":"open_access","relation":"main_file","file_id":"5041","content_type":"application/pdf","date_updated":"2020-07-14T12:47:35Z"}],"year":"2017","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","project":[{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"language":[{"iso":"eng"}],"volume":4,"abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"date_created":"2018-12-11T11:47:48Z","date_updated":"2023-09-07T12:00:25Z","oa":1,"citation":{"ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” <i>Cell Systems</i>, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. 2017;4(4):393-403. doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>"},"publisher":"Cell Press","_id":"666","pubrep_id":"901","day":"26","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"publist_id":"7061","type":"journal_article","page":"393 - 403","scopus_import":1,"status":"public","title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","publication_identifier":{"issn":["24054712"]},"file_date_updated":"2020-07-14T12:47:35Z","ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"4"},{"quality_controlled":"1","month":"12","author":[{"last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"last_name":"Urbanke","full_name":"Urbanke, Ruediger","first_name":"Ruediger"},{"last_name":"Gross","full_name":"Gross, Warren","first_name":"Warren"}],"citation":{"apa":"Hashemi, S. A., Mondelli, M., Hassani, H., Urbanke, R., &#38; Gross, W. (2017). Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. In <i>2017 IEEE Global Communications Conference</i> (pp. 1–7). Singapore, Singapore: IEEE. <a href=\"https://doi.org/10.1109/glocom.2017.8254940\">https://doi.org/10.1109/glocom.2017.8254940</a>","ama":"Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. In: <i>2017 IEEE Global Communications Conference</i>. IEEE; 2017:1-7. doi:<a href=\"https://doi.org/10.1109/glocom.2017.8254940\">10.1109/glocom.2017.8254940</a>","short":"S.A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, W. Gross, in:, 2017 IEEE Global Communications Conference, IEEE, 2017, pp. 1–7.","mla":"Hashemi, Seyyed Ali, et al. “Partitioned List Decoding of Polar Codes: Analysis and Improvement of Finite Length Performance.” <i>2017 IEEE Global Communications Conference</i>, IEEE, 2017, pp. 1–7, doi:<a href=\"https://doi.org/10.1109/glocom.2017.8254940\">10.1109/glocom.2017.8254940</a>.","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Hamed Hassani, Ruediger Urbanke, and Warren Gross. “Partitioned List Decoding of Polar Codes: Analysis and Improvement of Finite Length Performance.” In <i>2017 IEEE Global Communications Conference</i>, 1–7. IEEE, 2017. <a href=\"https://doi.org/10.1109/glocom.2017.8254940\">https://doi.org/10.1109/glocom.2017.8254940</a>.","ista":"Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. 2017. Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. 2017 IEEE Global Communications Conference. GLOBECOM: Global Communications Conference, 1–7.","ieee":"S. A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, and W. Gross, “Partitioned list decoding of polar codes: Analysis and improvement of finite length performance,” in <i>2017 IEEE Global Communications Conference</i>, Singapore, Singapore, 2017, pp. 1–7."},"day":"01","publisher":"IEEE","_id":"6679","extern":"1","publication":"2017 IEEE Global Communications Conference","external_id":{"arxiv":["1705.05497"]},"date_updated":"2021-01-12T08:08:34Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05497"}],"conference":{"location":"Singapore, Singapore","name":"GLOBECOM: Global Communications Conference","end_date":"2017-12-08","start_date":"2017-12-04"},"oa":1,"date_published":"2017-12-01T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2019-07-24T13:55:25Z","arxiv":1,"abstract":[{"lang":"eng","text":"Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption [1]. In this paper, we examine the paradigm of PSCL decoding from both theoretical and practical standpoints: (i) by changing the construction of the code, we are able to improve the performance at no additional computational, latency or memory cost, (ii) we present an optimal scheme to allocate cyclic redundancy checks (CRCs), and (iii) we provide an upper bound on the list size that allows MAP performance."}],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"conference","doi":"10.1109/glocom.2017.8254940","year":"2017","status":"public","title":"Partitioned list decoding of polar codes: Analysis and improvement of finite length performance","page":"1-7"}]