[{"oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.1371/journal.pbio.1002299","volume":13,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"}],"date_updated":"2026-10-31T23:30:51Z","ec_funded":1,"date_published":"2015-11-18T00:00:00Z","publication_status":"published","publication":"PLoS Biology","quality_controlled":"1","abstract":[{"lang":"eng","text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9711"},{"relation":"research_data","status":"public","id":"9765"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","full_name":"Chevereau, Guillaume","first_name":"Guillaume"},{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","full_name":"Dravecka, Marta","last_name":"Dravecka"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"first_name":"Aysegul","full_name":"Guvenek, Aysegul","last_name":"Guvenek"},{"first_name":"Dilay","last_name":"Ayhan","full_name":"Ayhan, Dilay"},{"first_name":"Erdal","last_name":"Toprak","full_name":"Toprak, Erdal"},{"first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","external_id":{"isi":["000365898900011"]},"isi":1,"_id":"1619","month":"11","corr_author":"1","intvolume":" 13","scopus_import":"1","citation":{"apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.","ieee":"G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015)."},"publisher":"Public Library of Science","publist_id":"5547","article_number":"e1002299","file_date_updated":"2020-07-14T12:45:07Z","status":"public","ddc":["570"],"issue":"11","file":[{"file_size":1387760,"relation":"main_file","date_updated":"2020-07-14T12:45:07Z","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","file_id":"4723","date_created":"2018-12-12T10:09:00Z","access_level":"open_access","checksum":"0e82e3279f50b15c6c170c042627802b","content_type":"application/pdf","creator":"system"}],"license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1371/journal.pbio.1002299","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","date_created":"2018-12-11T11:53:04Z","pubrep_id":"468","oa_version":"Published Version","title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","day":"18"},{"citation":{"ieee":"D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the simplification of the Morse-Smale complex,” in Topological Methods in Data Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.","short":"D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.","mla":"Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.” Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.","ista":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization III. , 135–150.","ama":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9","chicago":"Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf. “Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9.","apa":"Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9"},"scopus_import":"1","place":"Cham","month":"03","status":"public","publisher":"Springer Nature","type":"book_chapter","language":[{"iso":"eng"}],"date_created":"2022-03-04T08:33:57Z","doi":"10.1007/978-3-319-04099-8_9","department":[{"_id":"HeEd"}],"day":"19","page":"135-150","title":"Notes on the simplification of the Morse-Smale complex","acknowledgement":"This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.","publication_identifier":{"issn":["1612-3786"],"isbn":["9783319040981"],"eissn":["2197-666X"],"eisbn":["9783319040998"]},"oa_version":"None","fulldoi":"https://doi.org/10.1007/978-3-319-04099-8_9","editor":[{"full_name":"Bremer, Peer-Timo","last_name":"Bremer","first_name":"Peer-Timo"},{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"},{"last_name":"Pascucci","full_name":"Pascucci, Valerio","first_name":"Valerio"},{"last_name":"Peikert","full_name":"Peikert, Ronald","first_name":"Ronald"}],"series_title":"Mathematics and Visualization","article_processing_charge":"No","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"publication_status":"published","date_published":"2014-03-19T00:00:00Z","date_updated":"2025-04-15T08:37:54Z","ec_funded":1,"year":"2014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10817","abstract":[{"lang":"eng","text":"The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption."}],"quality_controlled":"1","publication":"Topological Methods in Data Analysis and Visualization III.","author":[{"first_name":"David","last_name":"Günther","full_name":"Günther, David"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"first_name":"Hans-Peter","last_name":"Seidel","full_name":"Seidel, Hans-Peter"},{"last_name":"Weinkauf","full_name":"Weinkauf, Tino","first_name":"Tino"}]},{"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"conference":{"start_date":"2014-01-19","end_date":"2014-01-21","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","location":"San Diego, CA, United States"},"volume":8318,"fulldoi":"https://doi.org/10.1007/978-3-642-54013-4_15","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1311.4425"}],"oa":1,"article_processing_charge":"No","external_id":{"arxiv":["1311.4425"]},"_id":"10884","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","author":[{"first_name":"Benjamin","last_name":"Aminof","full_name":"Aminof, Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Swen","last_name":"Jacobs","full_name":"Jacobs, Swen"},{"first_name":"Ayrat","full_name":"Khalimov, Ayrat","last_name":"Khalimov"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","full_name":"Rubin, Sasha","last_name":"Rubin","first_name":"Sasha"}],"quality_controlled":"1","publication":"Verification, Model Checking, and Abstract Interpretation","abstract":[{"lang":"eng","text":"We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token."}],"publication_status":"published","date_updated":"2025-04-15T06:29:59Z","ec_funded":1,"date_published":"2014-01-30T00:00:00Z","arxiv":1,"status":"public","publisher":"Springer Nature","scopus_import":"1","citation":{"ista":"Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281.","ama":"Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15","chicago":"Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In Verification, Model Checking, and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15.","apa":"Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized model checking of token-passing systems. In Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15","short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","ieee":"B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15."},"intvolume":" 8318","month":"01","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783642540134"],"issn":["0302-9743"],"isbn":["9783642540127"]},"acknowledgement":"This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005.","title":"Parameterized model checking of token-passing systems","page":"262-281","day":"30","oa_version":"Preprint","alternative_title":["LNCS"],"date_created":"2022-03-18T13:01:22Z","language":[{"iso":"eng"}],"type":"conference","doi":"10.1007/978-3-642-54013-4_15","department":[{"_id":"KrCh"}]},{"date_updated":"2026-04-16T10:00:03Z","OA_type":"green","ec_funded":1,"date_published":"2014-01-30T00:00:00Z","publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"681"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"first_name":"Emmanuel","full_name":"Filiot, Emmanuel","last_name":"Filiot"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"publication":"VMCAI 2014: Verification, Model Checking, and Abstract Interpretation","quality_controlled":"1","abstract":[{"lang":"eng","text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.\r\nIn this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.\r\nWe present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games."}],"external_id":{"arxiv":["1311.3238"]},"_id":"10885","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","year":"2014","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1311.3238"}],"article_processing_charge":"No","oa":1,"conference":{"start_date":"2014-01-19","end_date":"2014-01-21","location":"San Diego, CA, United States","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation"},"fulldoi":"https://doi.org/10.1007/978-3-642-54013-4_5","volume":8318,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"}],"doi":"10.1007/978-3-642-54013-4_5","alternative_title":["LNCS"],"date_created":"2022-03-18T13:03:15Z","language":[{"iso":"eng"}],"type":"conference","oa_version":"Preprint","publication_identifier":{"issn":["0302-9743"],"isbn":["9783642540127"],"eissn":["1611-3349"],"eisbn":["9783642540134"]},"acknowledgement":" Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","page":"78-97","title":"Doomsday equilibria for omega-regular games","day":"30","month":"01","scopus_import":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 78–97, doi:10.1007/978-3-642-54013-4_5.","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria for omega-regular games,” in VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 78–97.","short":"K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular games. In: VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:78-97. doi:10.1007/978-3-642-54013-4_5","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François Raskin. “Doomsday Equilibria for Omega-Regular Games.” In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, 8318:78–97. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_5.","apa":"Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J.-F. (2014). Doomsday equilibria for omega-regular games. In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 78–97). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_5","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 78–97."},"intvolume":" 8318","publisher":"Springer Nature","arxiv":1,"status":"public"},{"page":"249-262","title":"Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"19","year":"2014","publication_identifier":{"eisbn":["9783319040998"],"eissn":["2197-666X"],"issn":["1612-3786"],"isbn":["9783319040981"]},"acknowledgement":"This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.","_id":"10886","publication":"Topological Methods in Data Analysis and Visualization III ","quality_controlled":"1","abstract":[{"text":"We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set.","lang":"eng"}],"oa_version":"None","author":[{"full_name":"Zobel, Valentin","last_name":"Zobel","first_name":"Valentin"},{"first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"}],"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","alternative_title":["Mathematics and Visualization"],"date_created":"2022-03-18T13:05:39Z","department":[{"_id":"HeEd"}],"doi":"10.1007/978-3-319-04099-8_16","date_updated":"2023-09-05T14:13:16Z","date_published":"2014-03-19T00:00:00Z","status":"public","publisher":"Springer","fulldoi":"https://doi.org/10.1007/978-3-319-04099-8_16","scopus_import":"1","citation":{"chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In Topological Methods in Data Analysis and Visualization III , 249–62. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_16.","apa":"Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In Topological Methods in Data Analysis and Visualization III (pp. 249–262). Springer. https://doi.org/10.1007/978-3-319-04099-8_16","ama":"Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In: Topological Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16","ista":"Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. Topological Methods in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262.","mla":"Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature,” in Topological Methods in Data Analysis and Visualization III , 2014, pp. 249–262.","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–262."},"article_processing_charge":"No","month":"03"},{"publication":"25th International Symposium, ISAAC 2014","quality_controlled":"1","abstract":[{"text":"In this paper, we introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist.\r\nUsing our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.","lang":"eng"}],"related_material":{"record":[{"id":"481","status":"public","relation":"later_version"}]},"author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"last_name":"Huber","full_name":"Huber, Stefan","first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814"},{"first_name":"Peter","last_name":"Palfrader","full_name":"Palfrader, Peter"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","external_id":{"isi":["000354865900010"]},"isi":1,"_id":"10892","date_updated":"2025-09-29T13:22:55Z","date_published":"2014-11-08T00:00:00Z","publication_status":"published","article_processing_charge":"No","volume":8889,"fulldoi":"https://doi.org/10.1007/978-3-319-13075-0_10","conference":{"name":"ISAAC: International Symposium on Algorithms and Computation","location":"Jeonju, Korea","start_date":"2014-12-15","end_date":"2014-12-17"},"oa_version":"None","title":"Planar matchings for weighted straight skeletons","page":"117-127","day":"08","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783319130750"],"issn":["0302-9743"],"isbn":["9783319130743"]},"acknowledgement":"T. Biedl was supported by NSERC and the Ross and Muriel Cheriton Fellowship. P. Palfrader was supported by Austrian Science Fund (FWF): P25816-N15.","doi":"10.1007/978-3-319-13075-0_10","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"type":"conference","date_created":"2022-03-21T07:09:03Z","alternative_title":["LNCS"],"publisher":"Springer Nature","status":"public","month":"11","corr_author":"1","intvolume":" 8889","scopus_import":"1","citation":{"ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” in 25th International Symposium, ISAAC 2014, Jeonju, Korea, 2014, vol. 8889, pp. 117–127.","short":"T. Biedl, S. Huber, P. Palfrader, in:, 25th International Symposium, ISAAC 2014, Springer Nature, 2014, pp. 117–127.","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” 25th International Symposium, ISAAC 2014, vol. 8889, Springer Nature, 2014, pp. 117–27, doi:10.1007/978-3-319-13075-0_10.","ista":"Biedl T, Huber S, Palfrader P. 2014. Planar matchings for weighted straight skeletons. 25th International Symposium, ISAAC 2014. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 8889, 117–127.","apa":"Biedl, T., Huber, S., & Palfrader, P. (2014). Planar matchings for weighted straight skeletons. In 25th International Symposium, ISAAC 2014 (Vol. 8889, pp. 117–127). Jeonju, Korea: Springer Nature. https://doi.org/10.1007/978-3-319-13075-0_10","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” In 25th International Symposium, ISAAC 2014, 8889:117–27. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13075-0_10.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. In: 25th International Symposium, ISAAC 2014. Vol 8889. Springer Nature; 2014:117-127. doi:10.1007/978-3-319-13075-0_10"}},{"author":[{"full_name":"Kasten, Jens","last_name":"Kasten","first_name":"Jens"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan","first_name":"Jan"},{"last_name":"Reich","full_name":"Reich, Wieland","first_name":"Wieland"},{"first_name":"Gerik","last_name":"Scheuermann","full_name":"Scheuermann, Gerik"}],"publication":"Topological Methods in Data Analysis and Visualization III ","quality_controlled":"1","abstract":[{"lang":"eng","text":"Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data."}],"_id":"10893","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","date_updated":"2025-04-15T08:37:54Z","ec_funded":1,"date_published":"2014-03-19T00:00:00Z","publication_status":"published","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","editor":[{"full_name":"Bremer, Peer-Timo","last_name":"Bremer","first_name":"Peer-Timo"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"last_name":"Pascucci","full_name":"Pascucci, Valerio","first_name":"Valerio"},{"full_name":"Peikert, Ronald","last_name":"Peikert","first_name":"Ronald"}],"fulldoi":"https://doi.org/10.1007/978-3-319-04099-8_4","volume":1,"series_title":"Mathematics and Visualization","oa_version":"None","publication_identifier":{"eissn":["2197-666X"],"eisbn":["9783319040998"],"isbn":["9783319040981"],"issn":["1612-3786"]},"acknowledgement":"First, we thank the reviewers of this paper for their ideas and critical comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions. This research is supported by the European Commission under the TOPOSYS project FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the European Science Foundation under the ACAT Research Network Program.","title":"Toward the extraction of saddle periodic orbits","page":"55-69","day":"19","department":[{"_id":"HeEd"}],"doi":"10.1007/978-3-319-04099-8_4","date_created":"2022-03-21T07:11:23Z","language":[{"iso":"eng"}],"type":"book_chapter","publisher":"Springer","status":"public","month":"03","place":"Cham","scopus_import":"1","citation":{"mla":"Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4.","ieee":"J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer, 2014, pp. 55–69.","short":"J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III , Springer, Cham, 2014, pp. 55–69.","chicago":"Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_4.","apa":"Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4","ama":"Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization. Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4","ista":"Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization III . vol. 1, 55–69."},"intvolume":" 1"},{"oa_version":"None","title":"PHAT – Persistent Homology Algorithms Toolbox","page":"137-143","day":"01","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662441985"],"eissn":["1611-3349"],"eisbn":["9783662441992"]},"department":[{"_id":"HeEd"}],"doi":"10.1007/978-3-662-44199-2_24","language":[{"iso":"eng"}],"type":"conference","date_created":"2022-03-21T07:12:16Z","publisher":"Springer Berlin Heidelberg","status":"public","month":"09","place":"Berlin, Heidelberg","intvolume":" 8592","scopus_import":"1","citation":{"ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software. ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.","apa":"Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2014). PHAT – Persistent Homology Algorithms Toolbox. In ICMS 2014: International Congress on Mathematical Software (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-662-44199-2_24","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT – Persistent Homology Algorithms Toolbox.” In ICMS 2014: International Congress on Mathematical Software, 8592:137–43. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. https://doi.org/10.1007/978-3-662-44199-2_24.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms Toolbox. In: ICMS 2014: International Congress on Mathematical Software. Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143. doi:10.1007/978-3-662-44199-2_24","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, pp. 137–143.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology Algorithms Toolbox,” in ICMS 2014: International Congress on Mathematical Software, Seoul, South Korea, 2014, vol. 8592, pp. 137–143.","mla":"Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” ICMS 2014: International Congress on Mathematical Software, vol. 8592, Springer Berlin Heidelberg, 2014, pp. 137–43, doi:10.1007/978-3-662-44199-2_24."},"quality_controlled":"1","publication":"ICMS 2014: International Congress on Mathematical Software","abstract":[{"lang":"eng","text":"PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations."}],"related_material":{"record":[{"status":"public","id":"1433","relation":"later_version"}]},"author":[{"orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan","first_name":"Jan"},{"first_name":"Hubert","full_name":"Wagner, Hubert","last_name":"Wagner"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2014","_id":"10894","date_updated":"2026-06-18T17:35:15Z","date_published":"2014-09-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","fulldoi":"https://doi.org/10.1007/978-3-662-44199-2_24","volume":8592,"series_title":"LNCS","conference":{"start_date":"2014-08-05","end_date":"2014-08-09","name":"ICMS: International Congress on Mathematical Software","location":"Seoul, South Korea"}},{"month":"04","scopus_import":1,"citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. “Perfect-Information Stochastic Mean-Payoff Parity Games,” 8412:210–25. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_14.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2014). Perfect-information stochastic mean-payoff parity games (Vol. 8412, pp. 210–225). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_14","ama":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-information stochastic mean-payoff parity games. In: Vol 8412. Springer; 2014:210-225. doi:10.1007/978-3-642-54830-7_14","ista":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2014. Perfect-information stochastic mean-payoff parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 210–225.","mla":"Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff Parity Games. Vol. 8412, Springer, 2014, pp. 210–25, doi:10.1007/978-3-642-54830-7_14.","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, “Perfect-information stochastic mean-payoff parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 210–225.","short":"K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, in:, Springer, 2014, pp. 210–225."},"intvolume":" 8412","publist_id":"4758","publisher":"Springer","status":"public","department":[{"_id":"KrCh"}],"doi":"10.1007/978-3-642-54830-7_14","date_created":"2018-12-11T11:56:21Z","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"type":"conference","oa_version":"None","acknowledgement":"This research was supported by European project Cassting (FP7-601148).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/128.","page":"210 - 225","title":"Perfect-information stochastic mean-payoff parity games","day":"01","conference":{"start_date":"2014-04-05","end_date":"2014-04-13","location":"Grenoble, France","name":"FoSSaCS: Foundations of Software Science and Computation Structures"},"fulldoi":"https://doi.org/10.1007/978-3-642-54830-7_14","volume":8412,"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"date_updated":"2023-02-23T12:24:50Z","date_published":"2014-04-01T00:00:00Z","publication_status":"published","related_material":{"record":[{"status":"public","id":"5405","relation":"earlier_version"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Gimbert","full_name":"Gimbert, Hugo","first_name":"Hugo"},{"first_name":"Youssouf","full_name":"Oualhadj, Youssouf","last_name":"Oualhadj"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2 1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic). We present an algorithm running in time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which the objective can be ensured with probability 1, where n is the number of states of the game, d the number of priorities of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states in 2 1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective). "}],"_id":"2212","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014"},{"ec_funded":1,"date_updated":"2023-02-23T12:24:58Z","date_published":"2014-04-01T00:00:00Z","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5408"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"first_name":"Sumit","full_name":"Nain, Sumit","last_name":"Nain"},{"first_name":"Moshe","last_name":"Vardi","full_name":"Vardi, Moshe"}],"quality_controlled":"1","abstract":[{"text":"We consider two-player partial-observation stochastic games on finitestate graphs where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are ε-regular conditions specified as parity objectives. The qualitative-analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). These qualitative-analysis problems are known to be undecidable. However in many applications the relevant question is the existence of finite-memory strategies, and the qualitative-analysis problems under finite-memory strategies was recently shown to be decidable in 2EXPTIME.We improve the complexity and show that the qualitative-analysis problems for partial-observation stochastic parity games under finite-memory strategies are EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis.","lang":"eng"}],"external_id":{"arxiv":["1401.3289"]},"_id":"2213","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.3289"}],"oa":1,"conference":{"location":"Grenoble, France","name":"FoSSaCS: Foundations of Software Science and Computation Structures","start_date":"2014-04-05","end_date":"2014-04-13"},"fulldoi":"https://doi.org/10.1007/978-3-642-54830-7_16","volume":8412,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"doi":"10.1007/978-3-642-54830-7_16","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:56:21Z","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"type":"conference","oa_version":"Preprint","acknowledgement":"This research was supported by European project Cassting (FP7-601148), NSF grants CNS 1049862 and CCF-1139011, by NSF Expe ditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","page":"242 - 257","title":"The complexity of partial-observation stochastic parity games with finite-memory strategies","day":"01","month":"04","scopus_import":1,"citation":{"mla":"Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. Vol. 8412, Springer, 2014, pp. 242–57, doi:10.1007/978-3-642-54830-7_16.","ieee":"K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, “The complexity of partial-observation stochastic parity games with finite-memory strategies,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 242–257.","short":"K. Chatterjee, L. Doyen, S. Nain, M. Vardi, in:, Springer, 2014, pp. 242–257.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. “The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies,” 8412:242–57. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_16.","apa":"Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2014). The complexity of partial-observation stochastic parity games with finite-memory strategies (Vol. 8412, pp. 242–257). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_16","ama":"Chatterjee K, Doyen L, Nain S, Vardi M. The complexity of partial-observation stochastic parity games with finite-memory strategies. In: Vol 8412. Springer; 2014:242-257. doi:10.1007/978-3-642-54830-7_16","ista":"Chatterjee K, Doyen L, Nain S, Vardi M. 2014. The complexity of partial-observation stochastic parity games with finite-memory strategies. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 242–257."},"intvolume":" 8412","publist_id":"4757","publisher":"Springer","arxiv":1,"status":"public"},{"month":"01","citation":{"chicago":"Stoler Barak, Liat, Christine Moussion, Elias Shezen, Miki Hatzav, Michael K Sixt, and Ronen Alon. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0085699.","apa":"Stoler Barak, L., Moussion, C., Shezen, E., Hatzav, M., Sixt, M. K., & Alon, R. (2014). Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0085699","ama":"Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085699","ista":"Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. 2014. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. 9(1), e85699.","mla":"Stoler Barak, Liat, et al. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” PLoS One, vol. 9, no. 1, e85699, Public Library of Science, 2014, doi:10.1371/journal.pone.0085699.","short":"L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M.K. Sixt, R. Alon, PLoS One 9 (2014).","ieee":"L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M. K. Sixt, and R. Alon, “Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects,” PLoS One, vol. 9, no. 1. Public Library of Science, 2014."},"scopus_import":"1","intvolume":" 9","publist_id":"4756","publisher":"Public Library of Science","issue":"1","ddc":["570"],"status":"public","file_date_updated":"2020-07-14T12:45:33Z","article_number":"e85699","doi":"10.1371/journal.pone.0085699","department":[{"_id":"MiSi"}],"file":[{"creator":"system","content_type":"application/pdf","checksum":"84a8033bda2e07e39405f5acc85f4eca","access_level":"open_access","date_created":"2018-12-12T10:07:48Z","file_id":"4646","file_size":12634775,"date_updated":"2020-07-14T12:45:33Z","relation":"main_file","file_name":"IST-2016-433-v1+1_journal.pone.0085699.pdf"}],"date_created":"2018-12-11T11:56:22Z","pubrep_id":"433","has_accepted_license":"1","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledgement":"Michael Sixt's research is supported by the European Research Council (ERC Starting grant).","day":"22","title":"Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects","oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":9,"fulldoi":"https://doi.org/10.1371/journal.pone.0085699","project":[{"grant_number":"289720","_id":"25A76F58-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Stromal Cell-immune Cell Interactions in Health and Disease"}],"date_published":"2014-01-22T00:00:00Z","date_updated":"2025-09-29T11:30:42Z","ec_funded":1,"publication_status":"published","author":[{"first_name":"Liat","full_name":"Stoler Barak, Liat","last_name":"Stoler Barak"},{"first_name":"Christine","full_name":"Moussion, Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shezen","full_name":"Shezen, Elias","first_name":"Elias"},{"full_name":"Hatzav, Miki","last_name":"Hatzav","first_name":"Miki"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"full_name":"Alon, Ronen","last_name":"Alon","first_name":"Ronen"}],"abstract":[{"lang":"eng","text":"A hallmark of immune cell trafficking is directional guidance via gradients of soluble or surface bound chemokines. Vascular endothelial cells produce, transport and deposit either their own chemokines or chemokines produced by the underlying stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold for these chemokine pools, but it is unclear how steep chemokine gradients are sustained between the lumenal and ablumenal aspects of blood vessels. Addressing this question by semi-quantitative immunostaining of HS moieties around blood vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal lamina of resting and inflamed post capillary skin venules, as well as in high endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx probe further suggested that their lumenal glycocalyx contains much lower HS density than their basolateral extracellular matrix (ECM). This polarized HS pattern was observed also in isolated resting and inflamed microvascular dermal cells. Notably, progressive skin inflammation resulted in massive ECM deposition and in further HS enrichment around skin post capillary venules and their associated pericytes. Inflammation-dependent HS enrichment was not compromised in mice deficient in the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature patterns steep gradients of HS scaffolds between their lumenal and basolateral endothelial aspects, and that inflammatory processes can further enrich the HS content nearby inflamed vessels. We propose that chemokine gradients between the lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold gradients."}],"quality_controlled":"1","publication":"PLoS One","isi":1,"_id":"2214","external_id":{"isi":["000330283100061"]},"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"publication_status":"published","date_published":"2014-05-14T00:00:00Z","date_updated":"2025-09-29T11:30:10Z","year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"_id":"2215","external_id":{"isi":["000337245500009"]},"abstract":[{"lang":"eng","text":"Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events."}],"publication":"Nature Reviews Molecular Cell Biology","quality_controlled":"1","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","first_name":"Jörg"},{"first_name":"Claudio","full_name":"Lademann, Claudio","last_name":"Lademann"},{"last_name":"Jentsch","full_name":"Jentsch, Stefan","first_name":"Stefan"}],"volume":15,"fulldoi":"https://doi.org/10.1038/nrm3805","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:22Z","department":[{"_id":"MiSi"}],"doi":"10.1038/nrm3805","day":"14","title":"Mechanisms and principles of homology search during recombination","page":"369 - 383","acknowledgement":"J.R. was supported by a Boehringer Ingelheim Fonds PhD stipend.","oa_version":"None","intvolume":" 15","citation":{"mla":"Renkawitz, Jörg, et al. “Mechanisms and Principles of Homology Search during Recombination.” Nature Reviews Molecular Cell Biology, vol. 15, no. 6, Nature Publishing Group, 2014, pp. 369–83, doi:10.1038/nrm3805.","short":"J. Renkawitz, C. Lademann, S. Jentsch, Nature Reviews Molecular Cell Biology 15 (2014) 369–383.","ieee":"J. Renkawitz, C. Lademann, and S. Jentsch, “Mechanisms and principles of homology search during recombination,” Nature Reviews Molecular Cell Biology, vol. 15, no. 6. Nature Publishing Group, pp. 369–383, 2014.","ama":"Renkawitz J, Lademann C, Jentsch S. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 2014;15(6):369-383. doi:10.1038/nrm3805","chicago":"Renkawitz, Jörg, Claudio Lademann, and Stefan Jentsch. “Mechanisms and Principles of Homology Search during Recombination.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/nrm3805.","apa":"Renkawitz, J., Lademann, C., & Jentsch, S. (2014). Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3805","ista":"Renkawitz J, Lademann C, Jentsch S. 2014. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 15(6), 369–383."},"scopus_import":"1","month":"05","status":"public","issue":"6","publisher":"Nature Publishing Group","publist_id":"4755"},{"publisher":"Springer","publist_id":"4752","status":"public","oa":1,"main_file_link":[{"url":"https://dl.acm.org/citation.cfm?doid=2562059.2562141","open_access":"1"}],"month":"01","fulldoi":"https://doi.org/10.1145/2562059.2562141","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","location":"Berlin, Germany","start_date":"2017-04-15","end_date":"2017-04-17"},"citation":{"mla":"Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. Springer, 2014, pp. 303–12, doi:10.1145/2562059.2562141.","short":"K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, in:, Springer, 2014, pp. 303–312.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, “Edit distance for timed automata,” presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany, 2014, pp. 303–312.","ama":"Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit distance for timed automata. In: Springer; 2014:303-312. doi:10.1145/2562059.2562141","apa":"Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2014). Edit distance for timed automata (pp. 303–312). Presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562141","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Ritankar Majumdar. “Edit Distance for Timed Automata,” 303–12. Springer, 2014. https://doi.org/10.1145/2562059.2562141.","ista":"Chatterjee K, Ibsen-Jensen R, Majumdar R. 2014. Edit distance for timed automata. HSCC: Hybrid Systems - Computation and Control, 303–312."},"scopus_import":"1","abstract":[{"lang":"eng","text":"The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in time stamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than δ away from the parameter, for δ > 0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and analogous decidability results hold for rectangular automata."}],"quality_controlled":"1","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar","last_name":"Majumdar"}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"earlier_version","id":"5409","status":"public"}]},"year":"2014","day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Edit distance for timed automata","page":"303 - 312","_id":"2216","department":[{"_id":"KrCh"}],"doi":"10.1145/2562059.2562141","date_published":"2014-01-01T00:00:00Z","date_updated":"2024-10-21T06:02:53Z","type":"conference","publication_status":"published","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:22Z"},{"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://doi.org/10.15479/AT:IST-2014-171-v1-1","open_access":"1"}],"article_processing_charge":"No","oa":1,"conference":{"name":"HSCC: Hybrid Systems - Computation and Control","location":"Berlin, Germany","end_date":"2014-04-17","start_date":"2014-04-15"},"fulldoi":"https://doi.org/10.1145/2562059.2562130","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"5416","status":"public","relation":"earlier_version"}]},"abstract":[{"text":"As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.\r\n\r\nThe contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem.","lang":"eng"}],"quality_controlled":"1","publication":"Proceedings of the 17th international conference on Hybrid systems: computation and control","_id":"2217","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","date_published":"2014-04-01T00:00:00Z","ec_funded":1,"OA_type":"green","date_updated":"2025-06-26T08:32:32Z","publication_status":"published","publist_id":"4751","publisher":"Springer","status":"public","month":"04","citation":{"apa":"Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems. In Proceedings of the 17th international conference on Hybrid systems: computation and control (pp. 213–222). Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562130","chicago":"Henzinger, Thomas A, and Jan Otop. “Model Measuring for Hybrid Systems.” In Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, 213–22. Springer, 2014. https://doi.org/10.1145/2562059.2562130.","ama":"Henzinger TA, Otop J. Model measuring for hybrid systems. In: Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control. Springer; 2014:213-222. doi:10.1145/2562059.2562130","ista":"Henzinger TA, Otop J. 2014. Model measuring for hybrid systems. Proceedings of the 17th international conference on Hybrid systems: computation and control. HSCC: Hybrid Systems - Computation and Control, 213–222.","mla":"Henzinger, Thomas A., and Jan Otop. “Model Measuring for Hybrid Systems.” Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–22, doi:10.1145/2562059.2562130.","short":"T.A. Henzinger, J. Otop, in:, Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–222.","ieee":"T. A. Henzinger and J. Otop, “Model measuring for hybrid systems,” in Proceedings of the 17th international conference on Hybrid systems: computation and control, Berlin, Germany, 2014, pp. 213–222."},"scopus_import":"1","oa_version":"Preprint","acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/171","day":"01","title":"Model measuring for hybrid systems","page":"213 - 222","doi":"10.1145/2562059.2562130","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:56:23Z","type":"conference","language":[{"iso":"eng"}]},{"alternative_title":["LNCS"],"date_created":"2018-12-11T11:56:23Z","pubrep_id":"297","has_accepted_license":"1","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"doi":"10.1007/978-3-319-08867-9_38","file":[{"checksum":"a631d3105509f239724644e77a1212e2","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:33Z","file_size":416732,"relation":"main_file","file_name":"IST-2014-297-v1+1_cav14-final.pdf","file_id":"4995","access_level":"open_access","date_created":"2018-12-12T10:13:14Z"},{"creator":"system","content_type":"application/pdf","checksum":"f8b0f748cc9fa697ca992cc56c87bc4e","access_level":"open_access","date_created":"2018-12-12T10:13:15Z","file_id":"4996","relation":"main_file","file_size":616293,"date_updated":"2020-07-14T12:45:33Z","file_name":"IST-2014-297-v2+1_cav14-final2.pdf"}],"publication_identifier":{"isbn":["978-331908866-2"]},"day":"22","page":"568 - 584","title":"Regression-free synthesis for concurrency","oa_version":"Submitted Version","citation":{"short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2014, pp. 568–584.","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free synthesis for concurrency,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 568–584.","mla":"Cerny, Pavol, et al. Regression-Free Synthesis for Concurrency. Vol. 8559, Springer, 2014, pp. 568–84, doi:10.1007/978-3-319-08867-9_38.","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559, 568–584.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_38.","ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:10.1007/978-3-319-08867-9_38","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach, T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_38"},"scopus_import":"1","intvolume":" 8559","month":"07","ddc":["000"],"status":"public","file_date_updated":"2020-07-14T12:45:33Z","publist_id":"4749","publisher":"Springer","publication_status":"published","date_published":"2014-07-22T00:00:00Z","date_updated":"2026-04-09T10:54:00Z","ec_funded":1,"_id":"2218","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Pavol","full_name":"Cerny, Pavol","last_name":"Cerny"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun"},{"last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid","first_name":"Leonid"},{"orcid":"0000-0003-4409-8487","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","full_name":"Tarrach, Thorsten","last_name":"Tarrach"}],"related_material":{"record":[{"status":"public","id":"1130","relation":"dissertation_contains"}]},"abstract":[{"text":"While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs.","lang":"eng"}],"quality_controlled":"1","conference":{"end_date":"2014-07-22","start_date":"2014-07-18","location":"Vienna, Austria","name":"CAV: Computer Aided Verification"},"fulldoi":"https://doi.org/10.1007/978-3-319-08867-9_38","volume":8559,"main_file_link":[{"open_access":"1","url":"https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38"}],"oa":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"}]},{"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/401"}],"oa":1,"conference":{"name":"IACR: International Conference on Practice and Theory in Public-Key Cryptography"},"fulldoi":"https://doi.org/10.1007/978-3-642-54631-0_1","volume":8383,"date_updated":"2021-01-12T06:56:05Z","date_published":"2014-03-01T00:00:00Z","publication_status":"published","author":[{"full_name":"Kiltz, Eike","last_name":"Kiltz","first_name":"Eike"},{"full_name":"Masny, Daniel","last_name":"Masny","first_name":"Daniel"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"quality_controlled":"1","abstract":[{"text":"Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext (IND-CCA) secure public-key encryption scheme from the learning parity with noise (LPN) assumption. In this work we give an alternative scheme which is conceptually simpler and more efficient. At the core of our construction is a trapdoor technique originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which we adapt to the LPN setting. The main technical tool is a new double-trapdoor mechanism, together with a trapdoor switching lemma based on a computational variant of the leftover hash lemma.","lang":"eng"}],"_id":"2219","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","month":"03","scopus_import":1,"citation":{"ista":"Kiltz E, Masny D, Pietrzak KZ. 2014. Simple chosen-ciphertext security from low noise LPN. IACR: International Conference on Practice and Theory in Public-Key Cryptography, LNCS, vol. 8383, 1–18.","ama":"Kiltz E, Masny D, Pietrzak KZ. Simple chosen-ciphertext security from low noise LPN. In: Vol 8383. Springer; 2014:1-18. doi:10.1007/978-3-642-54631-0_1","apa":"Kiltz, E., Masny, D., & Pietrzak, K. Z. (2014). Simple chosen-ciphertext security from low noise LPN (Vol. 8383, pp. 1–18). Presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, Springer. https://doi.org/10.1007/978-3-642-54631-0_1","chicago":"Kiltz, Eike, Daniel Masny, and Krzysztof Z Pietrzak. “Simple Chosen-Ciphertext Security from Low Noise LPN,” 8383:1–18. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_1.","short":"E. Kiltz, D. Masny, K.Z. Pietrzak, in:, Springer, 2014, pp. 1–18.","ieee":"E. Kiltz, D. Masny, and K. Z. Pietrzak, “Simple chosen-ciphertext security from low noise LPN,” presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, 2014, vol. 8383, pp. 1–18.","mla":"Kiltz, Eike, et al. Simple Chosen-Ciphertext Security from Low Noise LPN. Vol. 8383, Springer, 2014, pp. 1–18, doi:10.1007/978-3-642-54631-0_1."},"intvolume":" 8383","publist_id":"4748","publisher":"Springer","status":"public","department":[{"_id":"KrPi"}],"doi":"10.1007/978-3-642-54631-0_1","date_created":"2018-12-11T11:56:24Z","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"type":"conference","oa_version":"Submitted Version","publication_identifier":{"isbn":["978-364254630-3"]},"title":"Simple chosen-ciphertext security from low noise LPN","page":"1 - 18","day":"01"},{"isi":1,"_id":"2220","external_id":{"pmid":["24766845"],"isi":["000335431300005"]},"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","full_name":"De Vos, Marjon","first_name":"Marjon"},{"first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"In this issue of Chemistry & Biology, Cokol and colleagues report a systematic study of drug interactions between antifungal compounds. Suppressive drug interactions occur more frequently than previously realized and come in different flavors with interesting implications.","lang":"eng"}],"quality_controlled":"1","publication":"Chemistry and Biology","pmid":1,"publication_status":"published","date_published":"2014-04-24T00:00:00Z","date_updated":"2025-09-29T11:28:57Z","volume":21,"fulldoi":"https://doi.org/10.1016/j.chembiol.2014.04.004","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/24766845","open_access":"1"}],"oa":1,"article_processing_charge":"No","publication_identifier":{"issn":["1074-5521"]},"day":"24","title":"Suppressive drug interactions between antifungals","page":"439 - 440","oa_version":"Published Version","date_created":"2018-12-11T11:56:24Z","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"doi":"10.1016/j.chembiol.2014.04.004","issue":"4","status":"public","publist_id":"4747","publisher":"Cell Press","citation":{"ista":"de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals. Chemistry and Biology. 21(4), 439–440.","chicago":"Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology. Cell Press, 2014. https://doi.org/10.1016/j.chembiol.2014.04.004.","ama":"de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals. Chemistry and Biology. 2014;21(4):439-440. doi:10.1016/j.chembiol.2014.04.004","apa":"de Vos, M., & Bollenbach, M. T. (2014). Suppressive drug interactions between antifungals. Chemistry and Biology. Cell Press. https://doi.org/10.1016/j.chembiol.2014.04.004","short":"M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440.","ieee":"M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,” Chemistry and Biology, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.","mla":"de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology, vol. 21, no. 4, Cell Press, 2014, pp. 439–40, doi:10.1016/j.chembiol.2014.04.004."},"scopus_import":"1","intvolume":" 21","corr_author":"1","month":"04"},{"page":"750 - 763","title":"VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis","day":"01","publication_identifier":{"issn":["0032-0781"]},"oa_version":"None","language":[{"iso":"eng"}],"type":"journal_article","date_created":"2018-12-11T11:56:24Z","doi":"10.1093/pcp/pcu012","department":[{"_id":"JiFr"}],"status":"public","issue":"4","publisher":"Oxford University Press","publist_id":"4742","intvolume":" 55","scopus_import":"1","citation":{"ista":"Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763.","ama":"Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 2014;55(4):750-763. doi:10.1093/pcp/pcu012","apa":"Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml, J., & Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcu012","chicago":"Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka, Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pcu012.","ieee":"S. Naramoto et al., “VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis,” Plant and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014.","short":"S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml, H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763.","mla":"Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:10.1093/pcp/pcu012."},"month":"04","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","external_id":{"isi":["000334679500009"]},"_id":"2222","isi":1,"publication":"Plant and Cell Physiology","quality_controlled":"1","abstract":[{"lang":"eng","text":"Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation."}],"author":[{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Tomoko","full_name":"Dainobu, Tomoko","last_name":"Dainobu"},{"first_name":"Hirotomo","last_name":"Takatsuka","full_name":"Takatsuka, Hirotomo"},{"last_name":"Okada","full_name":"Okada, Teruyo","first_name":"Teruyo"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Fukuda, Hiroo","last_name":"Fukuda","first_name":"Hiroo"}],"publication_status":"published","ec_funded":1,"date_updated":"2025-09-29T11:28:27Z","date_published":"2014-04-01T00:00:00Z","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"volume":55,"fulldoi":"https://doi.org/10.1093/pcp/pcu012","article_processing_charge":"No"},{"date_published":"2014-04-01T00:00:00Z","date_updated":"2025-09-29T11:27:52Z","ec_funded":1,"pmid":1,"publication_status":"published","abstract":[{"text":"Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes.","lang":"eng"}],"publication":"Plant and Cell Physiology","quality_controlled":"1","author":[{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"full_name":"Feraru, Mugurel","last_name":"Feraru","first_name":"Mugurel"},{"last_name":"Sasabe","full_name":"Sasabe, Michiko","first_name":"Michiko"},{"first_name":"Tomomi","full_name":"Ishikawa, Tomomi","last_name":"Ishikawa"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"first_name":"Tatsuo","full_name":"Kakimoto, Tatsuo","last_name":"Kakimoto"},{"first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"_id":"2223","external_id":{"isi":["000334679500008"],"pmid":["24369434"]},"article_processing_charge":"No","oa":1,"fulldoi":"https://doi.org/10.1093/pcp/pct196","volume":55,"tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"_id":"256BDAB0-B435-11E9-9278-68D0E5697425","name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.1093/pcp/pct196","department":[{"_id":"JiFr"}],"file":[{"file_name":"IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf","relation":"main_file","date_updated":"2020-07-14T12:45:34Z","file_size":2028111,"file_id":"5076","access_level":"open_access","date_created":"2018-12-12T10:14:25Z","checksum":"b781a76b32ac35a520256453c3ba9433","content_type":"application/pdf","creator":"system"}],"type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:25Z","pubrep_id":"431","oa_version":"Published Version","day":"01","page":"737 - 749","title":"BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis","publication_identifier":{"issn":["0032-0781"]},"month":"04","intvolume":" 55","citation":{"ieee":"H. Tanaka et al., “BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis,” Plant and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 737–749, 2014.","short":"H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa, J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749.","mla":"Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49, doi:10.1093/pcp/pct196.","ista":"Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 55(4), 737–749.","chicago":"Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pct196.","ama":"Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 2014;55(4):737-749. doi:10.1093/pcp/pct196","apa":"Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa, T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pct196"},"scopus_import":"1","publisher":"Oxford University Press","publist_id":"4741","status":"public","file_date_updated":"2020-07-14T12:45:34Z","issue":"4","ddc":["570"]},{"article_number":"025503","status":"public","issue":"2","publisher":"IOP Publishing","publist_id":"4740","intvolume":" 46","scopus_import":"1","citation":{"mla":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” Fluid Dynamics Research, vol. 46, no. 2, 025503, IOP Publishing, 2014, doi:10.1088/0169-5983/46/2/025503.","ieee":"S. Altmeyer, “On secondary instabilities generating footbridges between spiral vortex flow,” Fluid Dynamics Research, vol. 46, no. 2. IOP Publishing, 2014.","short":"S. Altmeyer, Fluid Dynamics Research 46 (2014).","chicago":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” Fluid Dynamics Research. IOP Publishing, 2014. https://doi.org/10.1088/0169-5983/46/2/025503.","ama":"Altmeyer S. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 2014;46(2). doi:10.1088/0169-5983/46/2/025503","apa":"Altmeyer, S. (2014). On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. IOP Publishing. https://doi.org/10.1088/0169-5983/46/2/025503","ista":"Altmeyer S. 2014. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 46(2), 025503."},"month":"04","corr_author":"1","title":"On secondary instabilities generating footbridges between spiral vortex flow","day":"01","publication_identifier":{"issn":["0169-5983"]},"oa_version":"None","language":[{"iso":"eng"}],"type":"journal_article","date_created":"2018-12-11T11:56:25Z","doi":"10.1088/0169-5983/46/2/025503","department":[{"_id":"BjHo"}],"fulldoi":"https://doi.org/10.1088/0169-5983/46/2/025503","volume":46,"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2014","external_id":{"isi":["000334075800003"]},"_id":"2224","isi":1,"quality_controlled":"1","publication":"Fluid Dynamics Research","abstract":[{"lang":"eng","text":"This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet."}],"author":[{"orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian"}],"publication_status":"published","date_updated":"2026-04-16T10:07:46Z","date_published":"2014-04-01T00:00:00Z"}]