[{"publist_id":"3795","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A chain rule for an entropy notion H(.) states that the entropy H(X) of a variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)>= H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)>= H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability entropy and several variants of HILL entropy) satisfy the chain rule for conditional entropy, though here not only the quantity decreases by l, but also the quality of the entropy decreases exponentially in l. However, for \r\nthe standard notion of conditional HILL entropy (the computational equivalent of min-entropy) the existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that for conditional HILL entropy no meaningful chain rule exists, assuming the existence of one-way permutations: there exist distributions X,Y,A, where A is a distribution over a single bit, but $H(X|Y)>>H(X|Y,A)$, even if we simultaneously allow for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying our construction is based on a surprising connection between the chain rule for HILL entropy and deniable encryption. "}],"has_accepted_license":"1","publication_status":"published","status":"public","date_published":"2013-01-29T00:00:00Z","date_created":"2018-12-11T12:00:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","intvolume":" 7785","quality_controlled":"1","_id":"2940","day":"29","type":"conference","oa":1,"editor":[{"first_name":"Amit","full_name":"Sahai, Amit","last_name":"Sahai"}],"publisher":"Springer","volume":7785,"department":[{"_id":"KrPi"}],"year":"2013","citation":{"short":"S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp. 23–39.","apa":"Krenn, S., Pietrzak, K. Z., & Wadia, A. (2013). A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-642-36594-2_2","mla":"Krenn, Stephan, et al. A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It. Edited by Amit Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:10.1007/978-3-642-36594-2_2.","ista":"Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. TCC: Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.","ama":"Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed. Vol 7785. Springer; 2013:23-39. doi:10.1007/978-3-642-36594-2_2","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. https://doi.org/10.1007/978-3-642-36594-2_2.","ieee":"S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it,” presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol. 7785, pp. 23–39."},"scopus_import":1,"doi":"10.1007/978-3-642-36594-2_2","date_updated":"2025-09-18T11:37:22Z","ec_funded":1,"ddc":["000"],"file_date_updated":"2020-07-14T12:45:54Z","related_material":{"record":[{"status":"public","id":"1479","relation":"later_version"}]},"title":"A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it","page":"23 - 39","author":[{"last_name":"Krenn","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","full_name":"Krenn, Stephan","orcid":"0000-0003-2835-9093","first_name":"Stephan"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Akshay","full_name":"Wadia, Akshay","last_name":"Wadia"}],"file":[{"access_level":"open_access","checksum":"beb0cc1c0579da2d2e84394230a5da78","content_type":"application/pdf","creator":"dernst","file_id":"5875","relation":"main_file","date_updated":"2020-07-14T12:45:54Z","file_name":"2013_LNCS_Krenn.pdf","date_created":"2019-01-22T14:11:11Z","file_size":414823}],"conference":{"name":"TCC: Theory of Cryptography Conference","end_date":"2013-03-06","start_date":"2013-03-03","location":"Tokyo, Japan"},"fulldoi":"https://doi.org/10.1007/978-3-642-36594-2_2","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}]},{"date_published":"2013-02-01T00:00:00Z","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"publication_status":"published","status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"article_processing_charge":"No","oa_version":"None","language":[{"iso":"eng"}],"publist_id":"3788","quality_controlled":"1","corr_author":"1","type":"journal_article","_id":"2944","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T12:00:28Z","intvolume":" 22","month":"02","scopus_import":"1","external_id":{"isi":["000314220900008"]},"doi":"10.1111/mec.12165","date_updated":"2025-09-29T13:25:36Z","publisher":"Wiley-Blackwell","volume":22,"year":"2013","citation":{"mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.","apa":"Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013."},"department":[{"_id":"NiBa"}],"publication":"Molecular Ecology","author":[{"full_name":"Aeschbacher, Simon","first_name":"Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"},{"last_name":"Beaumont","first_name":"Mark","full_name":"Beaumont, Mark"}],"fulldoi":"https://doi.org/10.1111/mec.12165","page":"987 - 1002","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","related_material":{"record":[{"relation":"research_data","id":"9758","status":"public"}]},"acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","issue":"4"},{"intvolume":" 7724","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:30Z","series_title":"Lecture Notes in Computer Science","oa":1,"_id":"2948","type":"conference","day":"04","quality_controlled":"1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publist_id":"3784","date_published":"2013-04-04T00:00:00Z","abstract":[{"lang":"eng","text":"Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance."}],"publication_status":"published","has_accepted_license":"1","status":"public","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:55Z","acknowledgement":"This work was supported by the PASCAL 2 Network of Excellence (TT) and by the Newton International Fellowship (NQ)","ddc":["000"],"fulldoi":"https://doi.org/10.1007/978-3-642-37331-2_1","conference":{"start_date":"2012-11-05","name":"ACCV: Asian Conference on Computer Vision","end_date":"2012-11-09","location":"Daejeon, Korea"},"file":[{"access_level":"open_access","checksum":"a0a7234a89e2192af655b0d0ae3bf445","date_updated":"2020-07-14T12:45:55Z","relation":"main_file","file_id":"5874","creator":"dernst","content_type":"application/pdf","file_name":"2012_ACCV_Tommasi.pdf","date_created":"2019-01-22T14:03:11Z","file_size":1513620}],"author":[{"full_name":"Tommasi, Tatiana","first_name":"Tatiana","last_name":"Tommasi"},{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"last_name":"Caputo","full_name":"Caputo, Barbara","first_name":"Barbara"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"page":"1 - 15","title":"Beyond dataset bias: Multi-task unaligned shared knowledge transfer","year":"2013","citation":{"mla":"Tommasi, Tatiana, et al. Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer. Vol. 7724, Springer, 2013, pp. 1–15, doi:10.1007/978-3-642-37331-2_1.","short":"T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15.","apa":"Tommasi, T., Quadrianto, N., Caputo, B., & Lampert, C. (2013). Beyond dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. https://doi.org/10.1007/978-3-642-37331-2_1","chicago":"Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert. “Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-37331-2_1.","ista":"Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 7724, 1–15.","ama":"Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 2013;7724:1-15. doi:10.1007/978-3-642-37331-2_1","ieee":"T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013."},"department":[{"_id":"ChLa"}],"publisher":"Springer","volume":7724,"date_updated":"2020-08-11T10:09:54Z","doi":"10.1007/978-3-642-37331-2_1","scopus_import":1},{"title":"Quantitative abstraction refinement","corr_author":"1","page":"115 - 128","quality_controlled":"1","type":"conference","_id":"2182","day":"01","author":[{"first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Arjun","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"}],"publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"}],"fulldoi":"https://doi.org/10.1145/2429069.2429085","conference":{"start_date":"2013-07-23","name":"POPL: Principles of Programming Languages","end_date":"2013-01-25","location":"Rome, Italy"},"date_created":"2018-12-11T11:56:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","scopus_import":1,"oa_version":"None","doi":"10.1145/2429069.2429085","date_updated":"2024-10-09T20:55:21Z","status":"public","abstract":[{"lang":"eng","text":"We propose a general framework for abstraction with respect to quantitative properties, such as worst-case execution time, or power consumption. Our framework provides a systematic way for counter-example guided abstraction refinement for quantitative properties. The salient aspect of the framework is that it allows anytime verification, that is, verification algorithms that can be stopped at any time (for example, due to exhaustion of memory), and report approximations that improve monotonically when the algorithms are given more time. We instantiate the framework with a number of quantitative abstractions and refinement schemes, which differ in terms of how much quantitative information they keep from the original system. We introduce both state-based and trace-based quantitative abstractions, and we describe conditions that define classes of quantitative properties for which the abstractions provide over-approximations. We give algorithms for evaluating the quantitative properties on the abstract systems. We present algorithms for counter-example based refinements for quantitative properties for both state-based and segment-based abstractions. We perform a case study on worst-case execution time of executables to evaluate the anytime verification aspect and the quantitative abstractions we proposed."}],"publication_status":"published","date_published":"2013-01-01T00:00:00Z","ec_funded":1,"publist_id":"4800","language":[{"iso":"eng"}],"publisher":"ACM","department":[{"_id":"ToHe"}],"year":"2013","citation":{"mla":"Cerny, Pavol, et al. “Quantitative Abstraction Refinement.” Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 115–28, doi:10.1145/2429069.2429085.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 115–128.","apa":"Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2013). Quantitative abstraction refinement. In Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language (pp. 115–128). Rome, Italy: ACM. https://doi.org/10.1145/2429069.2429085","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative Abstraction Refinement.” In Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, 115–28. ACM, 2013. https://doi.org/10.1145/2429069.2429085.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2013. Quantitative abstraction refinement. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 115–128.","ama":"Cerny P, Henzinger TA, Radhakrishna A. Quantitative abstraction refinement. In: Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language. ACM; 2013:115-128. doi:10.1145/2429069.2429085","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative abstraction refinement,” in Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language, Rome, Italy, 2013, pp. 115–128."}},{"alternative_title":["LIPIcs"],"publist_id":"5837","language":[{"iso":"eng"}],"abstract":[{"text":"We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.","lang":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","date_published":"2013-09-01T00:00:00Z","oa_version":"Published Version","month":"09","intvolume":" 23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:39Z","tmp":{"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)","image":"/images/cc_by.png"},"series_title":"Leibniz International Proceedings in Informatics","oa":1,"_id":"1374","day":"01","type":"conference","corr_author":"1","quality_controlled":"1","department":[{"_id":"KrCh"}],"citation":{"ieee":"K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,” in 22nd EACSL Annual Conference on Computer Science Logic, Torino, Italy, 2013, vol. 23, pp. 181–196.","ama":"Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In: 22nd EACSL Annual Conference on Computer Science Logic. Vol 23. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2013:181-196. doi:10.4230/LIPIcs.CSL.2013.181","ista":"Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions. 22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” In 22nd EACSL Annual Conference on Computer Science Logic, 23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.181.","short":"K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.","apa":"Chatterjee, K., & Fijalkow, N. (2013). Infinite-state games with finitary conditions. In 22nd EACSL Annual Conference on Computer Science Logic (Vol. 23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2013.181","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” 22nd EACSL Annual Conference on Computer Science Logic, vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96, doi:10.4230/LIPIcs.CSL.2013.181."},"year":"2013","volume":23,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"date_updated":"2024-10-09T20:55:23Z","doi":"10.4230/LIPIcs.CSL.2013.181","scopus_import":1,"file_date_updated":"2020-07-14T12:44:47Z","ddc":["000"],"pubrep_id":"624","file":[{"date_created":"2018-12-12T10:13:38Z","file_name":"IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf","file_size":547296,"access_level":"open_access","checksum":"b7091a3866db573c0db5ec486952255e","content_type":"application/pdf","creator":"system","file_id":"5023","relation":"main_file","date_updated":"2020-07-14T12:44:47Z"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.4230/LIPIcs.CSL.2013.181","conference":{"location":"Torino, Italy","start_date":"203-09-02","end_date":"2013-09-05","name":"CSL: Computer Science Logic"},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Nathanaël","full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow"}],"publication":"22nd EACSL Annual Conference on Computer Science Logic","title":"Infinite-state games with finitary conditions","page":"181 - 196"},{"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas"}],"publication":"13th International Conference on Formal Methods in Computer-Aided Design","conference":{"location":"Portland, OR, United States","name":"FMCAD: Formal Methods in Computer-Aided Design","end_date":"2013-10-23","start_date":"2013-10-20"},"fulldoi":"https://doi.org/10.1109/FMCAD.2013.6679386","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"title":"Distributed synthesis for LTL fragments","page":"18 - 25","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5406"}]},"ec_funded":1,"scopus_import":"1","date_updated":"2025-06-26T08:33:43Z","doi":"10.1109/FMCAD.2013.6679386","publisher":"IEEE","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25, doi:10.1109/FMCAD.2013.6679386.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In 13th International Conference on Formal Methods in Computer-Aided Design (pp. 18–25). Portland, OR, United States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679386","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In 13th International Conference on Formal Methods in Computer-Aided Design, 18–25. IEEE, 2013. https://doi.org/10.1109/FMCAD.2013.6679386.","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.","ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: 13th International Conference on Formal Methods in Computer-Aided Design. IEEE; 2013:18-25. doi:10.1109/FMCAD.2013.6679386","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in 13th International Conference on Formal Methods in Computer-Aided Design, Portland, OR, United States, 2013, pp. 18–25."},"year":"2013","OA_place":"repository","oa":1,"corr_author":"1","quality_controlled":"1","_id":"1376","day":"11","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:40Z","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15479/AT:IST-2013-130-v1-1"}],"OA_type":"green","status":"public","abstract":[{"text":"We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.","lang":"eng"}],"publication_status":"published","date_published":"2013-12-11T00:00:00Z","article_processing_charge":"No","oa_version":"Preprint","publist_id":"5835","language":[{"iso":"eng"}]},{"oa":1,"corr_author":"1","supervisor":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","_id":"1405","day":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:51:50Z","month":"09","main_file_link":[{"url":"http://dzufferey.github.io/files/2013_thesis.pdf"}],"date_published":"2013-09-05T00:00:00Z","status":"public","has_accepted_license":"1","abstract":[{"text":"Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"publist_id":"5802","author":[{"orcid":"0000-0002-3197-8736","first_name":"Damien","full_name":"Zufferey, Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.15479/at:ista:1405","file":[{"file_size":1514906,"file_name":"2013_Zufferey_thesis_final.pdf","date_created":"2021-02-22T11:28:36Z","success":1,"checksum":"ed2d7b52933d134e8dc69d569baa284e","file_id":"9176","date_updated":"2021-02-22T11:28:36Z","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access"},{"checksum":"cecc4c4b14225bee973d32e3dba91a55","content_type":"application/pdf","file_id":"10298","creator":"cchlebak","date_updated":"2021-11-17T13:47:58Z","relation":"main_file","access_level":"closed","file_size":1378313,"date_created":"2021-11-16T14:42:52Z","file_name":"2013_Zufferey_thesis_final_pdfa.pdf"}],"page":"134","title":"Analysis of dynamic message passing programs","related_material":{"record":[{"status":"public","id":"4361","relation":"part_of_dissertation"},{"status":"public","id":"3251","relation":"part_of_dissertation"},{"id":"2847","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"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 Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. ","ddc":["000"],"file_date_updated":"2021-11-17T13:47:58Z","ec_funded":1,"doi":"10.15479/at:ista:1405","date_updated":"2026-04-09T14:35:24Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","citation":{"short":"D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013.","apa":"Zufferey, D. (2013). Analysis of dynamic message passing programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1405","mla":"Zufferey, Damien. Analysis of Dynamic Message Passing Programs. Institute of Science and Technology Austria, 2013, doi:10.15479/at:ista:1405.","ieee":"D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013.","ista":"Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria.","ama":"Zufferey D. Analysis of dynamic message passing programs. 2013. doi:10.15479/at:ista:1405","chicago":"Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. https://doi.org/10.15479/at:ista:1405."},"year":"2013","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"OA_place":"publisher"},{"date_updated":"2025-09-30T07:30:04Z","doi":"10.3389/fnbeh.2013.00217","external_id":{"isi":["000329175600001"]},"department":[{"_id":"JoCs"}],"citation":{"short":"D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).","apa":"Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217","mla":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research Foundation, 2013, doi:10.3389/fnbeh.2013.00217.","ama":"Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217","ista":"Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 7(DEC).","chicago":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.","ieee":"D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research Foundation, 2013."},"year":"2013","volume":7,"publisher":"Frontiers Research Foundation","title":"Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions","file":[{"file_size":530134,"date_created":"2018-12-12T10:15:10Z","file_name":"IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf","content_type":"application/pdf","relation":"main_file","creator":"system","file_id":"5128","date_updated":"2020-07-14T12:46:35Z","checksum":"cd7183121e56251176100ccac165c95c","access_level":"open_access"}],"fulldoi":"https://doi.org/10.3389/fnbeh.2013.00217","author":[{"last_name":"Dickerson","id":"444EB89E-F248-11E8-B48F-1D18A9856A87","first_name":"Desiree","full_name":"Dickerson, Desiree"},{"last_name":"Bilkey","first_name":"David","full_name":"Bilkey, David"}],"publication":"Frontiers in Behavioral Neuroscience","file_date_updated":"2020-07-14T12:46:35Z","issue":"DEC","ddc":["571"],"pubrep_id":"953","oa_version":"Published Version","article_processing_charge":"No","isi":1,"publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. "}],"has_accepted_license":"1","date_published":"2013-12-27T00:00:00Z","publist_id":"7346","language":[{"iso":"eng"}],"_id":"476","day":"27","type":"journal_article","quality_controlled":"1","oa":1,"tmp":{"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)","image":"/images/cc_by.png"},"month":"12","intvolume":" 7","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:41Z"},{"status":"public","abstract":[{"text":"Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing "persisters." Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure.","lang":"eng"}],"publication_status":"published","date_published":"2013-01-04T00:00:00Z","article_processing_charge":"No","isi":1,"oa_version":"None","publist_id":"7321","language":[{"iso":"eng"}],"quality_controlled":"1","_id":"499","day":"04","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:48Z","month":"01","intvolume":" 339","scopus_import":"1","date_updated":"2025-09-30T07:29:30Z","doi":"10.1126/science.1229858","external_id":{"isi":["000312985800059"]},"publisher":"American Association for the Advancement of Science","volume":339,"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2013","citation":{"short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","apa":"Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858","mla":"Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:10.1126/science.1229858.","ista":"Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.","ama":"Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858","chicago":"Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1229858.","ieee":"Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,” Science, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013."},"publication":"Science","author":[{"last_name":"Wakamoto","first_name":"Yurichi","full_name":"Wakamoto, Yurichi"},{"full_name":"Dhar, Neraaj","first_name":"Neraaj","last_name":"Dhar"},{"full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katrin","full_name":"Schneider, Katrin","last_name":"Schneider"},{"first_name":"François","full_name":"Signorino Gelo, François","last_name":"Signorino Gelo"},{"last_name":"Leibler","full_name":"Leibler, Stanislas","first_name":"Stanislas"},{"first_name":"John","full_name":"Mckinney, John","last_name":"Mckinney"}],"fulldoi":"https://doi.org/10.1126/science.1229858","title":"Dynamic persistence of antibiotic-stressed mycobacteria","page":"91 - 95","issue":"6115"},{"author":[{"last_name":"Ward","full_name":"Ward, Melissa","first_name":"Melissa"},{"first_name":"Samantha","full_name":"Lycett, Samantha","last_name":"Lycett"},{"last_name":"Avila","first_name":"Dorita","full_name":"Avila, Dorita"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"full_name":"Leigh Brown, Andrew","first_name":"Andrew","last_name":"Leigh Brown"}],"publication":"BMC Evolutionary Biology","file":[{"file_size":1150052,"date_created":"2018-12-12T10:08:59Z","file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","checksum":"52cf48a7c1794676ae8b0029573a84a9","relation":"main_file","date_updated":"2020-07-14T12:46:36Z","file_id":"4722","creator":"system","content_type":"application/pdf","access_level":"open_access"}],"fulldoi":"https://doi.org/10.1186/1471-2148-13-222","title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","ddc":["576"],"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n","pubrep_id":"941","issue":"1","file_date_updated":"2020-07-14T12:46:36Z","scopus_import":"1","date_updated":"2025-09-30T07:28:51Z","doi":"10.1186/1471-2148-13-222","external_id":{"isi":["000326620200001"]},"publisher":"BioMed Central","volume":13,"department":[{"_id":"JoBo"}],"year":"2013","citation":{"ieee":"M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.","ista":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222.","ama":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-222","chicago":"Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222.","short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013).","apa":"Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222","mla":"Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no. 1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222."},"oa":1,"quality_controlled":"1","day":"09","_id":"500","type":"journal_article","date_created":"2018-12-11T11:46:49Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","intvolume":" 13","tmp":{"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)","image":"/images/cc_by.png"},"publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution."}],"has_accepted_license":"1","date_published":"2013-10-09T00:00:00Z","article_processing_charge":"No","isi":1,"oa_version":"Published Version","article_number":"222","publist_id":"7320","language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","_id":"501","day":"01","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:49Z","month":"12","intvolume":" 94","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"text":"All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.","lang":"eng"}],"date_published":"2013-12-01T00:00:00Z","article_processing_charge":"No","isi":1,"oa_version":"Published Version","publist_id":"7319","language":[{"iso":"eng"}],"author":[{"first_name":"Mario","full_name":"Cozzuol, Mario","last_name":"Cozzuol"},{"last_name":"Clozato","first_name":"Camila","full_name":"Clozato, Camila"},{"full_name":"Holanda, Elizete","first_name":"Elizete","last_name":"Holanda"},{"full_name":"Rodrigues, Flávio","first_name":"Flávio","last_name":"Rodrigues"},{"last_name":"Nienow","full_name":"Nienow, Samuel","first_name":"Samuel"},{"first_name":"Benoit","full_name":"De Thoisy, Benoit","last_name":"De Thoisy"},{"last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A"},{"last_name":"Santos","full_name":"Santos, Fabrício","first_name":"Fabrício"}],"publication":"Journal of Mammalogy","file":[{"checksum":"8007815078dccac21ecd1cf73a269dc6","creator":"system","date_updated":"2020-07-14T12:46:36Z","file_id":"4980","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":1040765,"file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf","date_created":"2018-12-12T10:12:59Z"}],"fulldoi":"https://doi.org/10.1644/12-MAMM-A-169.1","title":"A new species of tapir from the Amazon","page":"1331 - 1345","ddc":["570"],"pubrep_id":"940","file_date_updated":"2020-07-14T12:46:36Z","issue":"6","scopus_import":"1","doi":"10.1644/12-MAMM-A-169.1","date_updated":"2025-09-30T07:28:20Z","external_id":{"isi":["000329010200015"]},"volume":94,"publisher":"Oxford University Press","department":[{"_id":"JoBo"}],"citation":{"chicago":"Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.","ista":"Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345.","ama":"Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1","ieee":"M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.","mla":"Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:10.1644/12-MAMM-A-169.1.","short":"M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.","apa":"Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1"},"year":"2013"},{"publist_id":"7318","language":[{"iso":"eng"}],"volume":21,"publisher":"IOS Press","department":[{"_id":"KrPi"}],"citation":{"mla":"Blazy, Olivier, et al. “Short Blind Signatures.” Journal of Computer Security, vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:10.3233/JCS-130477.","apa":"Blazy, O., Fuchsbauer, G., Pointcheval, D., & Vergnaud, D. (2013). Short blind signatures. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-130477","short":"O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer Security 21 (2013) 627–661.","chicago":"Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud. “Short Blind Signatures.” Journal of Computer Security. IOS Press, 2013. https://doi.org/10.3233/JCS-130477.","ama":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. Journal of Computer Security. 2013;21(5):627-661. doi:10.3233/JCS-130477","ista":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures. Journal of Computer Security. 21(5), 627–661.","ieee":"O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,” Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013."},"year":"2013","scopus_import":1,"oa_version":"None","doi":"10.3233/JCS-130477","date_updated":"2021-01-12T08:01:09Z","publication_status":"published","abstract":[{"text":"Blind signatures allow users to obtain signatures on messages hidden from the signer; moreover, the signer cannot link the resulting message/signature pair to the signing session. This paper presents blind signature schemes, in which the number of interactions between the user and the signer is minimal and whose blind signatures are short. Our schemes are defined over bilinear groups and are proved secure in the common-reference-string model without random oracles and under standard assumptions: CDH and the decision-linear assumption. (We also give variants over asymmetric groups based on similar assumptions.) The blind signatures are Waters signatures, which consist of 2 group elements. Moreover, we instantiate partially blind signatures, where the message consists of a part hidden from the signer and a commonly known public part, and schemes achieving perfect blindness. We propose new variants of blind signatures, such as signer-friendly partially blind signatures, where the public part can be chosen by the signer without prior agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated messages provided by independent sources. We also extend Waters signatures to non-binary alphabets by proving a new result on the underlying hash function. ","lang":"eng"}],"status":"public","date_published":"2013-11-22T00:00:00Z","issue":"5","date_created":"2018-12-11T11:46:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","intvolume":" 21","title":"Short blind signatures","quality_controlled":"1","page":"627 - 661","_id":"502","day":"22","type":"journal_article","publication":"Journal of Computer Security","author":[{"last_name":"Blazy","first_name":"Olivier","full_name":"Blazy, Olivier"},{"last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Fuchsbauer, Georg"},{"last_name":"Pointcheval","first_name":"David","full_name":"Pointcheval, David"},{"last_name":"Vergnaud","first_name":"Damien","full_name":"Vergnaud, Damien"}],"fulldoi":"https://doi.org/10.3233/JCS-130477"},{"isi":1,"article_processing_charge":"No","date_published":"2013-02-01T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts."}],"oa_version":"None","language":[{"iso":"eng"}],"publist_id":"7313","_id":"505","day":"01","type":"journal_article","quality_controlled":"1","intvolume":" 15","month":"02","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:51Z","external_id":{"isi":["000314185900015"]},"date_updated":"2025-09-30T07:27:28Z","doi":"10.1039/c2gc36666e","scopus_import":"1","citation":{"ieee":"K. Greimel et al., “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.","chicago":"Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel, Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36666e.","ama":"Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 2013;15(2):381-388. doi:10.1039/c2gc36666e","ista":"Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.","mla":"Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 381–88, doi:10.1039/c2gc36666e.","apa":"Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz, G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36666e","short":"K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero, I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388."},"year":"2013","department":[{"_id":"HaJa"}],"publisher":"Royal Society of Chemistry","volume":15,"fulldoi":"https://doi.org/10.1039/c2gc36666e","author":[{"full_name":"Greimel, Katrin","first_name":"Katrin","last_name":"Greimel"},{"full_name":"Perz, Veronika","first_name":"Veronika","last_name":"Perz"},{"last_name":"Koren","id":"382FBD6A-F248-11E8-B48F-1D18A9856A87","first_name":"Klaus","full_name":"Koren, Klaus"},{"last_name":"Feola","full_name":"Feola, Roland","first_name":"Roland"},{"first_name":"Armin","full_name":"Temel, Armin","last_name":"Temel"},{"last_name":"Sohar","full_name":"Sohar, Christian","first_name":"Christian"},{"last_name":"Herrero Acero","full_name":"Herrero Acero, Enrique","first_name":"Enrique"},{"first_name":"Ingo","full_name":"Klimant, Ingo","last_name":"Klimant"},{"last_name":"Guebitz","first_name":"Georg","full_name":"Guebitz, Georg"}],"publication":"Green Chemistry","page":"381 - 388","title":"Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins","issue":"2","acknowledgement":"This study was performed within the Austrian Centre of Indus-\r\ntrial Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology Agency of the City of Vienna through the\r\nCOMET-Funding Program managed by the Austrian Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with the CLSM measurements."},{"oa_version":"Submitted Version","status":"public","abstract":[{"lang":"eng","text":"Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs."}],"publication_status":"published","date_published":"2013-08-01T00:00:00Z","article_processing_charge":"No","isi":1,"publist_id":"7312","language":[{"iso":"eng"}],"quality_controlled":"1","_id":"507","day":"01","type":"journal_article","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:52Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/","open_access":"1"}],"month":"08","intvolume":" 25","scopus_import":"1","doi":"10.1105/tpc.113.114264","date_updated":"2025-09-30T07:17:15Z","pmid":1,"external_id":{"pmid":["23975898"],"isi":["000324920500019"]},"volume":25,"publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"year":"2013","citation":{"chicago":"Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114264.","ista":"Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.","ama":"Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 2013;25(8):2970-2985. doi:10.1105/tpc.113.114264","ieee":"S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.","mla":"Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” Plant Cell, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:10.1105/tpc.113.114264.","short":"S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.","apa":"Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114264"},"title":"Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis","page":"2970 - 2985","publication":"Plant Cell","author":[{"first_name":"Soo","full_name":"Kim, Soo","last_name":"Kim"},{"full_name":"Xu, Zheng","first_name":"Zheng","last_name":"Xu"},{"last_name":"Song","first_name":"Kyungyoung","full_name":"Song, Kyungyoung"},{"first_name":"Dae","full_name":"Kim, Dae","last_name":"Kim"},{"first_name":"Hyangju","full_name":"Kang, Hyangju","last_name":"Kang"},{"full_name":"Reichardt, Ilka","first_name":"Ilka","last_name":"Reichardt"},{"full_name":"Sohn, Eun","first_name":"Eun","last_name":"Sohn"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Juergens, Gerd","first_name":"Gerd","last_name":"Juergens"},{"full_name":"Hwang, Inhwan","first_name":"Inhwan","last_name":"Hwang"}],"fulldoi":"https://doi.org/10.1105/tpc.113.114264","issue":"8"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/","open_access":"1"}],"month":"09","intvolume":" 30","date_created":"2018-12-11T11:46:52Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"508","type":"journal_article","day":"01","quality_controlled":"1","oa":1,"publist_id":"7310","language":[{"iso":"eng"}],"oa_version":"Submitted Version","article_processing_charge":"No","isi":1,"abstract":[{"lang":"eng","text":"The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases."}],"status":"public","publication_status":"published","date_published":"2013-09-01T00:00:00Z","issue":"9","title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","page":"2157 - 2167","fulldoi":"https://doi.org/10.1093/molbev/mst119","author":[{"last_name":"Tarazona Santos","first_name":"Eduardo","full_name":"Tarazona Santos, Eduardo"},{"full_name":"Machado, Moara","first_name":"Moara","last_name":"Machado"},{"last_name":"Magalhães","first_name":"Wagner","full_name":"Magalhães, Wagner"},{"first_name":"Renee","full_name":"Chen, Renee","last_name":"Chen"},{"full_name":"Lyon, Fernanda","first_name":"Fernanda","last_name":"Lyon"},{"first_name":"Laurie","full_name":"Burdett, Laurie","last_name":"Burdett"},{"first_name":"Andrew","full_name":"Crenshaw, Andrew","last_name":"Crenshaw"},{"full_name":"Fabbri, Cristina","first_name":"Cristina","last_name":"Fabbri"},{"first_name":"Latife","full_name":"Pereira, Latife","last_name":"Pereira"},{"full_name":"Pinto, Laelia","first_name":"Laelia","last_name":"Pinto"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A"},{"first_name":"Ben","full_name":"Sestanovich, Ben","last_name":"Sestanovich"},{"first_name":"Meredith","full_name":"Yeager, Meredith","last_name":"Yeager"},{"first_name":"Stephen","full_name":"Chanock, Stephen","last_name":"Chanock"}],"publication":"Molecular Biology and Evolution","department":[{"_id":"JoBo"}],"year":"2013","citation":{"ieee":"E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.","chicago":"Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.","ama":"Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119","ista":"Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.","mla":"Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:10.1093/molbev/mst119.","short":"E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.","apa":"Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119"},"volume":30,"publisher":"Oxford University Press","date_updated":"2025-09-30T07:13:08Z","doi":"10.1093/molbev/mst119","external_id":{"pmid":["23821607"],"isi":["000323616600014"]},"pmid":1,"scopus_import":"1"},{"oa":1,"quality_controlled":"1","type":"journal_article","_id":"509","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:52Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/"}],"month":"08","intvolume":" 25","abstract":[{"text":"Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. ","lang":"eng"}],"status":"public","publication_status":"published","date_published":"2013-08-01T00:00:00Z","article_processing_charge":"No","isi":1,"oa_version":"Submitted Version","publist_id":"7311","language":[{"iso":"eng"}],"publication":"Plant Cell","author":[{"full_name":"Di Rubbo, Simone","first_name":"Simone","last_name":"Di Rubbo"},{"last_name":"Irani","first_name":"Niloufer","full_name":"Irani, Niloufer"},{"full_name":"Kim, Soo","first_name":"Soo","last_name":"Kim"},{"full_name":"Xu, Zheng","first_name":"Zheng","last_name":"Xu"},{"full_name":"Gadeyne, Astrid","first_name":"Astrid","last_name":"Gadeyne"},{"last_name":"Dejonghe","full_name":"Dejonghe, Wim","first_name":"Wim"},{"full_name":"Vanhoutte, Isabelle","first_name":"Isabelle","last_name":"Vanhoutte"},{"last_name":"Persiau","full_name":"Persiau, Geert","first_name":"Geert"},{"last_name":"Eeckhout","full_name":"Eeckhout, Dominique","first_name":"Dominique"},{"orcid":"0000-0002-1998-6741","first_name":"Sibu","full_name":"Simon, Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kyungyoung","full_name":"Song, Kyungyoung","last_name":"Song"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Jaeger, Geert","first_name":"Geert","last_name":"De Jaeger"},{"first_name":"Daniël","full_name":"Van Damme, Daniël","last_name":"Van Damme"},{"full_name":"Hwang, Inhwan","first_name":"Inhwan","last_name":"Hwang"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"fulldoi":"https://doi.org/10.1105/tpc.113.114058","title":"The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis","page":"2986 - 2997","issue":"8","scopus_import":"1","doi":"10.1105/tpc.113.114058","date_updated":"2025-09-30T07:15:45Z","external_id":{"isi":["000324920500020"],"pmid":["23975899"]},"pmid":1,"publisher":"American Society of Plant Biologists","volume":25,"department":[{"_id":"JiFr"}],"citation":{"mla":"Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:10.1105/tpc.113.114058.","short":"S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte, G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger, D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997.","apa":"Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova, E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114058","ieee":"S. Di Rubbo et al., “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013.","chicago":"Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114058.","ista":"Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.","ama":"Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 2013;25(8):2986-2997. doi:10.1105/tpc.113.114058"},"year":"2013"},{"publist_id":"7309","language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","abstract":[{"text":"The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.","lang":"eng"}],"publication_status":"published","date_published":"2013-10-01T00:00:00Z","article_processing_charge":"No","isi":1,"date_created":"2018-12-11T11:46:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"www.doi.org/10.1105/tpc.113.114421","open_access":"1"}],"month":"10","intvolume":" 25","quality_controlled":"1","_id":"511","day":"01","type":"journal_article","oa":1,"volume":25,"publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"citation":{"chicago":"Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon, Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114421.","ama":"Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 2013;25(10):3858-3870. doi:10.1105/tpc.113.114421","ista":"Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10), 3858–3870.","ieee":"A. Pěnčík et al., “Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid,” Plant Cell, vol. 25, no. 10. American Society of Plant Biologists, pp. 3858–3870, 2013.","mla":"Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” Plant Cell, vol. 25, no. 10, American Society of Plant Biologists, 2013, pp. 3858–70, doi:10.1105/tpc.113.114421.","apa":"Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham, K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114421","short":"A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham, Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung, Plant Cell 25 (2013) 3858–3870."},"year":"2013","scopus_import":"1","doi":"10.1105/tpc.113.114421","date_updated":"2026-06-18T18:52:18Z","pmid":1,"external_id":{"isi":["000327723100019"],"pmid":["24163311"]},"ddc":["580"],"issue":"10","title":"Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid","page":"3858 - 3870","publication":"Plant Cell","author":[{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"last_name":"Simonovik","full_name":"Simonovik, Biljana","first_name":"Biljana"},{"last_name":"Petersson","first_name":"Sara","full_name":"Petersson, Sara"},{"full_name":"Henyková, Eva","first_name":"Eva","last_name":"Henyková"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Greenham","first_name":"Kathleen","full_name":"Greenham, Kathleen"},{"last_name":"Zhang","full_name":"Zhang, Yi","first_name":"Yi"},{"full_name":"Kowalczyk, Mariusz","first_name":"Mariusz","last_name":"Kowalczyk"},{"last_name":"Estelle","first_name":"Mark","full_name":"Estelle, Mark"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"first_name":"Göran","full_name":"Sandberg, Göran","last_name":"Sandberg"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"}],"fulldoi":"https://doi.org/10.1105/tpc.113.114421"},{"pubrep_id":"936","ddc":["581"],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:46:36Z","issue":"1","title":"A map of cell type‐specific auxin responses","author":[{"first_name":"Bastiaan","full_name":"Bargmann, Bastiaan","last_name":"Bargmann"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Gabriel","full_name":"Krouk, Gabriel","last_name":"Krouk"},{"last_name":"Nawy","first_name":"Tal","full_name":"Nawy, Tal"},{"last_name":"Efroni","first_name":"Idan","full_name":"Efroni, Idan"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"},{"last_name":"Choe","first_name":"Goh","full_name":"Choe, Goh"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Bergmann","full_name":"Bergmann, Dominique","first_name":"Dominique"},{"full_name":"Estelle, Mark","first_name":"Mark","last_name":"Estelle"},{"full_name":"Birnbaum, Kenneth","first_name":"Kenneth","last_name":"Birnbaum"}],"publication":"Molecular Systems Biology","fulldoi":"https://doi.org/10.1038/msb.2013.40","file":[{"file_id":"4644","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:46:36Z","content_type":"application/pdf","checksum":"9c4fbe793af4bb22b3fe50cc677a39bf","access_level":"open_access","file_size":3257692,"date_created":"2018-12-12T10:07:46Z","file_name":"IST-2018-936-v1+1_2008_Barton_A_map.pdf"}],"publisher":"Nature Publishing Group","volume":9,"year":"2013","citation":{"mla":"Bargmann, Bastiaan, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular Systems Biology, vol. 9, no. 1, 688, Nature Publishing Group, 2013, doi:10.1038/msb.2013.40.","apa":"Bargmann, B., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., … Birnbaum, K. (2013). A map of cell type‐specific auxin responses. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2013.40","short":"B. Bargmann, S. Vanneste, G. Krouk, T. Nawy, I. Efroni, E. Shani, G. Choe, J. Friml, D. Bergmann, M. Estelle, K. Birnbaum, Molecular Systems Biology 9 (2013).","ieee":"B. Bargmann et al., “A map of cell type‐specific auxin responses,” Molecular Systems Biology, vol. 9, no. 1. Nature Publishing Group, 2013.","chicago":"Bargmann, Bastiaan, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.40.","ista":"Bargmann B, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann D, Estelle M, Birnbaum K. 2013. A map of cell type‐specific auxin responses. Molecular Systems Biology. 9(1), 688.","ama":"Bargmann B, Vanneste S, Krouk G, et al. A map of cell type‐specific auxin responses. Molecular Systems Biology. 2013;9(1). doi:10.1038/msb.2013.40"},"department":[{"_id":"JiFr"}],"scopus_import":"1","external_id":{"isi":["000325297700001"]},"doi":"10.1038/msb.2013.40","date_updated":"2025-09-30T07:11:42Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:55Z","intvolume":" 9","month":"09","quality_controlled":"1","type":"journal_article","_id":"516","day":"10","oa":1,"article_number":"688","language":[{"iso":"eng"}],"publist_id":"7303","oa_version":"Published Version","date_published":"2013-09-10T00:00:00Z","abstract":[{"lang":"eng","text":"In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development."}],"status":"public","publication_status":"published","has_accepted_license":"1","isi":1,"article_processing_charge":"No"},{"fulldoi":"https://doi.org/10.1016/j.imlet.2013.07.007","publication":"Immunology Letters","author":[{"last_name":"Fuertbauer","full_name":"Fuertbauer, Elke","first_name":"Elke"},{"last_name":"Zaujec","full_name":"Zaujec, Jan","first_name":"Jan"},{"last_name":"Uhrin","full_name":"Uhrin, Pavel","first_name":"Pavel"},{"first_name":"Ingrid","full_name":"Raab, Ingrid","last_name":"Raab"},{"full_name":"Weber, Michele","first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber"},{"last_name":"Schachner","first_name":"Helga","full_name":"Schachner, Helga"},{"first_name":"Miroslav","full_name":"Bauer, Miroslav","last_name":"Bauer"},{"last_name":"Schütz","full_name":"Schütz, Gerhard","first_name":"Gerhard"},{"full_name":"Binder, Bernd","first_name":"Bernd","last_name":"Binder"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"},{"full_name":"Stockinger, Hannes","first_name":"Hannes","last_name":"Stockinger"}],"title":"Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells","page":"31 - 41","issue":"1-2","date_updated":"2025-09-30T07:11:09Z","doi":"10.1016/j.imlet.2013.07.007","external_id":{"isi":["000326559400006"]},"scopus_import":"1","department":[{"_id":"MiSi"}],"year":"2013","citation":{"mla":"Fuertbauer, Elke, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” Immunology Letters, vol. 154, no. 1–2, Elsevier, 2013, pp. 31–41, doi:10.1016/j.imlet.2013.07.007.","short":"E. Fuertbauer, J. Zaujec, P. Uhrin, I. Raab, M. Weber, H. Schachner, M. Bauer, G. Schütz, B. Binder, M.K. Sixt, D. Kerjaschki, H. Stockinger, Immunology Letters 154 (2013) 31–41.","apa":"Fuertbauer, E., Zaujec, J., Uhrin, P., Raab, I., Weber, M., Schachner, H., … Stockinger, H. (2013). Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. Elsevier. https://doi.org/10.1016/j.imlet.2013.07.007","chicago":"Fuertbauer, Elke, Jan Zaujec, Pavel Uhrin, Ingrid Raab, Michele Weber, Helga Schachner, Miroslav Bauer, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” Immunology Letters. Elsevier, 2013. https://doi.org/10.1016/j.imlet.2013.07.007.","ista":"Fuertbauer E, Zaujec J, Uhrin P, Raab I, Weber M, Schachner H, Bauer M, Schütz G, Binder B, Sixt MK, Kerjaschki D, Stockinger H. 2013. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 154(1–2), 31–41.","ama":"Fuertbauer E, Zaujec J, Uhrin P, et al. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 2013;154(1-2):31-41. doi:10.1016/j.imlet.2013.07.007","ieee":"E. Fuertbauer et al., “Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells,” Immunology Letters, vol. 154, no. 1–2. Elsevier, pp. 31–41, 2013."},"volume":154,"publisher":"Elsevier","day":"01","_id":"522","type":"journal_article","quality_controlled":"1","month":"07","intvolume":" 154","date_created":"2018-12-11T11:46:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","isi":1,"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic endothelial cells and responsible for separation of blood and lymphatic circulation through activation of platelets. Here we show that podoplanin is also expressed by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell type associated with thymic conduits, and involved in development of natural regulatory T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes in the medulla. This might be due to CCL21 that delocalizes upon deletion of the CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not remain devoid of nTreg but generate them delayed within the first month resulting in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype of Foxp3-deficient Scurfy mice."}],"date_published":"2013-07-01T00:00:00Z","oa_version":"None","publist_id":"7300","language":[{"iso":"eng"}]},{"ec_funded":1,"date_updated":"2025-09-30T07:10:38Z","doi":"10.1016/j.cub.2013.10.038","external_id":{"isi":["000328918900032"]},"scopus_import":"1","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"citation":{"ieee":"K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the establishment of the apical-basal embryonic axis in plants,” Current Biology, vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013.","ista":"Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518.","ama":"Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 2013;23(24):2513-2518. doi:10.1016/j.cub.2013.10.038","chicago":"Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.10.038.","apa":"Wabnik, K. T., Robert, H., Smith, R., & Friml, J. (2013). Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.10.038","short":"K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518.","mla":"Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” Current Biology, vol. 23, no. 24, Cell Press, 2013, pp. 2513–18, doi:10.1016/j.cub.2013.10.038."},"year":"2013","volume":23,"publisher":"Cell Press","fulldoi":"https://doi.org/10.1016/j.cub.2013.10.038","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"author":[{"first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hélène","full_name":"Robert, Hélène","last_name":"Robert"},{"last_name":"Smith","full_name":"Smith, Richard","first_name":"Richard"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"Current Biology","title":"Modeling framework for the establishment of the apical-basal embryonic axis in plants","page":"2513 - 2518","issue":"24","article_processing_charge":"No","isi":1,"status":"public","publication_status":"published","abstract":[{"text":"The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development.","lang":"eng"}],"date_published":"2013-12-16T00:00:00Z","oa_version":"None","publist_id":"7292","language":[{"iso":"eng"}],"_id":"527","type":"journal_article","day":"16","corr_author":"1","quality_controlled":"1","month":"12","intvolume":" 23","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:58Z"}]