[{"project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","name":"Design for Embedded Systems"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. Randomness for Free. Vol. 6281, Springer, 2010, pp. 246–57, doi:10.1007/978-3-642-15155-2_23.","short":"K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, in:, Springer, 2010, pp. 246–257.","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and T. A. Henzinger, “Randomness for free,” presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic, 2010, vol. 6281, pp. 246–257.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., & Henzinger, T. A. (2010). Randomness for free (Vol. 6281, pp. 246–257). Presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-15155-2_23","ama":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. Randomness for free. In: Vol 6281. Springer; 2010:246-257. doi:10.1007/978-3-642-15155-2_23","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Thomas A Henzinger. “Randomness for Free,” 6281:246–57. Springer, 2010. https://doi.org/10.1007/978-3-642-15155-2_23.","ista":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2010. Randomness for free. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6281, 246–257."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2325","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Gimbert","full_name":"Gimbert, Hugo","first_name":"Hugo"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"title":"Randomness for free","acknowledgement":"This research was supported by the European Union project COMBEST and the European Network of Excellence ArtistDesign.","publisher":"Springer","quality_controlled":"1","oa":1,"year":"2010","day":"06","page":"246 - 257","date_published":"2010-09-06T00:00:00Z","doi":"10.1007/978-3-642-15155-2_23","date_created":"2018-12-11T12:05:32Z","_id":"3856","type":"conference","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2010-08-23","end_date":"2010-08-27","location":"Brno, Czech Republic"},"status":"public","pubrep_id":"60","date_updated":"2023-02-23T10:12:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"text":"We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (players interact simultaneously); and (b) turn-based (players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. We present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function (probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. ","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1006.0673v1","open_access":"1"}],"month":"09","intvolume":" 6281","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"1731","status":"public"}]},"volume":6281,"ec_funded":1},{"year":"2010","publication_status":"published","language":[{"iso":"eng"}],"day":"20","date_created":"2018-12-11T12:05:33Z","volume":6246,"related_material":{"link":[{"description":"eBook available via IST BookList","relation":"other","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=12721"}]},"doi":"10.1007/978-3-642-15297-9","date_published":"2010-09-20T00:00:00Z","abstract":[{"lang":"eng","text":"This book constitutes the proceedings of the 8th International Conference on Formal Modeling and Analysis of Timed Systems, FORMATS 2010, held in Klosterneuburg, Austria in September 2010. The 14 papers presented were carefully reviewed and selected from 31 submissions. In addition, the volume contains 3 invited talks and 2 invited tutorials.The aim of FORMATS is to promote the study of fundamental and practical aspects of timed systems, and to bring together researchers from different disciplines that share an interest in the modeling and analysis of timed systems. Typical topics include foundations and semantics, methods and tools, and applications."}],"oa_version":"None","alternative_title":["LNCS"],"quality_controlled":"1","publisher":"Springer","intvolume":" 6246","month":"09","citation":{"chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger, eds. Formal Modeling and Analysis of Timed Systems. Vol. 6246. Springer, 2010. https://doi.org/10.1007/978-3-642-15297-9.","ista":"Chatterjee K, Henzinger TA eds. 2010. Formal modeling and analysis of timed systems, Springer,p.","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger, editors. Formal Modeling and Analysis of Timed Systems. Vol. 6246, Springer, 2010, doi:10.1007/978-3-642-15297-9.","ama":"Chatterjee K, Henzinger TA, eds. Formal Modeling and Analysis of Timed Systems. Vol 6246. Springer; 2010. doi:10.1007/978-3-642-15297-9","apa":"Chatterjee, K., & Henzinger, T. A. (Eds.). (2010). Formal modeling and analysis of timed systems (Vol. 6246). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-15297-9","short":"K. Chatterjee, T.A. Henzinger, eds., Formal Modeling and Analysis of Timed Systems, Springer, 2010.","ieee":"K. Chatterjee and T. A. Henzinger, Eds., Formal modeling and analysis of timed systems, vol. 6246. Springer, 2010."},"date_updated":"2019-11-14T08:42:42Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"2322","editor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Formal modeling and analysis of timed systems","_id":"3859","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2010-09-08","location":"Klosterneuburg, Austria","end_date":"2010-09-10"},"type":"conference_editor","status":"public"},{"author":[{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Karin","last_name":"Greimel","full_name":"Greimel, Karin"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"publist_id":"2310","editor":[{"first_name":"Tayssir","full_name":"Touili, Tayssir","last_name":"Touili"},{"first_name":"Byron","full_name":"Cook, Byron","last_name":"Cook"},{"full_name":"Jackson, Paul","last_name":"Jackson","first_name":"Paul"}],"title":"Robustness in the presence of liveness","citation":{"short":"R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, T. Touili, B. Cook, P. Jackson (Eds.), Springer, 2010, pp. 410–424.","ieee":"R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Robustness in the presence of liveness,” presented at the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 410–424.","ama":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Robustness in the presence of liveness. In: Touili T, Cook B, Jackson P, eds. Vol 6174. Springer; 2010:410-424. doi:10.1007/978-3-642-14295-6_36","apa":"Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann, B. (2010). Robustness in the presence of liveness. In T. Touili, B. Cook, & P. Jackson (Eds.) (Vol. 6174, pp. 410–424). Presented at the CAV: Computer Aided Verification, Edinburgh, UK: Springer. https://doi.org/10.1007/978-3-642-14295-6_36","mla":"Bloem, Roderick, et al. Robustness in the Presence of Liveness. Edited by Tayssir Touili et al., vol. 6174, Springer, 2010, pp. 410–24, doi:10.1007/978-3-642-14295-6_36.","ista":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2010. Robustness in the presence of liveness. CAV: Computer Aided Verification, LNCS, vol. 6174, 410–424.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Robustness in the Presence of Liveness.” edited by Tayssir Touili, Byron Cook, and Paul Jackson, 6174:410–24. Springer, 2010. https://doi.org/10.1007/978-3-642-14295-6_36."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"410 - 424","date_published":"2010-07-01T00:00:00Z","doi":"10.1007/978-3-642-14295-6_36","date_created":"2018-12-11T12:05:36Z","has_accepted_license":"1","year":"2010","day":"01","publisher":"Springer","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:46:19Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T07:52:47Z","ddc":["004"],"type":"conference","conference":{"start_date":"2010-07-15","location":"Edinburgh, UK","end_date":"2010-07-19","name":"CAV: Computer Aided Verification"},"status":"public","pubrep_id":"54","_id":"3866","volume":6174,"ec_funded":1,"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9d204611c8d7855bed8134f8708a0010","file_id":"5243","creator":"system","date_updated":"2020-07-14T12:46:19Z","file_size":213083,"date_created":"2018-12-12T10:16:52Z","file_name":"IST-2012-54-v1+1_Robustness_in_the_presence_of_liveness.pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["LNCS"],"month":"07","intvolume":" 6174","abstract":[{"lang":"eng","text":"Systems ought to behave reasonably even in circumstances that are not anticipated in their specifications. We propose a definition of robustness for liveness specifications which prescribes, for any number of environment assumptions that are violated, a minimal number of system guarantees that must still be fulfilled. This notion of robustness can be formulated and realized using a Generalized Reactivity formula. We present an algorithm for synthesizing robust systems from such formulas. For the important special case of Generalized Reactivity formulas of rank 1, our algorithm improves the complexity of [PPS06] for large specifications with a small number of assumptions and guarantees."}],"oa_version":"Submitted Version"},{"_id":"3868","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"status":"public","pubrep_id":"370","date_updated":"2023-02-23T11:30:18Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:19Z","abstract":[{"text":"Simulation and bisimulation metrics for stochastic systems provide a quantitative generalization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative mu-calculus and related probabilistic logics. We first show that the metrics provide a bound for the difference in long-run average and discounted average behavior across states, indicating that the metrics can be used both in system verification, and in performance evaluation. For turn-based games and MDPs, we provide a polynomial-time algorithm for the computation of the one-step metric distance between states. The algorithm is based on linear programming; it improves on the previous known exponential-time algorithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known algorithms for Markov chains. For the bisimulation kernel of the metric our algorithm works in time O(n(4)) for both turn-based games and MDPs; improving the previously best known O(n(9).log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance be tween states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be done via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(vertical bar G vertical bar(O(vertical bar G vertical bar 5))) time complexity, improving the previously known reduction, which yielded O(vertical bar G vertical bar(O(vertical bar G vertical bar 7))) time complexity. These algorithms can be iterated to approximate the metrics using binary search","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"09","intvolume":" 6","publication_status":"published","file":[{"file_name":"IST-2015-370-v1+1_0809.4326.pdf","date_created":"2018-12-12T10:08:11Z","file_size":346527,"date_updated":"2020-07-14T12:46:19Z","creator":"system","checksum":"a18988135fef3016c93808ecb15b55f5","file_id":"4671","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"3","related_material":{"record":[{"status":"public","id":"3504","relation":"earlier_version"}]},"volume":6,"citation":{"ista":"Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2010. Algorithms for game metrics. Logical Methods in Computer Science. 6(3), 1–27.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath Raman. “Algorithms for Game Metrics.” Logical Methods in Computer Science. International Federation of Computational Logic, 2010. https://doi.org/10.2168/LMCS-6(3:13)2010.","apa":"Chatterjee, K., De Alfaro, L., Majumdar, R., & Raman, V. (2010). Algorithms for game metrics. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-6(3:13)2010","ama":"Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics. Logical Methods in Computer Science. 2010;6(3):1-27. doi:10.2168/LMCS-6(3:13)2010","ieee":"K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game metrics,” Logical Methods in Computer Science, vol. 6, no. 3. International Federation of Computational Logic, pp. 1–27, 2010.","short":"K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, Logical Methods in Computer Science 6 (2010) 1–27.","mla":"Chatterjee, Krishnendu, et al. “Algorithms for Game Metrics.” Logical Methods in Computer Science, vol. 6, no. 3, International Federation of Computational Logic, 2010, pp. 1–27, doi:10.2168/LMCS-6(3:13)2010."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Luca","full_name":"De Alfaro, Luca","last_name":"De Alfaro"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar","last_name":"Majumdar"},{"first_name":"Vishwanath","last_name":"Raman","full_name":"Raman, Vishwanath"}],"publist_id":"2312","title":"Algorithms for game metrics","publisher":"International Federation of Computational Logic","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2010","day":"01","publication":"Logical Methods in Computer Science","page":"1 - 27","date_published":"2010-09-01T00:00:00Z","doi":"10.2168/LMCS-6(3:13)2010","date_created":"2018-12-11T12:05:36Z"},{"_id":"3899","type":"book","status":"public","date_updated":"2021-12-21T12:26:50Z","citation":{"ieee":"H. Edelsbrunner and J. Harer, Computational Topology: An Introduction, vol. 69. American Mathematical Society, 2010.","short":"H. Edelsbrunner, J. Harer, Computational Topology: An Introduction, American Mathematical Society, 2010.","ama":"Edelsbrunner H, Harer J. Computational Topology: An Introduction. Vol 69. American Mathematical Society; 2010. doi:10.1090/mbk/069","apa":"Edelsbrunner, H., & Harer, J. (2010). Computational Topology: An Introduction (Vol. 69). American Mathematical Society. https://doi.org/10.1090/mbk/069","mla":"Edelsbrunner, Herbert, and John Harer. Computational Topology: An Introduction. Vol. 69, American Mathematical Society, 2010, doi:10.1090/mbk/069.","ista":"Edelsbrunner H, Harer J. 2010. Computational Topology: An Introduction, American Mathematical Society, XII, 241p.","chicago":"Edelsbrunner, Herbert, and John Harer. Computational Topology: An Introduction. Vol. 69. American Mathematical Society, 2010. https://doi.org/10.1090/mbk/069."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","article_processing_charge":"No","publist_id":"2258","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Harer","full_name":"Harer, John","first_name":"John"}],"title":"Computational Topology: An Introduction","abstract":[{"lang":"eng","text":"Combining concepts from topology and algorithms, this book delivers what its title promises: an introduction to the field of computational topology. Starting with motivating problems in both mathematics and computer science and building up from classic topics in geometric and algebraic topology, the third part of the text advances to persistent homology. This point of view is critically important in turning a mostly theoretical field of mathematics into one that is relevant to a multitude of disciplines in the sciences and engineering. The main approach is the discovery of topology through algorithms. The book is ideal for teaching a graduate or advanced undergraduate course in computational topology, as it develops all the background of both the mathematical and algorithmic aspects of the subject from first principles. Thus the text could serve equally well in a course taught in a mathematics department or computer science department."}],"oa_version":"None","main_file_link":[{"url":"https://www.ams.org/books/mbk/069/"}],"quality_controlled":"1","publisher":"American Mathematical Society","intvolume":" 69","month":"01","publication_status":"published","year":"2010","publication_identifier":{"eisbn":["978-1-4704-1208-1"],"isbn":["978-0-8218-4925-5"]},"language":[{"iso":"eng"}],"day":"15","page":"XII, 241","date_created":"2018-12-11T12:05:46Z","related_material":{"link":[{"description":"available via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=3289","relation":"other"}]},"doi":"10.1090/mbk/069","date_published":"2010-01-15T00:00:00Z","volume":69},{"oa_version":"None","abstract":[{"lang":"eng","text":"Almost all species of the orchid genus Ophrys are pollinated by sexual deception. The orchids mimic the sex pheromone of receptive female insects, mainly hymenopterans, in order to attract males seeking to copulate. Most Ophrys species have achromatic flowers, but some exhibit a coloured perianth and a bright, conspicuous labellum pattern. We recently showed that the pink perianth of Ophrys heldreichii flowers increases detectability by its pollinator, males of the long-horned bee Eucera berlandi. Here we tested the hypothesis that the bright, complex labellum pattern mimics the female of the pollinator to increase attractiveness toward males. In a dual-choice test we offered E. berlandi males an O. heldreichii flower and a flower from O. dictynnae, which also exhibits a pinkish perianth but no conspicuous labellum pattern. Both flowers were housed in UV-transmitting acrylic glass boxes to exclude olfactory signals. Males significantly preferred O. heldreichii to O. dictynnae flowers. In a second experiment, we replaced the perianth of both flowers with identical artificial perianths made from pink card, so that only the labellum differed between the two flower stimuli. Males then chose between both stimuli at random, suggesting that the presence of a labellum pattern does not affect their choice. Spectral measurements revealed higher colour contrast with the background of the perianth of O. heldreichii compared to O. dictynnae, but no difference in green receptor-specific contrast or brightness. Our results show that male choice is guided by the chromatic contrast of the perianth during the initial flower approach but is not affected by the presence of a labellum pattern. Instead, we hypothesise that the labellum pattern is involved in aversive learning during post-copulatory behaviour and used by the orchid as a strategy to increase outcrossing."}],"intvolume":" 4","month":"01","publisher":"Springer","language":[{"iso":"eng"}],"publication":"Arthropod-Plant Interactions","day":"01","publication_status":"published","year":"2010","date_created":"2018-12-11T12:06:08Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.1007/s11829-010-9093-4","issue":"3","volume":4,"date_published":"2010-01-01T00:00:00Z","page":"141 - 148","_id":"3963","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T07:53:30Z","citation":{"short":"M. Streinzer, T. Ellis, H. Paulus, J. Spaethe, Arthropod-Plant Interactions 4 (2010) 141–148.","ieee":"M. Streinzer, T. Ellis, H. Paulus, and J. Spaethe, “Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator,” Arthropod-Plant Interactions, vol. 4, no. 3. Springer, pp. 141–148, 2010.","apa":"Streinzer, M., Ellis, T., Paulus, H., & Spaethe, J. (2010). Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions. Springer. https://doi.org/10.1007/s11829-010-9093-4","ama":"Streinzer M, Ellis T, Paulus H, Spaethe J. Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions. 2010;4(3):141-148. doi:10.1007/s11829-010-9093-4","mla":"Streinzer, M., et al. “Visual Discrimination between Two Sexually Deceptive Ophrys Species by a Bee Pollinator.” Arthropod-Plant Interactions, vol. 4, no. 3, Springer, 2010, pp. 141–48, doi:10.1007/s11829-010-9093-4.","ista":"Streinzer M, Ellis T, Paulus H, Spaethe J. 2010. Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions. 4(3), 141–148.","chicago":"Streinzer, M., Thomas Ellis, H. Paulus, and J. Spaethe. “Visual Discrimination between Two Sexually Deceptive Ophrys Species by a Bee Pollinator.” Arthropod-Plant Interactions. Springer, 2010. https://doi.org/10.1007/s11829-010-9093-4."},"title":"Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator","article_processing_charge":"No","publist_id":"2164","author":[{"first_name":"M.","last_name":"Streinzer","full_name":"Streinzer, M."},{"last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paulus, H.","last_name":"Paulus","first_name":"H."},{"first_name":"J.","full_name":"Spaethe, J.","last_name":"Spaethe"}]},{"publisher":"Cell Press","intvolume":" 32","month":"05","abstract":[{"lang":"eng","text":"Chemokines orchestrate immune cell trafficking by eliciting either directed or random migration and by activating integrins in order to induce cell adhesion. Analyzing dendritic cell (DC) migration, we showed that these distinct cellular responses depended on the mode of chemokine presentation within tissues. The surface-immobilized form of the chemokine CCL21, the heparan sulfate-anchoring ligand of the CC-chemokine receptor 7 (CCR7), caused random movement of DCs that was confined to the chemokine-presenting surface because it triggered integrin-mediated adhesion. Upon direct contact with CCL21, DCs truncated the anchoring residues of CCL21, thereby releasing it from the solid phase. Soluble CCL21 functionally resembles the second CCR7 ligand, CCL19, which lacks anchoring residues and forms soluble gradients. Both soluble CCR7 ligands triggered chemotactic movement, but not surface adhesion. Adhesive random migration and directional steering cooperate to produce dynamic but spatially restricted locomotion patterns closely resembling the cellular dynamics observed in secondary lymphoid organs."}],"oa_version":"None","page":"703 - 713","date_created":"2018-12-11T12:06:07Z","doi":"10.1016/j.immuni.2010.04.017","issue":"5","date_published":"2010-05-28T00:00:00Z","volume":32,"year":"2010","publication_status":"published","publication":"Immunity","language":[{"iso":"eng"}],"day":"28","type":"journal_article","status":"public","_id":"3959","publist_id":"2168","author":[{"full_name":"Schumann, Kathrin","last_name":"Schumann","first_name":"Kathrin","id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F"},{"first_name":"Tim","last_name":"Lämmermann","full_name":"Lämmermann, Tim"},{"first_name":"Markus","full_name":"Bruckner, Markus","last_name":"Bruckner"},{"full_name":"Legler, Daniel","last_name":"Legler","first_name":"Daniel"},{"last_name":"Polleux","full_name":"Polleux, Julien","first_name":"Julien"},{"first_name":"Joachim","last_name":"Spatz","full_name":"Spatz, Joachim"},{"last_name":"Schuler","full_name":"Schuler, Gerold","first_name":"Gerold"},{"first_name":"Reinhold","full_name":"Förster, Reinhold","last_name":"Förster"},{"last_name":"Lutz","full_name":"Lutz, Manfred","first_name":"Manfred"},{"first_name":"Lydia","last_name":"Sorokin","full_name":"Sorokin, Lydia"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"title":"Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells","citation":{"chicago":"Schumann, Kathrin, Tim Lämmermann, Markus Bruckner, Daniel Legler, Julien Polleux, Joachim Spatz, Gerold Schuler, et al. “Immobilized Chemokine Fields and Soluble Chemokine Gradients Cooperatively Shape Migration Patterns of Dendritic Cells.” Immunity. Cell Press, 2010. https://doi.org/10.1016/j.immuni.2010.04.017.","ista":"Schumann K, Lämmermann T, Bruckner M, Legler D, Polleux J, Spatz J, Schuler G, Förster R, Lutz M, Sorokin L, Sixt MK. 2010. Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells. Immunity. 32(5), 703–713.","mla":"Schumann, Kathrin, et al. “Immobilized Chemokine Fields and Soluble Chemokine Gradients Cooperatively Shape Migration Patterns of Dendritic Cells.” Immunity, vol. 32, no. 5, Cell Press, 2010, pp. 703–13, doi:10.1016/j.immuni.2010.04.017.","short":"K. Schumann, T. Lämmermann, M. Bruckner, D. Legler, J. Polleux, J. Spatz, G. Schuler, R. Förster, M. Lutz, L. Sorokin, M.K. Sixt, Immunity 32 (2010) 703–713.","ieee":"K. Schumann et al., “Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells,” Immunity, vol. 32, no. 5. Cell Press, pp. 703–713, 2010.","ama":"Schumann K, Lämmermann T, Bruckner M, et al. Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells. Immunity. 2010;32(5):703-713. doi:10.1016/j.immuni.2010.04.017","apa":"Schumann, K., Lämmermann, T., Bruckner, M., Legler, D., Polleux, J., Spatz, J., … Sixt, M. K. (2010). Immobilized chemokine fields and soluble chemokine gradients cooperatively shape migration patterns of dendritic cells. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2010.04.017"},"date_updated":"2021-01-12T07:53:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"type":"journal_article","status":"public","_id":"3958","author":[{"first_name":"Hema","last_name":"Mohan","full_name":"Mohan, Hema"},{"first_name":"Markus","full_name":"Krumbholz, Markus","last_name":"Krumbholz"},{"full_name":"Sharma, Rakhi","last_name":"Sharma","first_name":"Rakhi"},{"last_name":"Eisele","full_name":"Eisele, Sylvia","first_name":"Sylvia"},{"full_name":"Junker, Andreas","last_name":"Junker","first_name":"Andreas"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Michael Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Newcombe","full_name":"Newcombe, Jia","first_name":"Jia"},{"last_name":"Wekerle","full_name":"Wekerle, Hartmut","first_name":"Hartmut"},{"full_name":"Hohlfeld, Reinhard","last_name":"Hohlfeld","first_name":"Reinhard"},{"last_name":"Lassmann","full_name":"Lassmann, Hans","first_name":"Hans"},{"full_name":"Meinl, Edgar","last_name":"Meinl","first_name":"Edgar"}],"publist_id":"2169","title":"Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells","date_updated":"2021-01-12T07:53:28Z","citation":{"mla":"Mohan, Hema, et al. “Extracellular Matrix in Multiple Sclerosis Lesions: Fibrillar Collagens, Biglycan and Decorin Are Upregulated and Associated with Infiltrating Immune Cells.” Brain Pathology, vol. 20, no. 5, Wiley-Blackwell, 2010, pp. 966–75, doi:10.1111/j.1750-3639.2010.00399.x.","ama":"Mohan H, Krumbholz M, Sharma R, et al. Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells. Brain Pathology. 2010;20(5):966-975. doi:10.1111/j.1750-3639.2010.00399.x","apa":"Mohan, H., Krumbholz, M., Sharma, R., Eisele, S., Junker, A., Sixt, M. K., … Meinl, E. (2010). Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells. Brain Pathology. Wiley-Blackwell. https://doi.org/10.1111/j.1750-3639.2010.00399.x","short":"H. Mohan, M. Krumbholz, R. Sharma, S. Eisele, A. Junker, M.K. Sixt, J. Newcombe, H. Wekerle, R. Hohlfeld, H. Lassmann, E. Meinl, Brain Pathology 20 (2010) 966–975.","ieee":"H. Mohan et al., “Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells,” Brain Pathology, vol. 20, no. 5. Wiley-Blackwell, pp. 966–975, 2010.","chicago":"Mohan, Hema, Markus Krumbholz, Rakhi Sharma, Sylvia Eisele, Andreas Junker, Michael K Sixt, Jia Newcombe, et al. “Extracellular Matrix in Multiple Sclerosis Lesions: Fibrillar Collagens, Biglycan and Decorin Are Upregulated and Associated with Infiltrating Immune Cells.” Brain Pathology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1750-3639.2010.00399.x.","ista":"Mohan H, Krumbholz M, Sharma R, Eisele S, Junker A, Sixt MK, Newcombe J, Wekerle H, Hohlfeld R, Lassmann H, Meinl E. 2010. Extracellular matrix in multiple sclerosis lesions: fibrillar collagens, biglycan and decorin are upregulated and associated with infiltrating immune cells. Brain Pathology. 20(5), 966–975."},"extern":1,"publisher":"Wiley-Blackwell","quality_controlled":0,"intvolume":" 20","month":"09","abstract":[{"text":"Extracellular matrix (ECM) proteins can modify immune reactions, e.g. by sequestering or displaying growth factors and by interacting with immune and glial cells. Here we quantified by quantitative polymerase chain reaction (qPCR) expression of 50 ECM components and 34 ECM degrading enzymes in multiple sclerosis (MS) active and inactive white matter lesions. COL1A1, COL3A1, COL5A1 and COL5A2 chains were induced strongly in active lesions and even more in inactive lesions. These chains interact to form collagen types I, III and V, which are fibrillar collagens. Biglycan and decorin, which can decorate fibrillar collagens, were also induced strongly. The fibrillar collagens, biglycan and decorin were largely found between the endothelium and astrocytic glia limitans in the perivascular space where they formed a meshwork which was closely associated with infiltrating immune cells. In active lesions collagen V was also seen in the heavily infiltrated parenchyma. Fibrillar collagens I and III inhibited in vitro human monocyte production of CCL2 (MCP-1), an inflammatory chemokine involved in recruitment of immune cells. Together, ECM changes in lesions with different activities were quantified and proteins forming a perivascular fibrosis were identified. Induced fibrillar collagens may contribute to limiting enlargement of MS lesions by inhibiting the production of CCL2 by monocytes.","lang":"eng"}],"page":"966 - 975","date_created":"2018-12-11T12:06:07Z","doi":"10.1111/j.1750-3639.2010.00399.x","issue":"5","volume":20,"date_published":"2010-09-01T00:00:00Z","publication_status":"published","year":"2010","publication":"Brain Pathology","day":"01"},{"extern":1,"date_updated":"2021-01-12T07:53:30Z","citation":{"ista":"Renkawitz J, Sixt MK. 2010. Mechanisms of force generation and force transmission during interstitial leukocyte migration. EMBO Reports. 11(10), 744–750.","chicago":"Renkawitz, Jörg, and Michael K Sixt. “Mechanisms of Force Generation and Force Transmission during Interstitial Leukocyte Migration.” EMBO Reports. Wiley-Blackwell, 2010. https://doi.org/10.1038/embor.2010.147.","ieee":"J. Renkawitz and M. K. Sixt, “Mechanisms of force generation and force transmission during interstitial leukocyte migration,” EMBO Reports, vol. 11, no. 10. Wiley-Blackwell, pp. 744–750, 2010.","short":"J. Renkawitz, M.K. Sixt, EMBO Reports 11 (2010) 744–750.","ama":"Renkawitz J, Sixt MK. Mechanisms of force generation and force transmission during interstitial leukocyte migration. EMBO Reports. 2010;11(10):744-750. doi:10.1038/embor.2010.147","apa":"Renkawitz, J., & Sixt, M. K. (2010). Mechanisms of force generation and force transmission during interstitial leukocyte migration. EMBO Reports. Wiley-Blackwell. https://doi.org/10.1038/embor.2010.147","mla":"Renkawitz, Jörg, and Michael K. Sixt. “Mechanisms of Force Generation and Force Transmission during Interstitial Leukocyte Migration.” EMBO Reports, vol. 11, no. 10, Wiley-Blackwell, 2010, pp. 744–50, doi:10.1038/embor.2010.147."},"title":"Mechanisms of force generation and force transmission during interstitial leukocyte migration","publist_id":"2166","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","orcid":"0000-0003-2856-3369","full_name":"Jörg Renkawitz","last_name":"Renkawitz"},{"orcid":"0000-0002-6620-9179","full_name":"Michael Sixt","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"_id":"3961","status":"public","type":"journal_article","publication":"EMBO Reports","day":"24","publication_status":"published","year":"2010","date_created":"2018-12-11T12:06:08Z","issue":"10","volume":11,"doi":"10.1038/embor.2010.147","date_published":"2010-09-24T00:00:00Z","page":"744 - 750","acknowledgement":"We are grateful to Michele Weber for critical comments on the manuscript. Work in the laboratory of M.S. is supported by the German Research Foundation, the Peter Hans Hofschneider Foundation for Experimental Biomedicine and the Max Planck Society. J.R. is supported by a PhD fellowship of the Böhringer Ingelheim Fond. We thank Reinhard Fässler and Stefan Jentsch for their continuous support.","abstract":[{"lang":"eng","text":"For innate and adaptive immune responses it is essential that inflammatory cells use quick and flexible locomotion strategies. Accordingly, most leukocytes can efficiently infiltrate and traverse almost every physiological or artificial environment. Here, we review how leukocytes might achieve this task mechanistically, and summarize recent findings on the principles of cytoskeletal force generation and transduction at the leading edge of leukocytes. We propose a model in which the cells switch between adhesion-receptor-mediated force transmission and locomotion modes that are based on cellular deformations, but independent of adhesion receptors. This plasticity in migration strategies allows leukocytes to adapt to the geometry and molecular composition of their environment."}],"intvolume":" 11","month":"09","quality_controlled":0,"publisher":"Wiley-Blackwell"},{"extern":1,"date_updated":"2021-01-12T07:53:29Z","citation":{"chicago":"Weber, Michele, and Michael K Sixt. “MEK Signalling Tunes Actin Treadmilling for Interstitial Lymphocyte Migration.” EMBO Journal. Wiley-Blackwell, 2010. https://doi.org/10.1038/emboj.2010.183.","ista":"Weber M, Sixt MK. 2010. MEK signalling tunes actin treadmilling for interstitial lymphocyte migration. EMBO Journal. 29(17), 2861–2863.","mla":"Weber, Michele, and Michael K. Sixt. “MEK Signalling Tunes Actin Treadmilling for Interstitial Lymphocyte Migration.” EMBO Journal, vol. 29, no. 17, Wiley-Blackwell, 2010, pp. 2861–63, doi:10.1038/emboj.2010.183.","short":"M. Weber, M.K. Sixt, EMBO Journal 29 (2010) 2861–2863.","ieee":"M. Weber and M. K. Sixt, “MEK signalling tunes actin treadmilling for interstitial lymphocyte migration,” EMBO Journal, vol. 29, no. 17. Wiley-Blackwell, pp. 2861–2863, 2010.","ama":"Weber M, Sixt MK. MEK signalling tunes actin treadmilling for interstitial lymphocyte migration. EMBO Journal. 2010;29(17):2861-2863. doi:10.1038/emboj.2010.183","apa":"Weber, M., & Sixt, M. K. (2010). MEK signalling tunes actin treadmilling for interstitial lymphocyte migration. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2010.183"},"title":"MEK signalling tunes actin treadmilling for interstitial lymphocyte migration","author":[{"id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Weber","full_name":"Michele Weber"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Michael Sixt","last_name":"Sixt"}],"publist_id":"2167","_id":"3960","status":"public","type":"journal_article","publication":"EMBO Journal","day":"01","year":"2010","publication_status":"published","date_created":"2018-12-11T12:06:07Z","date_published":"2010-09-01T00:00:00Z","doi":"10.1038/emboj.2010.183","issue":"17","volume":29,"page":"2861 - 2863","abstract":[{"lang":"eng","text":"When lymphocytes follow chemotactic cues, they can adopt different migratory modes depending on the geometry and molecular composition of their extracellular environment. In this issue of The EMBO Journal, Klemke et al (2010) describe a novel Ras-dependent chemokine receptor signalling pathway that leads to activation of cofilin, which in turn amplifies actin turnover. This signalling module is exclusively required for lymphocyte migration in three-dimensional (3D) environments, but not for locomotion on two-dimensional (2D) surfaces."}],"intvolume":" 29","month":"09","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/issues/190105/","open_access":"1"}],"oa":1,"quality_controlled":0,"publisher":"Wiley-Blackwell"},{"quality_controlled":0,"publisher":"Springer","intvolume":" 10","month":"01","abstract":[{"lang":"eng","text":"We prove two stability results for Lipschitz functions on triangulable, compact metric spaces and consider applications of both to problems in systems biology. Given two functions, the first result is formulated in terms of the Wasserstein distance between their persistence diagrams and the second in terms of their total persistence."}],"acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057 and by CNRS under grant PICS-3416.","page":"127 - 139","date_created":"2018-12-11T12:06:09Z","doi":"10.1007/s10208-010-9060-6","issue":"2","date_published":"2010-01-28T00:00:00Z","volume":10,"publication_status":"published","year":"2010","publication":"Foundations of Computational Mathematics","day":"28","type":"journal_article","status":"public","_id":"3964","author":[{"last_name":"Cohen Steiner","full_name":"Cohen-Steiner, David","first_name":"David"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833"},{"first_name":"John","full_name":"Harer, John","last_name":"Harer"},{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"}],"publist_id":"2163","title":"Lipschitz functions have L_p-stable persistence","date_updated":"2021-01-12T07:53:31Z","citation":{"chicago":"Cohen Steiner, David, Herbert Edelsbrunner, John Harer, and Yuriy Mileyko. “Lipschitz Functions Have L_p-Stable Persistence.” Foundations of Computational Mathematics. Springer, 2010. https://doi.org/10.1007/s10208-010-9060-6.","ista":"Cohen Steiner D, Edelsbrunner H, Harer J, Mileyko Y. 2010. Lipschitz functions have L_p-stable persistence. Foundations of Computational Mathematics. 10(2), 127–139.","mla":"Cohen Steiner, David, et al. “Lipschitz Functions Have L_p-Stable Persistence.” Foundations of Computational Mathematics, vol. 10, no. 2, Springer, 2010, pp. 127–39, doi:10.1007/s10208-010-9060-6.","ama":"Cohen Steiner D, Edelsbrunner H, Harer J, Mileyko Y. Lipschitz functions have L_p-stable persistence. Foundations of Computational Mathematics. 2010;10(2):127-139. doi:10.1007/s10208-010-9060-6","apa":"Cohen Steiner, D., Edelsbrunner, H., Harer, J., & Mileyko, Y. (2010). Lipschitz functions have L_p-stable persistence. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-010-9060-6","ieee":"D. Cohen Steiner, H. Edelsbrunner, J. Harer, and Y. Mileyko, “Lipschitz functions have L_p-stable persistence,” Foundations of Computational Mathematics, vol. 10, no. 2. Springer, pp. 127–139, 2010.","short":"D. Cohen Steiner, H. Edelsbrunner, J. Harer, Y. Mileyko, Foundations of Computational Mathematics 10 (2010) 127–139."},"extern":1},{"_id":"3957","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T07:53:28Z","citation":{"ama":"Riedl J, Flynn K, Raducanu A, et al. Lifeact mice for studying F-actin dynamics. Nature Methods. 2010;7(3):168-169. doi:10.1038/nmeth0310-168","apa":"Riedl, J., Flynn, K., Raducanu, A., Gärtner, F. R., Beck, G., Bosl, M., … Wedlich Söldner, R. (2010). Lifeact mice for studying F-actin dynamics. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth0310-168","short":"J. Riedl, K. Flynn, A. Raducanu, F.R. Gärtner, G. Beck, M. Bosl, F. Bradke, S. Massberg, A. Aszodi, M.K. Sixt, R. Wedlich Söldner, Nature Methods 7 (2010) 168–169.","ieee":"J. Riedl et al., “Lifeact mice for studying F-actin dynamics,” Nature Methods, vol. 7, no. 3. Nature Publishing Group, pp. 168–169, 2010.","mla":"Riedl, Julia, et al. “Lifeact Mice for Studying F-Actin Dynamics.” Nature Methods, vol. 7, no. 3, Nature Publishing Group, 2010, pp. 168–69, doi:10.1038/nmeth0310-168.","ista":"Riedl J, Flynn K, Raducanu A, Gärtner FR, Beck G, Bosl M, Bradke F, Massberg S, Aszodi A, Sixt MK, Wedlich Söldner R. 2010. Lifeact mice for studying F-actin dynamics. Nature Methods. 7(3), 168–169.","chicago":"Riedl, Julia, Kevin Flynn, Aurelia Raducanu, Florian R Gärtner, Gisela Beck, Michael Bosl, Frank Bradke, et al. “Lifeact Mice for Studying F-Actin Dynamics.” Nature Methods. Nature Publishing Group, 2010. https://doi.org/10.1038/nmeth0310-168."},"title":"Lifeact mice for studying F-actin dynamics","author":[{"first_name":"Julia","last_name":"Riedl","full_name":"Riedl, Julia"},{"first_name":"Kevin","last_name":"Flynn","full_name":"Flynn, Kevin C"},{"first_name":"Aurelia","last_name":"Raducanu","full_name":"Raducanu, Aurelia"},{"orcid":"0000-0001-6120-3723","full_name":"Florian Gärtner","last_name":"Gärtner","first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beck, Gisela","last_name":"Beck","first_name":"Gisela"},{"first_name":"Michael","full_name":"Bosl, Michael","last_name":"Bosl"},{"full_name":"Bradke, Frank","last_name":"Bradke","first_name":"Frank"},{"first_name":"Steffen","full_name":"Massberg, Steffen","last_name":"Massberg"},{"last_name":"Aszodi","full_name":"Aszodi, Attila","first_name":"Attila"},{"full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wedlich-Söldner, Roland","last_name":"Wedlich Söldner","first_name":"Roland"}],"publist_id":"2171","intvolume":" 7","month":"03","publisher":"Nature Publishing Group","quality_controlled":0,"publication":"Nature Methods","day":"01","publication_status":"published","year":"2010","date_created":"2018-12-11T12:06:06Z","date_published":"2010-03-01T00:00:00Z","volume":7,"issue":"3","doi":"10.1038/nmeth0310-168","page":"168 - 169"},{"scopus_import":1,"intvolume":" 13","month":"03","abstract":[{"text":"All species are restricted in their distribution. Currently, ecological models can only explain such limits if patches vary in quality, leading to asymmetrical dispersal, or if genetic variation is too low at the margins for adaptation. However, population genetic models suggest that the increase in genetic variance resulting from dispersal should allow adaptation to almost any ecological gradient. Clearly therefore, these models miss something that prevents evolution in natural populations. We developed an individual-based simulation to explore stochastic effects in these models. At high carrying capacities, our simulations largely agree with deterministic predictions. However, when carrying capacity is low, the population fails to establish for a wide range of parameter values where adaptation was expected from previous models. Stochastic or transient effects appear critical around the boundaries in parameter space between simulation behaviours. Dispersal, gradient steepness, and population density emerge as key factors determining adaptation on an ecological gradient. ","lang":"eng"}],"oa_version":"None","ec_funded":1,"volume":13,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"4134","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:54:45Z","quality_controlled":"1","publisher":"Wiley-Blackwell","acknowledgement":"We are very grateful to Nick Barton.","page":"485 - 494","date_created":"2018-12-11T12:07:08Z","doi":"10.1111/j.1461-0248.2010.01442.x","date_published":"2010-03-15T00:00:00Z","year":"2010","publication":"Ecology Letters","day":"15","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"publist_id":"1987","author":[{"last_name":"Bridle","full_name":"Bridle, Jon","first_name":"Jon"},{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova"},{"last_name":"Kawata","full_name":"Kawata, Masakado","first_name":"Masakado"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"title":"Why is adaptation prevented at ecological margins? New insights from individual-based simulations","citation":{"ama":"Bridle J, Polechova J, Kawata M, Butlin R. Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. 2010;13(4):485-494. doi:10.1111/j.1461-0248.2010.01442.x","apa":"Bridle, J., Polechova, J., Kawata, M., & Butlin, R. (2010). Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/j.1461-0248.2010.01442.x","short":"J. Bridle, J. Polechova, M. Kawata, R. Butlin, Ecology Letters 13 (2010) 485–494.","ieee":"J. Bridle, J. Polechova, M. Kawata, and R. Butlin, “Why is adaptation prevented at ecological margins? New insights from individual-based simulations,” Ecology Letters, vol. 13, no. 4. Wiley-Blackwell, pp. 485–494, 2010.","mla":"Bridle, Jon, et al. “Why Is Adaptation Prevented at Ecological Margins? New Insights from Individual-Based Simulations.” Ecology Letters, vol. 13, no. 4, Wiley-Blackwell, 2010, pp. 485–94, doi:10.1111/j.1461-0248.2010.01442.x.","ista":"Bridle J, Polechova J, Kawata M, Butlin R. 2010. Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. 13(4), 485–494.","chicago":"Bridle, Jon, Jitka Polechova, Masakado Kawata, and Roger Butlin. “Why Is Adaptation Prevented at Ecological Margins? New Insights from Individual-Based Simulations.” Ecology Letters. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1461-0248.2010.01442.x."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"_id":"4163","type":"journal_article","status":"public","citation":{"ista":"Oteíza P, Koeppen M, Krieg M, Pulgar E, Farias C, Melo C, Preibisch S, Mueller D, Tada M, Hartel S, Heisenberg C-PJ, Concha M. 2010. Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ. Development. 137(20), 3459–3468.","chicago":"Oteíza, Pablo, Mathias Koeppen, Michael Krieg, Eduardo Pulgar, Cecilia Farias, Cristina Melo, Steffen Preibisch, et al. “Planar Cell Polarity Signalling Regulates Cell Adhesion Properties in Progenitors of the Zebrafish Laterality Organ.” Development. Company of Biologists, 2010. https://doi.org/10.1242/dev.049981.","apa":"Oteíza, P., Koeppen, M., Krieg, M., Pulgar, E., Farias, C., Melo, C., … Concha, M. (2010). Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ. Development. Company of Biologists. https://doi.org/10.1242/dev.049981","ama":"Oteíza P, Koeppen M, Krieg M, et al. Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ. Development. 2010;137(20):3459-3468. doi:10.1242/dev.049981","short":"P. Oteíza, M. Koeppen, M. Krieg, E. Pulgar, C. Farias, C. Melo, S. Preibisch, D. Mueller, M. Tada, S. Hartel, C.-P.J. Heisenberg, M. Concha, Development 137 (2010) 3459–3468.","ieee":"P. Oteíza et al., “Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ,” Development, vol. 137, no. 20. Company of Biologists, pp. 3459–3468, 2010.","mla":"Oteíza, Pablo, et al. “Planar Cell Polarity Signalling Regulates Cell Adhesion Properties in Progenitors of the Zebrafish Laterality Organ.” Development, vol. 137, no. 20, Company of Biologists, 2010, pp. 3459–68, doi:10.1242/dev.049981."},"date_updated":"2021-01-12T07:54:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"first_name":"Pablo","full_name":"Oteíza, Pablo","last_name":"Oteíza"},{"last_name":"Koeppen","full_name":"Koeppen, Mathias","first_name":"Mathias"},{"first_name":"Michael","last_name":"Krieg","full_name":"Krieg, Michael"},{"last_name":"Pulgar","full_name":"Pulgar, Eduardo","first_name":"Eduardo"},{"full_name":"Farias, Cecilia","last_name":"Farias","first_name":"Cecilia"},{"last_name":"Melo","full_name":"Melo, Cristina","first_name":"Cristina"},{"first_name":"Steffen","full_name":"Preibisch, Steffen","last_name":"Preibisch"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel"},{"last_name":"Tada","full_name":"Tada, Masazumi","first_name":"Masazumi"},{"first_name":"Steffen","full_name":"Hartel, Steffen","last_name":"Hartel"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Miguel","full_name":"Concha, Miguel","last_name":"Concha"}],"publist_id":"1958","title":"Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ","abstract":[{"text":"Organ formation requires the precise assembly of progenitor cells into a functional multicellular structure. Mechanical forces probably participate in this process but how they influence organ morphogenesis is still unclear. Here, we show that Wnt11- and Prickle1a-mediated planar cell polarity (PCP) signalling coordinates the formation of the zebrafish ciliated laterality organ (Kupffer's vesicle) by regulating adhesion properties between organ progenitor cells (the dorsal forerunner cells, DFCs). Combined inhibition of Wnt11 and Prickle1a reduces DFC cell-cell adhesion and impairs their compaction and arrangement during vesicle lumen formation. This leads to the formation of a mis-shapen vesicle with small fragmented lumina and shortened cilia, resulting in severely impaired organ function and, as a consequence, randomised laterality of both molecular and visceral asymmetries. Our results reveal a novel role for PCP-dependent cell adhesion in coordinating the supracellular organisation of progenitor cells during vertebrate laterality organ formation.","lang":"eng"}],"oa_version":"None","publisher":"Company of Biologists","intvolume":" 137","month":"10","year":"2010","publication_status":"published","language":[{"iso":"eng"}],"publication":"Development","day":"15","page":"3459 - 3468","date_created":"2018-12-11T12:07:20Z","issue":"20","doi":"10.1242/dev.049981","date_published":"2010-10-15T00:00:00Z","volume":137},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Barton NH, Etheridge A, Véber A. 2010. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 15(7), 162–216.","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/EJP.v15-741.","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “A new model for evolution in a spatial continuum,” Electronic Journal of Probability, vol. 15, no. 7. Institute of Mathematical Statistics, pp. 162–216, 2010.","short":"N.H. Barton, A. Etheridge, A. Véber, Electronic Journal of Probability 15 (2010) 162–216.","ama":"Barton NH, Etheridge A, Véber A. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 2010;15(7):162-216. doi:10.1214/EJP.v15-741","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2010). A new model for evolution in a spatial continuum. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v15-741","mla":"Barton, Nicholas H., et al. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability, vol. 15, no. 7, Institute of Mathematical Statistics, 2010, pp. 162–216, doi:10.1214/EJP.v15-741."},"title":"A new model for evolution in a spatial continuum","publist_id":"1863","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"}],"day":"03","publication":"Electronic Journal of Probability","has_accepted_license":"1","year":"2010","doi":"10.1214/EJP.v15-741","date_published":"2010-02-03T00:00:00Z","date_created":"2018-12-11T12:07:48Z","page":"162 - 216","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"ddc":["576"],"date_updated":"2021-01-12T07:55:34Z","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"NiBa"}],"_id":"4243","status":"public","pubrep_id":"369","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5140","checksum":"bab577546dd4e8f882e9a9dd645cd01e","creator":"system","file_size":450171,"date_updated":"2020-07-14T12:46:26Z","file_name":"IST-2015-369-v1+1_741-2535-1-PB.pdf","date_created":"2018-12-12T10:15:21Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":15,"issue":"7","oa_version":"Published Version","abstract":[{"text":"We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite number of individuals sampled uniformly at random (or more generally `far enough apart') from a two-dimensional torus of sidelength L as L tends to infinity. Under appropriate conditions (and on a suitable timescale) we can obtain as limiting genealogical processes a Kingman coalescent, a more general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local coalescence mechanism).","lang":"eng"}],"month":"02","intvolume":" 15","scopus_import":1},{"status":"public","type":"other_academic_publication","conference":{"name":"ELAG: European Library Automation Group"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"4340","file_date_updated":"2020-07-14T12:46:27Z","title":"Open bibliographic data","publist_id":"1234","author":[{"first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","last_name":"Danowski"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"date_updated":"2020-07-14T23:07:19Z","citation":{"chicago":"Danowski, Patrick. Open Bibliographic Data. European Library Automation Group (ELAG) 2010. Elsevier, 2010.","ista":"Danowski P. 2010. Open bibliographic data, Elsevier,p.","mla":"Danowski, Patrick. “Open Bibliographic Data.” European Library Automation Group (ELAG) 2010, Elsevier, 2010.","short":"P. Danowski, Open Bibliographic Data, Elsevier, 2010.","ieee":"P. Danowski, Open bibliographic data. Elsevier, 2010.","apa":"Danowski, P. (2010). Open bibliographic data. European Library Automation Group (ELAG) 2010. Elsevier.","ama":"Danowski P. Open Bibliographic Data. Elsevier; 2010."},"month":"06","publisher":"Elsevier","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.slideshare.net/PatrickD/open-bibliographic-data-elag2010"}],"oa_version":"None","abstract":[{"lang":"eng","text":"More and more libraries starting semantic web projects. The question about the license of the data\r\nis not discussed or the discussion is deferred to the end of project. in this paper is discussed why\r\nthe question of the license is so important in context of the semantic web that is should be one of the\r\nfirst aspects in a semantic web project. Also it will be shown why a public domain weaver is the\r\nonly solution that fulfill the the special requirements of the semantic web and that guaranties the\r\nreuseablitly of semantic library data for a sustainability of the projects. "}],"date_published":"2010-06-10T00:00:00Z","date_created":"2018-12-11T12:08:21Z","file":[{"creator":"system","date_updated":"2020-07-14T12:46:27Z","file_size":94982,"date_created":"2018-12-12T10:15:01Z","file_name":"IST-2012-51-v1+1_149-danowski-en.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7061756135333d73b26a84526fa654f5","file_id":"5118"}],"day":"10","language":[{"iso":"eng"}],"publication":"European Library Automation Group (ELAG) 2010","has_accepted_license":"1","year":"2010","publication_status":"published"},{"language":[{"iso":"ger"}],"publication_status":"published","publication_identifier":{"isbn":["9-783-1102-3209-7"],"eisbn":["9-783-1102-3210-3"]},"volume":" 41","oa_version":"Published Version","abstract":[{"lang":"eng","text":"With the term \"Library 2.0\" the editors mean an institution which applies the principles of the Web 2.0 such as openness, re-use, collaboration and interaction in the entire organization. Libraries are extending their service offerings and work processes to include the potential of Web 2.0 technologies. This changes the job description and self-image of librarians. The collective volume offers a complete overview of the topic Library 2.0 and the current state of developments from a technological, sociological, information theoretical and practice-oriented perspective."}],"month":"09","main_file_link":[{"url":"https://www.degruyter.com/document/doi/10.1515/9783110232103/html","open_access":"1"}],"alternative_title":["Bibliotheks- und Informationspraxis"],"date_updated":"2021-12-22T14:41:57Z","department":[{"_id":"E-Lib"}],"series_title":"Bibliothekspraxis","_id":"4346","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"book_editor","day":"01","year":"2010","date_created":"2018-12-11T12:08:23Z","doi":"10.1515/9783110232103","date_published":"2010-09-01T00:00:00Z","page":"405","oa":1,"quality_controlled":"1","publisher":"De Gruyter","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Danowski P, Bergmann J eds. 2010. Handbuch Bibliothek 2.0, De Gruyter, 405p.","chicago":"Danowski, Patrick, and Julia Bergmann, eds. Handbuch Bibliothek 2.0. Vol. 41. Bibliothekspraxis. De Gruyter, 2010. https://doi.org/10.1515/9783110232103.","ama":"Danowski P, Bergmann J, eds. Handbuch Bibliothek 2.0. Vol 41. De Gruyter; 2010. doi:10.1515/9783110232103","apa":"Danowski, P., & Bergmann, J. (Eds.). (2010). Handbuch Bibliothek 2.0 (Vol. 41). De Gruyter. https://doi.org/10.1515/9783110232103","ieee":"P. Danowski and J. Bergmann, Eds., Handbuch Bibliothek 2.0, vol. 41. De Gruyter, 2010.","short":"P. Danowski, J. Bergmann, eds., Handbuch Bibliothek 2.0, De Gruyter, 2010.","mla":"Danowski, Patrick, and Julia Bergmann, editors. Handbuch Bibliothek 2.0. Vol. 41, De Gruyter, 2010, doi:10.1515/9783110232103."},"title":"Handbuch Bibliothek 2.0","editor":[{"last_name":"Danowski","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bergmann, Julia","last_name":"Bergmann","first_name":"Julia"}],"article_processing_charge":"No","publist_id":"1228"},{"type":"conference","conference":{"name":"WLIC: World Library and Information Congress"},"status":"public","pubrep_id":"51","_id":"4341","author":[{"last_name":"Danowski","full_name":"Patrick Danowski","orcid":"0000-0002-6026-4409","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"1233","title":"Step one: blow up the silo! - Open bibliographic data, the first step towards Linked Open Data","citation":{"ista":"Danowski P. 2010. Step one: blow up the silo! - Open bibliographic data, the first step towards Linked Open Data. WLIC: World Library and Information Congress, IFLA , .","chicago":"Danowski, Patrick. “Step One: Blow up the Silo! - Open Bibliographic Data, the First Step towards Linked Open Data.” IFLA, 2010.","ieee":"P. Danowski, “Step one: blow up the silo! - Open bibliographic data, the first step towards Linked Open Data,” presented at the WLIC: World Library and Information Congress, 2010.","short":"P. Danowski, in:, IFLA, 2010.","ama":"Danowski P. Step one: blow up the silo! - Open bibliographic data, the first step towards Linked Open Data. In: IFLA; 2010.","apa":"Danowski, P. (2010). Step one: blow up the silo! - Open bibliographic data, the first step towards Linked Open Data. Presented at the WLIC: World Library and Information Congress, IFLA.","mla":"Danowski, Patrick. Step One: Blow up the Silo! - Open Bibliographic Data, the First Step towards Linked Open Data. IFLA, 2010."},"date_updated":"2021-01-12T07:56:16Z","extern":1,"alternative_title":["IFLA "],"publisher":"IFLA","quality_controlled":0,"main_file_link":[{"url":"http://www.ifla.org/files/hq/papers/ifla76/149-danowski-en.pdf","open_access":"0"}],"month":"08","abstract":[{"lang":"eng","text":"More and more libraries starting semantic web projects. The question about the license of the data is not discussed or the discussion is deferred to the end of project. in this paper is discussed why the question of the license is so important in context of the semantic web that is should be one of the first aspects in a semantic web project. Also it will be shown why a public domain weaver is the only solution that fulfill the the special requirements of the semantic web and that guaranties the reuseablitly of semantic library data for a sustainability of the projects."}],"date_published":"2010-08-01T00:00:00Z","date_created":"2018-12-11T12:08:21Z","year":"2010","publication_status":"published","day":"01"},{"project":[{"grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","grant_number":"214373"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Nickovic, Dejan, and Nir Piterman. From MTL to Deterministic Timed Automata. Edited by Thomas A. Henzinger and Krishnendu Chatterjee, vol. 6246, Springer, 2010, pp. 152–67, doi:10.1007/978-3-642-15297-9_13.","ama":"Nickovic D, Piterman N. From MTL to deterministic timed automata. In: Henzinger TA, Chatterjee K, eds. Vol 6246. Springer; 2010:152-167. doi:10.1007/978-3-642-15297-9_13","apa":"Nickovic, D., & Piterman, N. (2010). From MTL to deterministic timed automata. In T. A. Henzinger & K. Chatterjee (Eds.) (Vol. 6246, pp. 152–167). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-15297-9_13","ieee":"D. Nickovic and N. Piterman, “From MTL to deterministic timed automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg, Austria, 2010, vol. 6246, pp. 152–167.","short":"D. Nickovic, N. Piterman, in:, T.A. Henzinger, K. Chatterjee (Eds.), Springer, 2010, pp. 152–167.","chicago":"Nickovic, Dejan, and Nir Piterman. “From MTL to Deterministic Timed Automata.” edited by Thomas A. Henzinger and Krishnendu Chatterjee, 6246:152–67. Springer, 2010. https://doi.org/10.1007/978-3-642-15297-9_13.","ista":"Nickovic D, Piterman N. 2010. From MTL to deterministic timed automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 6246, 152–167."},"title":"From MTL to deterministic timed automata","editor":[{"full_name":"Henzinger, Thomas A.","last_name":"Henzinger","first_name":"Thomas A."},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"}],"publist_id":"1090","author":[{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"first_name":"Nir","full_name":"Piterman, Nir","last_name":"Piterman"}],"publisher":"Springer","quality_controlled":"1","oa":1,"day":"08","has_accepted_license":"1","year":"2010","doi":"10.1007/978-3-642-15297-9_13","date_published":"2010-09-08T00:00:00Z","date_created":"2018-12-11T12:08:30Z","page":"152 - 167","_id":"4369","status":"public","pubrep_id":"49","type":"conference","conference":{"location":"Klosterneuburg, Austria","end_date":"2010-09-10","start_date":"2010-09-08","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"ddc":["004"],"date_updated":"2021-01-12T07:56:27Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:27Z","oa_version":"Submitted Version","abstract":[{"text":"In this paper we propose a novel technique for constructing timed automata from properties expressed in the logic mtl, under bounded-variability assumptions. We handle full mtl and include all future operators. Our construction is based on separation of the continuous time monitoring of the input sequence and discrete predictions regarding the future. The separation of the continuous from the discrete allows us to determinize our automata in an exponential construction that does not increase the number of clocks. This leads to a doubly exponential construction from mtl to deterministic timed automata, compared with triply exponential using existing approaches. We offer an alternative to the existing approach to linear real-time model checking, which has never been implemented. It further offers a unified framework for model checking, runtime monitoring, and synthesis, in an approach that can reuse tools, implementations, and insights from the discrete setting.","lang":"eng"}],"month":"09","intvolume":" 6246","scopus_import":1,"alternative_title":["LNCS"],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5028","checksum":"b0ca5f5fbe8a3d20ccbc6f51a344a459","date_updated":"2020-07-14T12:46:27Z","file_size":249789,"creator":"system","date_created":"2018-12-12T10:13:43Z","file_name":"IST-2012-49-v1+1_From_MTL_to_deterministic_timed_automata.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6246,"ec_funded":1},{"author":[{"last_name":"Podelski","full_name":"Podelski,Andreas","first_name":"Andreas"},{"last_name":"Wies","full_name":"Thomas Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"1093","title":"Counterexample-guided focus","citation":{"chicago":"Podelski, Andreas, and Thomas Wies. “Counterexample-Guided Focus,” 249–60. ACM, 2010. https://doi.org/10.1145/1707801.1706330.","ista":"Podelski A, Wies T. 2010. Counterexample-guided focus. POPL: Principles of Programming Languages, 249–260.","mla":"Podelski, Andreas, and Thomas Wies. Counterexample-Guided Focus. ACM, 2010, pp. 249–60, doi:10.1145/1707801.1706330.","apa":"Podelski, A., & Wies, T. (2010). Counterexample-guided focus (pp. 249–260). Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/10.1145/1707801.1706330","ama":"Podelski A, Wies T. Counterexample-guided focus. In: ACM; 2010:249-260. doi:10.1145/1707801.1706330","short":"A. Podelski, T. Wies, in:, ACM, 2010, pp. 249–260.","ieee":"A. Podelski and T. Wies, “Counterexample-guided focus,” presented at the POPL: Principles of Programming Languages, 2010, pp. 249–260."},"date_updated":"2021-01-12T07:56:26Z","extern":1,"type":"conference","conference":{"name":"POPL: Principles of Programming Languages"},"status":"public","_id":"4364","page":"249 - 260","date_published":"2010-01-01T00:00:00Z","doi":"10.1145/1707801.1706330","date_created":"2018-12-11T12:08:28Z","year":"2010","publication_status":"published","day":"01","publisher":"ACM","quality_controlled":0,"month":"01"},{"date_updated":"2021-01-12T07:40:49Z","citation":{"chicago":"Růžička, Kamil, Lucia Strader, Aurélien Bailly, Haibing Yang, Joshua Blakeslee, Łukasz Łangowski, Eliška Nejedlá, et al. “Arabidopsis PIS1 Encodes the ABCG37 Transporter of Auxinic Compounds Including the Auxin Precursor Indole 3 Butyric Acid.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1005878107.","ista":"Růžička K, Strader L, Bailly A, Yang H, Blakeslee J, Łangowski Ł, Nejedlá E, Fujita H, Itoh H, Syōno K, Hejátko J, Gray W, Martinoia E, Geisler M, Bartel B, Murphy A, Friml J. 2010. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole 3 butyric acid. PNAS. 107(23), 10749–10753.","mla":"Růžička, Kamil, et al. “Arabidopsis PIS1 Encodes the ABCG37 Transporter of Auxinic Compounds Including the Auxin Precursor Indole 3 Butyric Acid.” PNAS, vol. 107, no. 23, National Academy of Sciences, 2010, pp. 10749–53, doi:10.1073/pnas.1005878107.","apa":"Růžička, K., Strader, L., Bailly, A., Yang, H., Blakeslee, J., Łangowski, Ł., … Friml, J. (2010). Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole 3 butyric acid. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1005878107","ama":"Růžička K, Strader L, Bailly A, et al. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole 3 butyric acid. PNAS. 2010;107(23):10749-10753. doi:10.1073/pnas.1005878107","ieee":"K. Růžička et al., “Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole 3 butyric acid,” PNAS, vol. 107, no. 23. National Academy of Sciences, pp. 10749–10753, 2010.","short":"K. Růžička, L. Strader, A. Bailly, H. Yang, J. Blakeslee, Ł. Łangowski, E. Nejedlá, H. Fujita, H. Itoh, K. Syōno, J. Hejátko, W. Gray, E. Martinoia, M. Geisler, B. Bartel, A. Murphy, J. Friml, PNAS 107 (2010) 10749–10753."},"extern":1,"author":[{"first_name":"Kamil","full_name":"Růžička, Kamil","last_name":"Růžička"},{"full_name":"Strader, Lucia C","last_name":"Strader","first_name":"Lucia"},{"full_name":"Bailly, Aurélien","last_name":"Bailly","first_name":"Aurélien"},{"first_name":"Haibing","last_name":"Yang","full_name":"Yang, Haibing"},{"first_name":"Joshua","last_name":"Blakeslee","full_name":"Blakeslee, Joshua"},{"last_name":"Łangowski","full_name":"Łangowski, Łukasz","first_name":"Łukasz"},{"first_name":"Eliška","full_name":"Nejedlá, Eliška","last_name":"Nejedlá"},{"first_name":"Hironori","full_name":"Fujita, Hironori","last_name":"Fujita"},{"full_name":"Itoh, Hironori","last_name":"Itoh","first_name":"Hironori"},{"first_name":"Kunihiko","full_name":"Syōno, Kunihiko","last_name":"Syōno"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"first_name":"William","full_name":"Gray, William M","last_name":"Gray"},{"first_name":"Enrico","full_name":"Martinoia, Enrico","last_name":"Martinoia"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"},{"first_name":"Bonnie","last_name":"Bartel","full_name":"Bartel, Bonnie"},{"first_name":"Angus","full_name":"Murphy, Angus S","last_name":"Murphy"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"}],"publist_id":"3633","title":"Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole 3 butyric acid","_id":"3068","type":"journal_article","status":"public","year":"2010","publication_status":"published","publication":"PNAS","day":"08","page":"10749 - 10753","date_created":"2018-12-11T12:01:11Z","volume":107,"doi":"10.1073/pnas.1005878107","date_published":"2010-06-08T00:00:00Z","issue":"23","abstract":[{"text":"Differential distribution of the plant hormone auxin within tissues mediates a variety of developmental processes. Cellular auxin levels are determined by metabolic processes including synthesis, degradation, and (de)conjugation, as well as by auxin transport across the plasma membrane. Whereas transport of free auxins such as naturally occurring indole-3-acetic acid (IAA) is well characterized, little is known about the transport of auxin precursors and metabolites. Here, we identify amutation in the ABCG37 gene of Arabidopsis that causes the polar auxin transport inhibitor sensitive1 (pis1) phenotype manifested by hypersensitivity to auxinic compounds. ABCG37 encodes the pleiotropic drug resistance transporter that transports a range of synthetic auxinic compounds as well as the endogenous auxin precursor indole-3-butyric acid (IBA), but not free IAA. ABCG37 and its homolog ABCG36 act redundantly at outermost root plasma membranes and,unlike established IAA transporters from the PIN and ABCB families, transport IBA out of the cells. Our findings explore possible novel modes of regulating auxin homeostasis and plant development by means of directional transport of the auxin precursor IBA and presumably also other auxin metabolites.","lang":"eng"}],"publisher":"National Academy of Sciences","quality_controlled":0,"intvolume":" 107","month":"06"},{"extern":1,"date_updated":"2021-01-12T07:40:49Z","citation":{"chicago":"Jelínková, Adriana, Kateřina Malínská, Sibu Simon, Jürgen Kleine Vehn, Markéta Pařezová, Přemysl Pejchar, Martin Kubeš, et al. “Probing Plant Membranes with FM Dyes: Tracking Dragging or Blocking?” Plant Journal. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-313X.2009.04102.x.","ista":"Jelínková A, Malínská K, Simon S, Kleine Vehn J, Pařezová M, Pejchar P, Kubeš M, Martinec J, Friml J, Zažímalová E, Petrášek J. 2010. Probing plant membranes with FM dyes: Tracking dragging or blocking? Plant Journal. 61(5), 883–892.","mla":"Jelínková, Adriana, et al. “Probing Plant Membranes with FM Dyes: Tracking Dragging or Blocking?” Plant Journal, vol. 61, no. 5, Wiley-Blackwell, 2010, pp. 883–92, doi:10.1111/j.1365-313X.2009.04102.x.","apa":"Jelínková, A., Malínská, K., Simon, S., Kleine Vehn, J., Pařezová, M., Pejchar, P., … Petrášek, J. (2010). Probing plant membranes with FM dyes: Tracking dragging or blocking? Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2009.04102.x","ama":"Jelínková A, Malínská K, Simon S, et al. Probing plant membranes with FM dyes: Tracking dragging or blocking? Plant Journal. 2010;61(5):883-892. doi:10.1111/j.1365-313X.2009.04102.x","ieee":"A. Jelínková et al., “Probing plant membranes with FM dyes: Tracking dragging or blocking?,” Plant Journal, vol. 61, no. 5. Wiley-Blackwell, pp. 883–892, 2010.","short":"A. Jelínková, K. Malínská, S. Simon, J. Kleine Vehn, M. Pařezová, P. Pejchar, M. Kubeš, J. Martinec, J. Friml, E. Zažímalová, J. Petrášek, Plant Journal 61 (2010) 883–892."},"title":"Probing plant membranes with FM dyes: Tracking dragging or blocking?","publist_id":"3635","author":[{"first_name":"Adriana","full_name":"Jelínková, Adriana","last_name":"Jelínková"},{"last_name":"Malínská","full_name":"Malínská, Kateřina","first_name":"Kateřina"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","full_name":"Sibu Simon","orcid":"0000-0002-1998-6741"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"last_name":"Pařezová","full_name":"Pařezová, Markéta","first_name":"Markéta"},{"last_name":"Pejchar","full_name":"Pejchar, Přemysl","first_name":"Přemysl"},{"first_name":"Martin","full_name":"Kubeš, Martin","last_name":"Kubeš"},{"last_name":"Martinec","full_name":"Martinec, Jan","first_name":"Jan"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"}],"_id":"3067","status":"public","type":"journal_article","publication":"Plant Journal","day":"01","publication_status":"published","year":"2010","date_created":"2018-12-11T12:01:10Z","doi":"10.1111/j.1365-313X.2009.04102.x","date_published":"2010-03-01T00:00:00Z","volume":61,"issue":"5","page":"883 - 892","abstract":[{"text":"Remarkable progress in various techniques of in vivo fluorescence microscopy has brought an urgent need for reliable markers for tracking cellular structures and processes. The goal of this manuscript is to describe unexplored effects of the FM (Fei Mao) styryl dyes, which are widely used probes that label processes of endocytosis and vesicle trafficking in eukaryotic cells. Although there are few reports on the effect of styryl dyes on membrane fluidity and the activity of mammalian receptors, FM dyes have been considered as reliable tools for tracking of plant endocytosis. Using plasma membrane-localized transporters for the plant hormone auxin in tobacco BY-2 and Arabidopsis thaliana cell suspensions, we show that routinely used concentrations of FM 4-64 and FM 5-95 trigger transient re-localization of these proteins, and FM 1-43 affects their activity. The active process of re-localization is blocked neither by inhibitors of endocytosis nor by cytoskeletal drugs. It does not occur in A. thaliana roots and depends on the degree of hydrophobicity (lipophilicity) of a particular FM dye. Our results emphasize the need for circumspection during in vivo studies of membrane proteins performed using simultaneous labelling with FM dyes.","lang":"eng"}],"intvolume":" 61","month":"03","quality_controlled":0,"publisher":"Wiley-Blackwell"},{"extern":1,"citation":{"chicago":"Žádníková, Petra, Jan Petrášek, Peter Marhavý, Vered Raz, Filip Vandenbussche, Zhaojun Ding, Kateřina Schwarzerová, et al. “Role of PIN-Mediated Auxin Efflux in Apical Hook Development of Arabidopsis Thaliana.” Development. Company of Biologists, 2010. https://doi.org/10.1242/dev.041277.","ista":"Žádníková P, Petrášek J, Marhavý P, Raz V, Vandenbussche F, Ding Z, Schwarzerová K, Morita M, Tasaka M, Hejátko J, Van Der Straeten D, Friml J, Benková E. 2010. Role of PIN-mediated auxin efflux in apical hook development of Arabidopsis thaliana. Development. 137(4), 607–617.","mla":"Žádníková, Petra, et al. “Role of PIN-Mediated Auxin Efflux in Apical Hook Development of Arabidopsis Thaliana.” Development, vol. 137, no. 4, Company of Biologists, 2010, pp. 607–17, doi:10.1242/dev.041277.","ama":"Žádníková P, Petrášek J, Marhavý P, et al. Role of PIN-mediated auxin efflux in apical hook development of Arabidopsis thaliana. Development. 2010;137(4):607-617. doi:10.1242/dev.041277","apa":"Žádníková, P., Petrášek, J., Marhavý, P., Raz, V., Vandenbussche, F., Ding, Z., … Benková, E. (2010). Role of PIN-mediated auxin efflux in apical hook development of Arabidopsis thaliana. Development. Company of Biologists. https://doi.org/10.1242/dev.041277","short":"P. Žádníková, J. Petrášek, P. Marhavý, V. Raz, F. Vandenbussche, Z. Ding, K. Schwarzerová, M. Morita, M. Tasaka, J. Hejátko, D. Van Der Straeten, J. Friml, E. Benková, Development 137 (2010) 607–617.","ieee":"P. Žádníková et al., “Role of PIN-mediated auxin efflux in apical hook development of Arabidopsis thaliana,” Development, vol. 137, no. 4. Company of Biologists, pp. 607–617, 2010."},"date_updated":"2021-01-12T07:40:48Z","title":"Role of PIN-mediated auxin efflux in apical hook development of Arabidopsis thaliana","publist_id":"3636","author":[{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Peter Marhavy","last_name":"Marhavy"},{"first_name":"Vered","full_name":"Raz, Vered","last_name":"Raz"},{"first_name":"Filip","last_name":"Vandenbussche","full_name":"Vandenbussche, Filip"},{"first_name":"Zhaojun","last_name":"Ding","full_name":"Ding, Zhaojun"},{"first_name":"Kateřina","full_name":"Schwarzerová, Kateřina","last_name":"Schwarzerová"},{"first_name":"Miyo","last_name":"Morita","full_name":"Morita, Miyo T"},{"first_name":"Masao","full_name":"Tasaka, Masao","last_name":"Tasaka"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"_id":"3065","status":"public","type":"journal_article","day":"15","publication":"Development","publication_status":"published","year":"2010","doi":"10.1242/dev.041277","date_published":"2010-02-15T00:00:00Z","issue":"4","volume":137,"date_created":"2018-12-11T12:01:09Z","page":"607 - 617","abstract":[{"text":"The apical hook of dark-grown Arabidopsis seedlings is a simple structure that develops soon after germination to protect the meristem tissues during emergence through the soil and that opens upon exposure to light. Differential growth at the apical hook proceeds in three sequential steps that are regulated by multiple hormones, principally auxin and ethylene. We show that the progress of the apical hook through these developmental phases depends on the dynamic, asymmetric distribution of auxin, which is regulated by auxin efflux carriers of the PIN family. Several PIN proteins exhibited specific, partially overlapping spatial and temporal expression patterns, and their subcellular localization suggested auxin fluxes during hook development. Genetic manipulation of individual PIN activities interfered with different stages of hook development, implying that specific combinations of PIN genes are required for progress of the apical hook through the developmental phases. Furthermore, ethylene might modulate apical hook development by prolonging the formation phase and strongly suppressing the maintenance phase. This ethylene effect is in part mediated by regulation of PIN-dependent auxin efflux and auxin signaling.","lang":"eng"}],"month":"02","intvolume":" 137","quality_controlled":0,"publisher":"Company of Biologists"},{"status":"public","type":"journal_article","_id":"3064","title":"PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport","author":[{"first_name":"Jing","full_name":"Zhang, Jing","last_name":"Zhang"},{"full_name":"Nodzyński, Thomasz","last_name":"Nodzyński","first_name":"Thomasz"},{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3637","extern":1,"citation":{"ista":"Zhang J, Nodzyński T, Pěnčík A, Rolčík J, Friml J. 2010. PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport. PNAS. 107(2), 918–922.","chicago":"Zhang, Jing, Thomasz Nodzyński, Aleš Pěnčík, Jakub Rolčík, and Jiří Friml. “PIN Phosphorylation Is Sufficient to Mediate PIN Polarity and Direct Auxin Transport.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.0909460107.","short":"J. Zhang, T. Nodzyński, A. Pěnčík, J. Rolčík, J. Friml, PNAS 107 (2010) 918–922.","ieee":"J. Zhang, T. Nodzyński, A. Pěnčík, J. Rolčík, and J. Friml, “PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport,” PNAS, vol. 107, no. 2. National Academy of Sciences, pp. 918–922, 2010.","apa":"Zhang, J., Nodzyński, T., Pěnčík, A., Rolčík, J., & Friml, J. (2010). PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0909460107","ama":"Zhang J, Nodzyński T, Pěnčík A, Rolčík J, Friml J. PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport. PNAS. 2010;107(2):918-922. doi:10.1073/pnas.0909460107","mla":"Zhang, Jing, et al. “PIN Phosphorylation Is Sufficient to Mediate PIN Polarity and Direct Auxin Transport.” PNAS, vol. 107, no. 2, National Academy of Sciences, 2010, pp. 918–22, doi:10.1073/pnas.0909460107."},"date_updated":"2021-01-12T07:40:47Z","month":"01","intvolume":" 107","quality_controlled":0,"publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"The plant hormone auxin plays a crucial role in regulating plant development and plant architecture. The directional auxin distribution within tissues depends on PIN transporters that are polarly localized on the plasmamembrane. The PINpolarity and the resulting auxin flow directionality aremediated by the antagonistic actions of PINOID kinase and protein phosphatase 2A. However, the contributionof the PINphosphorylationto the polar PINsortingis still unclear. Here, we identified an evolutionarily conserved phosphorylation site within the central hydrophilic loop of PIN proteins that is important for the apical and basal polar PIN localizations. Inactivation of the phosphorylation site in PIN1(Ala) resulted in a predominantly basal targeting and increased the auxinflowto the root tip. In contrast, the outcome of the phosphomimic PIN1(Asp) manipulation was a constitutive, PINOID-independent apical targeting of PIN1 and an increased auxin flow in the opposite direction. Furthermore, the PIN1(Asp) functionally replaced PIN2 in its endogenous expression domain, revealing that the phosphorylation-dependent polarity regulation contributes to functional diversification within the PIN family. Our data suggest that PINOID-independent PIN phosphorylation at one single site is adequate to change the PIN polarity and, consequently, to redirect auxin fluxes between cells and provide the conceptual possibility and means to manipulate auxin-dependent plant development and architecture."}],"issue":"2","volume":107,"doi":"10.1073/pnas.0909460107","date_published":"2010-01-12T00:00:00Z","date_created":"2018-12-11T12:01:09Z","page":"918 - 922","day":"12","publication":"PNAS","year":"2010","publication_status":"published"},{"publist_id":"3634","author":[{"first_name":"Łukasz","full_name":"Łangowski, Łukasz","last_name":"Łangowski"},{"last_name":"Růžička","full_name":"Růžička, Kamil","first_name":"Kamil"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"}],"title":"Trafficking to the outer polar domain defines the root soil interface","citation":{"ista":"Łangowski Ł, Růžička K, Naramoto S, Kleine Vehn J, Friml J. 2010. Trafficking to the outer polar domain defines the root soil interface. Current Biology. 20(10), 904–908.","chicago":"Łangowski, Łukasz, Kamil Růžička, Satoshi Naramoto, Jürgen Kleine Vehn, and Jiří Friml. “Trafficking to the Outer Polar Domain Defines the Root Soil Interface.” Current Biology. Cell Press, 2010. https://doi.org/10.1016/j.cub.2010.03.059.","apa":"Łangowski, Ł., Růžička, K., Naramoto, S., Kleine Vehn, J., & Friml, J. (2010). Trafficking to the outer polar domain defines the root soil interface. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2010.03.059","ama":"Łangowski Ł, Růžička K, Naramoto S, Kleine Vehn J, Friml J. Trafficking to the outer polar domain defines the root soil interface. Current Biology. 2010;20(10):904-908. doi:10.1016/j.cub.2010.03.059","short":"Ł. Łangowski, K. Růžička, S. Naramoto, J. Kleine Vehn, J. Friml, Current Biology 20 (2010) 904–908.","ieee":"Ł. Łangowski, K. Růžička, S. Naramoto, J. Kleine Vehn, and J. Friml, “Trafficking to the outer polar domain defines the root soil interface,” Current Biology, vol. 20, no. 10. Cell Press, pp. 904–908, 2010.","mla":"Łangowski, Łukasz, et al. “Trafficking to the Outer Polar Domain Defines the Root Soil Interface.” Current Biology, vol. 20, no. 10, Cell Press, 2010, pp. 904–08, doi:10.1016/j.cub.2010.03.059."},"date_updated":"2021-01-12T07:40:48Z","extern":1,"type":"journal_article","status":"public","_id":"3066","page":"904 - 908","issue":"10","volume":20,"date_published":"2010-05-25T00:00:00Z","doi":"10.1016/j.cub.2010.03.059","date_created":"2018-12-11T12:01:10Z","publication_status":"published","year":"2010","day":"25","publication":"Current Biology","publisher":"Cell Press","quality_controlled":0,"month":"05","intvolume":" 20","abstract":[{"lang":"eng","text":"In animals, the interface between organism and environment is constituted by the epithelium [1]. In plants, the exchange of nutrients and signals between root and soil is crucial for their survival, but the cellular mechanisms underlying the epithelium-like function and specific localization of proteins to the root surface have not been identified [2]. Here we analyze the mechanism of polar delivery to the root-soil interface of the proteins BOR4, ABCG37, and PEN3, which transport nutrients [2], transport plant hormones, and are required for pathogen defense [3], respectively. The simultaneous visualization of these proteins and the apical and basal cargos in a single cell demonstrates that the outermost cell side represents an additional polar domain. Delivery to this outer polar domain depends on ARF GEF [4] and actin [5-8] function but does not require known molecular components of the apical or basal targeting. The outer polar delivery is, in contrast to known basal and apical cargos [9, 10], mediated by the polar secretion. Our findings show that the outermost cell membranes of roots define an additional polar domain in plant cells along with a specific, previously uncharacterized, polar targeting mechanism that is important for defining the functional, epithelium-like root-soil interface."}]},{"page":"103 - 113","issue":"1","date_published":"2010-07-01T00:00:00Z","volume":19,"doi":"10.1016/j.devcel.2010.06.004","date_created":"2018-12-11T12:01:11Z","year":"2010","publication_status":"published","day":"01","publication":"Developmental Cell","quality_controlled":0,"publisher":"Cell Press","month":"07","intvolume":" 19","abstract":[{"lang":"eng","text":"Division of the Arabidopsis zygote defines two fundamentally different developmental domains, the proembryo and suspensor. The resulting boundary separates domain-specific gene expression, and a signal originating from the proembryo instructs the suspensor to generate the root stem cell niche. While root induction is known to require the phytohormone auxin and the Auxin Response Factor MONOPTEROS, it has remained largely elusive how the two domains involved in this process are initially specified. Here, we show that the GATA factor HANABA TARANU (HAN) is required to position the inductive proembryo boundary. Mutations in HAN cause a coordinated apical shift of gene expression patterns, revealing that HAN regulates transcription in the basal proembryo. Key auxin transporters are affected as early as the 8 cell stage, resulting in apical redistribution of auxin. Remarkably, han embryos eventually organize a root independent of MONOPTEROS and the suspensor around a new boundary marked by the auxin maximum."}],"author":[{"first_name":"Tal","full_name":"Nawy, Tal","last_name":"Nawy"},{"first_name":"Martin","last_name":"Bayer","full_name":"Bayer, Martin"},{"first_name":"Jozef","full_name":"Mravec, Jozef","last_name":"Mravec"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"},{"last_name":"Birnbaum","full_name":"Birnbaum, Kenneth D","first_name":"Kenneth"},{"full_name":"Lukowitz, Wolfgang","last_name":"Lukowitz","first_name":"Wolfgang"}],"publist_id":"3631","title":"The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo","date_updated":"2021-01-12T07:40:50Z","citation":{"mla":"Nawy, Tal, et al. “The GATA Factor HANABA TARANU Is Required to Position the Proembryo Boundary in the Early Arabidopsis Embryo.” Developmental Cell, vol. 19, no. 1, Cell Press, 2010, pp. 103–13, doi:10.1016/j.devcel.2010.06.004.","ama":"Nawy T, Bayer M, Mravec J, Friml J, Birnbaum K, Lukowitz W. The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. Developmental Cell. 2010;19(1):103-113. doi:10.1016/j.devcel.2010.06.004","apa":"Nawy, T., Bayer, M., Mravec, J., Friml, J., Birnbaum, K., & Lukowitz, W. (2010). The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2010.06.004","ieee":"T. Nawy, M. Bayer, J. Mravec, J. Friml, K. Birnbaum, and W. Lukowitz, “The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo,” Developmental Cell, vol. 19, no. 1. Cell Press, pp. 103–113, 2010.","short":"T. Nawy, M. Bayer, J. Mravec, J. Friml, K. Birnbaum, W. Lukowitz, Developmental Cell 19 (2010) 103–113.","chicago":"Nawy, Tal, Martin Bayer, Jozef Mravec, Jiří Friml, Kenneth Birnbaum, and Wolfgang Lukowitz. “The GATA Factor HANABA TARANU Is Required to Position the Proembryo Boundary in the Early Arabidopsis Embryo.” Developmental Cell. Cell Press, 2010. https://doi.org/10.1016/j.devcel.2010.06.004.","ista":"Nawy T, Bayer M, Mravec J, Friml J, Birnbaum K, Lukowitz W. 2010. The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. Developmental Cell. 19(1), 103–113."},"extern":1,"type":"journal_article","status":"public","_id":"3070"},{"_id":"3069","type":"journal_article","status":"public","date_updated":"2021-01-12T07:40:50Z","citation":{"chicago":"Ding, Zhaojun, and Jiří Friml. “Auxin Regulates Distal Stem Cell Differentiation in Arabidopsis Roots.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1000672107.","ista":"Ding Z, Friml J. 2010. Auxin regulates distal stem cell differentiation in Arabidopsis roots. PNAS. 107(26), 12046–12051.","mla":"Ding, Zhaojun, and Jiří Friml. “Auxin Regulates Distal Stem Cell Differentiation in Arabidopsis Roots.” PNAS, vol. 107, no. 26, National Academy of Sciences, 2010, pp. 12046–51, doi:10.1073/pnas.1000672107.","ama":"Ding Z, Friml J. Auxin regulates distal stem cell differentiation in Arabidopsis roots. PNAS. 2010;107(26):12046-12051. doi:10.1073/pnas.1000672107","apa":"Ding, Z., & Friml, J. (2010). Auxin regulates distal stem cell differentiation in Arabidopsis roots. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1000672107","ieee":"Z. Ding and J. Friml, “Auxin regulates distal stem cell differentiation in Arabidopsis roots,” PNAS, vol. 107, no. 26. National Academy of Sciences, pp. 12046–12051, 2010.","short":"Z. Ding, J. Friml, PNAS 107 (2010) 12046–12051."},"extern":1,"publist_id":"3632","author":[{"first_name":"Zhaojun","full_name":"Ding, Zhaojun","last_name":"Ding"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"Auxin regulates distal stem cell differentiation in Arabidopsis roots","abstract":[{"text":"The stem cell niche in the root meristem is critical for the development of the plant root system. The plant hormone auxin acts as a versatile trigger in many developmental processes, including the regulation of root growth, but its role in the control of the stem cell activity remains largely unclear. Here we show that local auxin levels, determined by biosynthesis and intercellular transport, mediate maintenance or differentiation of distal stem cells in the Arabidopsis thaliana roots. Genetic analysis shows that auxin acts upstream of the major regulators of the stem cell activity, the homeodomain transcription factor WOX5, and the AP-2 transcription factor PLETHORA. Auxin signaling for differentiation of distal stem cells requires the transcriptional repressor IAA17/AXR3 as well as the ARF10 and ARF16 auxin response factors. ARF10 and ARF16 activities repress the WOX5 transcription and restrict it to the quiescent center, where WOX5, in turn, is needed for the activity of PLETHORA. Our investigations reveal that long-distance auxin signals act upstream of the short-range network of transcriptional factors to mediate the differentiation of distal stem cells in roots.","lang":"eng"}],"publisher":"National Academy of Sciences","quality_controlled":0,"intvolume":" 107","month":"06","publication_status":"published","year":"2010","publication":"PNAS","day":"29","page":"12046 - 12051","date_created":"2018-12-11T12:01:11Z","doi":"10.1073/pnas.1000672107","volume":107,"issue":"26","date_published":"2010-06-29T00:00:00Z"},{"page":"231 - 235","date_created":"2018-12-11T12:01:09Z","issue":"2-3","doi":"10.1016/j.ejcb.2009.11.003","date_published":"2010-02-01T00:00:00Z","volume":89,"publication_status":"published","year":"2010","publication":"European Journal of Cell Biology","day":"01","quality_controlled":0,"publisher":"Elsevier","intvolume":" 89","month":"02","abstract":[{"text":"The directional transport of the plant hormone auxin is a unique process mediating a wide variety of developmental processes. Auxin movement between cells depends on AUX1/LAX, PGP and PIN protein families that mediate auxin transport across the plasma membrane. The directionality of auxin flow within tissues is largely determined by polar, subcellular localization of PIN auxin efflux carriers. PIN proteins undergo rapid subcellular dynamics that is important for the process of auxin transport and its directionality. Furthermore, various environmental and endogenous signals can modulate trafficking and polarity of PIN proteins and by this mechanism change auxin distribution. Thus, the subcellular dynamics of auxin transport proteins represents an important interface between cellular processes and development of the whole plant. This review summarizes our recent contributions to the field of PIN trafficking and auxin transport regulation. © 2009 Elsevier GmbH.","lang":"eng"}],"publist_id":"3638","author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"}],"title":"Subcellular trafficking of PIN auxin efflux carriers in auxin transport","date_updated":"2021-01-12T07:40:47Z","citation":{"ista":"Friml J. 2010. Subcellular trafficking of PIN auxin efflux carriers in auxin transport. European Journal of Cell Biology. 89(2–3), 231–235.","chicago":"Friml, Jiří. “Subcellular Trafficking of PIN Auxin Efflux Carriers in Auxin Transport.” European Journal of Cell Biology. Elsevier, 2010. https://doi.org/10.1016/j.ejcb.2009.11.003.","apa":"Friml, J. (2010). Subcellular trafficking of PIN auxin efflux carriers in auxin transport. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2009.11.003","ama":"Friml J. Subcellular trafficking of PIN auxin efflux carriers in auxin transport. European Journal of Cell Biology. 2010;89(2-3):231-235. doi:10.1016/j.ejcb.2009.11.003","short":"J. Friml, European Journal of Cell Biology 89 (2010) 231–235.","ieee":"J. Friml, “Subcellular trafficking of PIN auxin efflux carriers in auxin transport,” European Journal of Cell Biology, vol. 89, no. 2–3. Elsevier, pp. 231–235, 2010.","mla":"Friml, Jiří. “Subcellular Trafficking of PIN Auxin Efflux Carriers in Auxin Transport.” European Journal of Cell Biology, vol. 89, no. 2–3, Elsevier, 2010, pp. 231–35, doi:10.1016/j.ejcb.2009.11.003."},"extern":1,"type":"journal_article","status":"public","_id":"3063"},{"extern":1,"date_updated":"2021-01-12T07:40:55Z","citation":{"short":"S. Naramoto, J. Kleine Vehn, S. Robert, M. Fujimoto, T. Dainobu, T. Paciorek, T. Ueda, A. Nakano, M. Van Montagu, H. Fukuda, J. Friml, PNAS 107 (2010) 21890–21895.","ieee":"S. Naramoto et al., “ADP ribosylation factor machinery mediates endocytosis in plant cells,” PNAS, vol. 107, no. 50. National Academy of Sciences, pp. 21890–21895, 2010.","apa":"Naramoto, S., Kleine Vehn, J., Robert, S., Fujimoto, M., Dainobu, T., Paciorek, T., … Friml, J. (2010). ADP ribosylation factor machinery mediates endocytosis in plant cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1016260107","ama":"Naramoto S, Kleine Vehn J, Robert S, et al. ADP ribosylation factor machinery mediates endocytosis in plant cells. PNAS. 2010;107(50):21890-21895. doi:10.1073/pnas.1016260107","mla":"Naramoto, Satoshi, et al. “ADP Ribosylation Factor Machinery Mediates Endocytosis in Plant Cells.” PNAS, vol. 107, no. 50, National Academy of Sciences, 2010, pp. 21890–95, doi:10.1073/pnas.1016260107.","ista":"Naramoto S, Kleine Vehn J, Robert S, Fujimoto M, Dainobu T, Paciorek T, Ueda T, Nakano A, Van Montagu M, Fukuda H, Friml J. 2010. ADP ribosylation factor machinery mediates endocytosis in plant cells. PNAS. 107(50), 21890–21895.","chicago":"Naramoto, Satoshi, Jürgen Kleine Vehn, Stéphanie Robert, Masaru Fujimoto, Tomoko Dainobu, Tomasz Paciorek, Takashi Ueda, et al. “ADP Ribosylation Factor Machinery Mediates Endocytosis in Plant Cells.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1016260107."},"title":"ADP ribosylation factor machinery mediates endocytosis in plant cells","author":[{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Fujimoto, Masaru","last_name":"Fujimoto","first_name":"Masaru"},{"first_name":"Tomoko","last_name":"Dainobu","full_name":"Dainobu, Tomoko"},{"first_name":"Tomasz","full_name":"Paciorek, Tomasz","last_name":"Paciorek"},{"full_name":"Ueda, Takashi","last_name":"Ueda","first_name":"Takashi"},{"last_name":"Nakano","full_name":"Nakano, Akihiko","first_name":"Akihiko"},{"first_name":"Marc","full_name":"Van Montagu, Marc C","last_name":"Van Montagu"},{"first_name":"Hiroo","full_name":"Fukuda, Hiroo","last_name":"Fukuda"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"3621","_id":"3081","status":"public","type":"journal_article","day":"14","publication":"PNAS","year":"2010","publication_status":"published","volume":107,"issue":"50","date_published":"2010-12-14T00:00:00Z","doi":"10.1073/pnas.1016260107","date_created":"2018-12-11T12:01:15Z","page":"21890 - 21895","abstract":[{"text":"Endocytosis is crucial for various cellular functions and development of multicellular organisms. In mammals and yeast, ADP-ribosylation factor (ARF) GTPases, key components of vesicle formation, and their regulators ARF-guanine nucleotide exchange factors (GEFs) and ARF-GTPase-activating protein (GAPs) mediate endocytosis. A similar role has not been established in plants,mainly because of the lack of the canonical ARF and ARF-GEF components that are involved in endocytosis in other eukaryotes. In this study, we revealed a regulatory mechanism of endocytosis in plants based on ARF GTPase activity.Weidentified that ARF-GEFGNOMand ARF-GAP VASCULAR NETWORK DEFECTIVE 3 (VAN3), both of which are involved in polar auxin transport-dependent morphogenesis, localize at the plasma membranes as well as in intracellular structures. Variable angle epifluorescence microscopy revealed that GNOM and VAN3 localize to partially overlapping discrete foci at the plasmamembranes that are regularly associated with the endocytic vesicle coat clathrin. Genetic studies revealed that GNOM and VAN3 activities are required for endocytosis and internalization of plasma membrane proteins, including PIN-FORMED auxin transporters. These findings identified ARF GTPase-based regulatory mechanisms for endocytosis in plants. GNOMand VAN3 previously were proposed to function solely at the recycling endosomes and trans-Golgi networks, respectively. Therefore our findings uncovered an additional cellular function of these prominent developmental regulators.","lang":"eng"}],"month":"12","intvolume":" 107","publisher":"National Academy of Sciences","quality_controlled":0},{"date_updated":"2021-01-12T07:40:55Z","citation":{"ista":"Kleine Vehn J, Ding Z, Jones A, Tasaka M, Morita M, Friml J. 2010. Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells. PNAS. 107(51), 22344–22349.","chicago":"Kleine Vehn, Jürgen, Zhaojun Ding, Angharad Jones, Masao Tasaka, Miyo Morita, and Jiří Friml. “Gravity Induced PIN Transcytosis for Polarization of Auxin Fluxes in Gravity Sensing Root Cells.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1013145107.","short":"J. Kleine Vehn, Z. Ding, A. Jones, M. Tasaka, M. Morita, J. Friml, PNAS 107 (2010) 22344–22349.","ieee":"J. Kleine Vehn, Z. Ding, A. Jones, M. Tasaka, M. Morita, and J. Friml, “Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells,” PNAS, vol. 107, no. 51. National Academy of Sciences, pp. 22344–22349, 2010.","ama":"Kleine Vehn J, Ding Z, Jones A, Tasaka M, Morita M, Friml J. Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells. PNAS. 2010;107(51):22344-22349. doi:10.1073/pnas.1013145107","apa":"Kleine Vehn, J., Ding, Z., Jones, A., Tasaka, M., Morita, M., & Friml, J. (2010). Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1013145107","mla":"Kleine Vehn, Jürgen, et al. “Gravity Induced PIN Transcytosis for Polarization of Auxin Fluxes in Gravity Sensing Root Cells.” PNAS, vol. 107, no. 51, National Academy of Sciences, 2010, pp. 22344–49, doi:10.1073/pnas.1013145107."},"extern":1,"author":[{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"},{"last_name":"Jones","full_name":"Jones, Angharad R","first_name":"Angharad"},{"first_name":"Masao","full_name":"Tasaka, Masao","last_name":"Tasaka"},{"full_name":"Morita, Miyo T","last_name":"Morita","first_name":"Miyo"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3620","title":"Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells","_id":"3080","type":"journal_article","status":"public","publication_status":"published","year":"2010","day":"21","publication":"PNAS","page":"22344 - 22349","issue":"51","volume":107,"date_published":"2010-12-21T00:00:00Z","doi":"10.1073/pnas.1013145107","date_created":"2018-12-11T12:01:15Z","abstract":[{"lang":"eng","text":"Auxin is an essential plant-specific regulator of patterning processes that also controls directional growth of roots and shoots. In response to gravity stimulation, the PIN3 auxin transporter polarizes to the bottomside of gravity-sensing root cells, presumably redirecting the auxin flux toward the lower side of the root and triggering gravitropic bending. By combining live-cell imaging techniques with pharmacological and genetic approaches, we demonstrate that PIN3 polarization does not require secretion of de novo synthesized proteins or protein degradation, but instead involves rapid, transient stimulation of PIN endocytosis, presumably via a clathrin-dependent pathway. Moreover, gravity-induced PIN3 polarization requires the activity of the guanine nucleotide exchange factors for ARF GTPases (ARF-GEF) GNOM-dependent polar-targeting path-ways and might involve endosome-based PIN3 translocation from one cell side to another. Our data suggest that gravity perception acts at several instances of PIN3 trafficking, ultimately leading to the polarization of PIN3, which presumably aligns auxin fluxes with gravity vector and mediates downstream root gravitropic response."}],"quality_controlled":0,"publisher":"National Academy of Sciences","month":"12","intvolume":" 107"},{"abstract":[{"text":"Human immune cells have to penetrate an endothelial barrier during their beneficial pursuit of infection and their destructive infiltration of tissues in autoimmune diseases. This transmigration requires Rap1 GTPase to activate integrin affinity. We define a new model system for this process by demonstrating, with live imaging and genetics, that during embryonic development Drosophila melanogaster immune cells penetrate an epithelial, Drosophila E-cadherin (DE-cadherin)-based tissue barrier. A mutant in RhoL, a GTPase homologue that is specifically expressed in haemocytes, blocks this invasive step but not other aspects of guided migration. RhoL mediates integrin adhesion caused by Drosophila Rap1 overexpression and moves Rap1 away from a concentration in the cytoplasm to the leading edge during invasive migration. These findings indicate that a programmed migratory step during Drosophila development bears striking molecular similarities to vertebrate immune cell transmigration during inflammation, and identify RhoL as a new regulator of invasion, adhesion and Rap1 localization. Our work establishes the utility of Drosophila for identifying novel components of immune cell transmigration and for understanding the in vivo interplay of immune cells with the barriers they penetrate.","lang":"eng"}],"main_file_link":[{"open_access":"0","url":"10.1038/ncb2063 PubMed"}],"publisher":"Nature Publishing Group","quality_controlled":0,"intvolume":" 12","month":"06","publication_status":"published","year":"2010","publication":"Nature Cell Biology","day":"01","page":"605 - 610","date_created":"2018-12-11T12:01:42Z","volume":12,"issue":"6","date_published":"2010-06-01T00:00:00Z","_id":"3153","type":"journal_article","status":"public","date_updated":"2021-01-12T07:41:25Z","citation":{"ista":"Siekhaus DE, Haesemeyer M, Moffitt O, Lehmann R. 2010. RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila. Nature Cell Biology. 12(6), 605–610.","chicago":"Siekhaus, Daria E, Martin Haesemeyer, Olivia Moffitt, and Ruth Lehmann. “RhoL Controls Invasion and Rap1 Localization during Immune Cell Transmigration in Drosophila.” Nature Cell Biology. Nature Publishing Group, 2010.","ama":"Siekhaus DE, Haesemeyer M, Moffitt O, Lehmann R. RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila. Nature Cell Biology. 2010;12(6):605-610.","apa":"Siekhaus, D. E., Haesemeyer, M., Moffitt, O., & Lehmann, R. (2010). RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila. Nature Cell Biology. Nature Publishing Group.","short":"D.E. Siekhaus, M. Haesemeyer, O. Moffitt, R. Lehmann, Nature Cell Biology 12 (2010) 605–610.","ieee":"D. E. Siekhaus, M. Haesemeyer, O. Moffitt, and R. Lehmann, “RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila,” Nature Cell Biology, vol. 12, no. 6. Nature Publishing Group, pp. 605–610, 2010.","mla":"Siekhaus, Daria E., et al. “RhoL Controls Invasion and Rap1 Localization during Immune Cell Transmigration in Drosophila.” Nature Cell Biology, vol. 12, no. 6, Nature Publishing Group, 2010, pp. 605–10."},"extern":1,"publist_id":"3542","author":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Daria Siekhaus","orcid":"0000-0001-8323-8353"},{"full_name":"Haesemeyer, Martin","last_name":"Haesemeyer","first_name":"Martin"},{"first_name":"Olivia","last_name":"Moffitt","full_name":"Moffitt, Olivia"},{"first_name":"Ruth","full_name":"Lehmann, Ruth","last_name":"Lehmann"}],"title":"RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila"},{"title":"Cosegmentation revisited: Models and optimization","author":[{"full_name":"Vicente, Sara","last_name":"Vicente","first_name":"Sara"},{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"publist_id":"3479","extern":1,"citation":{"chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Cosegmentation Revisited: Models and Optimization,” 6312:465–79. Springer, 2010. https://doi.org/10.1007/978-3-642-15552-9_34.","ista":"Vicente S, Kolmogorov V, Rother C. 2010. Cosegmentation revisited: Models and optimization. ECCV: European Conference on Computer Vision, LNCS, vol. 6312, 465–479.","mla":"Vicente, Sara, et al. Cosegmentation Revisited: Models and Optimization. Vol. 6312, Springer, 2010, pp. 465–79, doi:10.1007/978-3-642-15552-9_34.","ama":"Vicente S, Kolmogorov V, Rother C. Cosegmentation revisited: Models and optimization. In: Vol 6312. Springer; 2010:465-479. doi:10.1007/978-3-642-15552-9_34","apa":"Vicente, S., Kolmogorov, V., & Rother, C. (2010). Cosegmentation revisited: Models and optimization (Vol. 6312, pp. 465–479). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-642-15552-9_34","ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Cosegmentation revisited: Models and optimization,” presented at the ECCV: European Conference on Computer Vision, 2010, vol. 6312, pp. 465–479.","short":"S. Vicente, V. Kolmogorov, C. Rother, in:, Springer, 2010, pp. 465–479."},"date_updated":"2021-01-12T07:41:46Z","status":"public","conference":{"name":"ECCV: European Conference on Computer Vision"},"type":"conference","_id":"3201","date_created":"2018-12-11T12:01:59Z","doi":"10.1007/978-3-642-15552-9_34","volume":6312,"date_published":"2010-08-30T00:00:00Z","page":"465 - 479","day":"30","publication_status":"published","year":"2010","intvolume":" 6312","month":"08","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.330.6803df","open_access":"0"}],"alternative_title":["LNCS"],"quality_controlled":0,"publisher":"Springer","abstract":[{"lang":"eng","text":"The problem of cosegmentation consists of segmenting the same object (or objects of the same class) in two or more distinct images. Recently a number of different models have been proposed for this problem. However, no comparison of such models and corresponding optimization techniques has been done so far. We analyze three existing models: the L1 norm model of Rother et al. [1], the L2 norm model of Mukherjee et al. [2] and the "reward" model of Hochbaum and Singh [3]. We also study a new model, which is a straightforward extension of the Boykov-Jolly model for single image segmentation [4]. In terms of optimization, we use a Dual Decomposition (DD) technique in addition to optimization methods in [1,2]. Experiments show a significant improvement of DD over published methods. Our main conclusion, however, is that the new model is the best overall because it: (i) has fewest parameters; (ii) is most robust in practice, and (iii) can be optimized well with an efficient EM-style procedure."}]},{"title":"Leakage resilient ElGamal encryption","author":[{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"publist_id":"3444","extern":1,"date_updated":"2021-01-12T07:42:01Z","citation":{"ista":"Kiltz E, Pietrzak KZ. 2010. Leakage resilient ElGamal encryption. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 6477, 595–612.","chicago":"Kiltz, Eike, and Krzysztof Z Pietrzak. “Leakage Resilient ElGamal Encryption,” 6477:595–612. Springer, 2010. https://doi.org/10.1007/978-3-642-17373-8_34.","ieee":"E. Kiltz and K. Z. Pietrzak, “Leakage resilient ElGamal encryption,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, 2010, vol. 6477, pp. 595–612.","short":"E. Kiltz, K.Z. Pietrzak, in:, Springer, 2010, pp. 595–612.","apa":"Kiltz, E., & Pietrzak, K. Z. (2010). Leakage resilient ElGamal encryption (Vol. 6477, pp. 595–612). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Springer. https://doi.org/10.1007/978-3-642-17373-8_34","ama":"Kiltz E, Pietrzak KZ. Leakage resilient ElGamal encryption. In: Vol 6477. Springer; 2010:595-612. doi:10.1007/978-3-642-17373-8_34","mla":"Kiltz, Eike, and Krzysztof Z. Pietrzak. Leakage Resilient ElGamal Encryption. Vol. 6477, Springer, 2010, pp. 595–612, doi:10.1007/978-3-642-17373-8_34."},"status":"public","type":"conference","conference":{"name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"_id":"3237","doi":"10.1007/978-3-642-17373-8_34","date_published":"2010-01-14T00:00:00Z","volume":6477,"date_created":"2018-12-11T12:02:11Z","page":"595 - 612","day":"14","publication_status":"published","year":"2010","month":"01","intvolume":" 6477","quality_controlled":0,"alternative_title":["LNCS"],"publisher":"Springer","abstract":[{"text":"Blinding is a popular and well-known countermeasure to protect public-key cryptosystems against side-channel attacks. The high level idea is to randomize an exponentiation in order to prevent multiple measurements of the same operation on different data, as such measurements might allow the adversary to learn the secret exponent. Several variants of blinding have been proposed in the literature, using additive or multiplicative secret-sharing to blind either the base or the exponent. These countermeasures usually aim at preventing particular side-channel attacks (mostly power analysis) and come without any formal security guarantee. In this work we investigate to which extend blinding can provide provable security against a general class of side-channel attacks. Surprisingly, it turns out that in the context of public-key encryption some blinding techniques are more suited than others. In particular, we consider a multiplicatively blinded version of ElGamal public-key encryption where - we prove that the scheme, instantiated over bilinear groups of prime order p (where p - 1 is not smooth) is leakage resilient in the generic-group model. Here we consider the model of chosen-ciphertext security in the presence of continuous leakage, i.e., the scheme remains chosen-ciphertext secure even if with every decryption query the adversary can learn a bounded amount (roughly log(p)/2 bits) of arbitrary, adversarially chosen information about the computation. - we conjecture that the scheme, instantiated over arbitrary groups of prime order p (where p - 1 is not smooth) is leakage resilient. Previous to this work no encryption scheme secure against continuous leakage was known. Constructing a scheme that can be proven secure in the standard model remains an interesting open problem. ","lang":"eng"}]},{"extern":1,"citation":{"chicago":"Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Leakage Resilient Pseudorandom Functions and Side Channel Attacks on Feistel Networks,” 6223:21–40. Springer, 2010. https://doi.org/10.1007/978-3-642-14623-7_2.","ista":"Dodis Y, Pietrzak KZ. 2010. Leakage resilient pseudorandom functions and side channel attacks on feistel networks. CRYPTO: International Cryptology Conference, LNCS, vol. 6223, 21–40.","mla":"Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. Leakage Resilient Pseudorandom Functions and Side Channel Attacks on Feistel Networks. Vol. 6223, Springer, 2010, pp. 21–40, doi:10.1007/978-3-642-14623-7_2.","ieee":"Y. Dodis and K. Z. Pietrzak, “Leakage resilient pseudorandom functions and side channel attacks on feistel networks,” presented at the CRYPTO: International Cryptology Conference, 2010, vol. 6223, pp. 21–40.","short":"Y. Dodis, K.Z. Pietrzak, in:, Springer, 2010, pp. 21–40.","apa":"Dodis, Y., & Pietrzak, K. Z. (2010). Leakage resilient pseudorandom functions and side channel attacks on feistel networks (Vol. 6223, pp. 21–40). Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/10.1007/978-3-642-14623-7_2","ama":"Dodis Y, Pietrzak KZ. Leakage resilient pseudorandom functions and side channel attacks on feistel networks. In: Vol 6223. Springer; 2010:21-40. doi:10.1007/978-3-642-14623-7_2"},"date_updated":"2021-01-12T07:42:00Z","title":"Leakage resilient pseudorandom functions and side channel attacks on feistel networks","publist_id":"3445","author":[{"full_name":"Dodis, Yevgeniy","last_name":"Dodis","first_name":"Yevgeniy"},{"last_name":"Pietrzak","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3235","status":"public","conference":{"name":"CRYPTO: International Cryptology Conference"},"type":"conference","day":"30","year":"2010","publication_status":"published","date_created":"2018-12-11T12:02:10Z","date_published":"2010-09-30T00:00:00Z","volume":6223,"doi":"10.1007/978-3-642-14623-7_2","page":"21 - 40","abstract":[{"lang":"eng","text":"A cryptographic primitive is leakage-resilient, if it remains secure even if an adversary can learn a bounded amount of arbitrary information about the computation with every invocation. As a consequence, the physical implementation of a leakage-resilient primitive is secure against every side-channel as long as the amount of information leaked per invocation is bounded. In this paper we prove positive and negative results about the feasibility of constructing leakage-resilient pseudorandom functions and permutations (i.e. block-ciphers). Our results are three fold: 1. We construct (from any standard PRF) a PRF which satisfies a relaxed notion of leakage-resilience where (1) the leakage function is fixed (and not adaptively chosen with each query.) and (2) the computation is split into several steps which leak individually (a "step" will be the invocation of the underlying PRF.) 2. We prove that a Feistel network with a super-logarithmic number of rounds, each instantiated with a leakage-resilient PRF, is a leakage resilient PRP. This reduction also holds for the non-adaptive notion just discussed, we thus get a block-cipher which is leakage-resilient (against non-adaptive leakage). 3. We propose generic side-channel attacks against Feistel networks. The attacks are generic in the sense that they work for any round functions (e.g. uniformly random functions) and only require some simple leakage from the inputs to the round functions. For example we show how to invert an r round Feistel network over 2n bits making 4•(n+1) r-2 forward queries, if with each query we are also given as leakage the Hamming weight of the inputs to the r round functions. This complements the result from the previous item showing that a super-constant number of rounds is necessary."}],"intvolume":" 6223","month":"09","publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":0},{"day":"26","publication_status":"published","year":"2010","date_created":"2018-12-11T12:02:10Z","doi":"10.1007/978-3-642-11799-2_21","volume":5978,"date_published":"2010-03-26T00:00:00Z","page":"343 - 360","abstract":[{"lang":"eng","text":"The strongest standard security notion for digital signature schemes is unforgeability under chosen message attacks. In practice, however, this notion can be insufficient due to "side-channel attacks" which exploit leakage of information about the secret internal state. In this work we put forward the notion of "leakage-resilient signatures," which strengthens the standard security notion by giving the adversary the additional power to learn a bounded amount of arbitrary information about the secret state that was accessed during every signature generation. This notion naturally implies security against all side-channel attacks as long as the amount of information leaked on each invocation is bounded and "only computation leaks information." The main result of this paper is a construction which gives a (tree-based, stateful) leakage-resilient signature scheme based on any 3-time signature scheme. The amount of information that our scheme can safely leak per signature generation is 1/3 of the information the underlying 3-time signature scheme can leak in total. Signature schemes that remain secure even if a bounded total amount of information is leaked were recently constructed, hence instantiating our construction with these schemes gives the first constructions of provably secure leakage-resilient signature schemes. The above construction assumes that the signing algorithm can sample truly random bits, and thus an implementation would need some special hardware (randomness gates). Simply generating this randomness using a leakage-resilient stream-cipher will in general not work. Our second contribution is a sound general principle to replace uniform random bits in any leakage-resilient construction with pseudorandom ones: run two leakage-resilient stream-ciphers (with independent keys) in parallel and then apply a two-source extractor to their outputs. "}],"intvolume":" 5978","month":"03","quality_controlled":0,"publisher":"Springer","alternative_title":["LNCS"],"extern":1,"citation":{"chicago":"Faust, Sebastian, Eike Kiltz, Krzysztof Z Pietrzak, and Guy Rothblum. “Leakage Resilient Signatures,” 5978:343–60. Springer, 2010. https://doi.org/10.1007/978-3-642-11799-2_21.","ista":"Faust S, Kiltz E, Pietrzak KZ, Rothblum G. 2010. Leakage resilient signatures. TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 343–360.","mla":"Faust, Sebastian, et al. Leakage Resilient Signatures. Vol. 5978, Springer, 2010, pp. 343–60, doi:10.1007/978-3-642-11799-2_21.","short":"S. Faust, E. Kiltz, K.Z. Pietrzak, G. Rothblum, in:, Springer, 2010, pp. 343–360.","ieee":"S. Faust, E. Kiltz, K. Z. Pietrzak, and G. Rothblum, “Leakage resilient signatures,” presented at the TCC: Theory of Cryptography Conference, 2010, vol. 5978, pp. 343–360.","apa":"Faust, S., Kiltz, E., Pietrzak, K. Z., & Rothblum, G. (2010). Leakage resilient signatures (Vol. 5978, pp. 343–360). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-11799-2_21","ama":"Faust S, Kiltz E, Pietrzak KZ, Rothblum G. Leakage resilient signatures. In: Vol 5978. Springer; 2010:343-360. doi:10.1007/978-3-642-11799-2_21"},"date_updated":"2021-01-12T07:41:59Z","title":"Leakage resilient signatures","author":[{"first_name":"Sebastian","full_name":"Faust, Sebastian","last_name":"Faust"},{"full_name":"Kiltz, Eike","last_name":"Kiltz","first_name":"Eike"},{"full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guy","full_name":"Rothblum, Guy N","last_name":"Rothblum"}],"publist_id":"3447","_id":"3234","status":"public","conference":{"name":"TCC: Theory of Cryptography Conference"},"type":"conference"},{"year":"2010","publication_status":"published","day":"26","page":"1 - 18","date_published":"2010-03-26T00:00:00Z","volume":5978,"doi":"10.1007/978-3-642-11799-2_1","date_created":"2018-12-11T12:02:10Z","abstract":[{"lang":"eng","text":"We present a general parallel-repetition theorem with an efficient reduction. As a corollary of this theorem we establish that parallel repetition reduces the soundness error at an exponential rate in any public-coin argument, and more generally, any argument where the verifier's messages, but not necessarily its decision to accept or reject, can be efficiently simulated with noticeable probability."}],"quality_controlled":0,"publisher":"Springer","alternative_title":["LNCS"],"month":"03","intvolume":" 5978","date_updated":"2021-01-12T07:41:59Z","citation":{"chicago":"Håstad, Johan, Rafael Pass, Douglas Wikström, and Krzysztof Z Pietrzak. “An Efficient Parallel Repetition Theorem,” 5978:1–18. Springer, 2010. https://doi.org/10.1007/978-3-642-11799-2_1.","ista":"Håstad J, Pass R, Wikström D, Pietrzak KZ. 2010. An efficient parallel repetition theorem. TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 1–18.","mla":"Håstad, Johan, et al. An Efficient Parallel Repetition Theorem. Vol. 5978, Springer, 2010, pp. 1–18, doi:10.1007/978-3-642-11799-2_1.","short":"J. Håstad, R. Pass, D. Wikström, K.Z. Pietrzak, in:, Springer, 2010, pp. 1–18.","ieee":"J. Håstad, R. Pass, D. Wikström, and K. Z. Pietrzak, “An efficient parallel repetition theorem,” presented at the TCC: Theory of Cryptography Conference, 2010, vol. 5978, pp. 1–18.","ama":"Håstad J, Pass R, Wikström D, Pietrzak KZ. An efficient parallel repetition theorem. In: Vol 5978. Springer; 2010:1-18. doi:10.1007/978-3-642-11799-2_1","apa":"Håstad, J., Pass, R., Wikström, D., & Pietrzak, K. Z. (2010). An efficient parallel repetition theorem (Vol. 5978, pp. 1–18). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-11799-2_1"},"extern":1,"publist_id":"3446","author":[{"first_name":"Johan","last_name":"Håstad","full_name":"Håstad, Johan"},{"first_name":"Rafael","full_name":"Pass, Rafael","last_name":"Pass"},{"full_name":"Wikström, Douglas","last_name":"Wikström","first_name":"Douglas"},{"last_name":"Pietrzak","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"title":"An efficient parallel repetition theorem","_id":"3233","type":"conference","conference":{"name":"TCC: Theory of Cryptography Conference"},"status":"public"},{"extern":1,"date_updated":"2023-02-23T11:19:20Z","citation":{"short":"V. Kolmogorov, in:, Neural Information Processing Systems, 2010.","ieee":"V. Kolmogorov, “Generalized roof duality and bisubmodular functions,” presented at the Neural Information Processing Systems, 2010.","apa":"Kolmogorov, V. (2010). Generalized roof duality and bisubmodular functions. Presented at the Neural Information Processing Systems, Neural Information Processing Systems.","ama":"Kolmogorov V. Generalized roof duality and bisubmodular functions. In: Neural Information Processing Systems; 2010.","mla":"Kolmogorov, Vladimir. Generalized Roof Duality and Bisubmodular Functions. Neural Information Processing Systems, 2010.","ista":"Kolmogorov V. 2010. Generalized roof duality and bisubmodular functions. Neural Information Processing Systems.","chicago":"Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Neural Information Processing Systems, 2010."},"title":"Generalized roof duality and bisubmodular functions","publist_id":"3802","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov"}],"_id":"2934","status":"public","type":"conference","conference":{"name":"Neural Information Processing Systems"},"day":"01","publication_status":"published","year":"2010","related_material":{"record":[{"relation":"later_version","status":"public","id":"3257"}]},"date_published":"2010-12-01T00:00:00Z","date_created":"2018-12-11T12:00:25Z","month":"12","quality_controlled":0,"publisher":"Neural Information Processing Systems"},{"_id":"3294","type":"journal_article","status":"public","date_updated":"2021-01-12T07:42:27Z","citation":{"ieee":"A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, and O. Siddiqi, “Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila,” PNAS, vol. 107, no. 21. National Academy of Sciences, pp. 9855–60, 2010.","short":"A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, O. Siddiqi, PNAS 107 (2010) 9855–60.","ama":"Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. PNAS. 2010;107(21):9855-9860. doi:10.1073/pnas.1003856107","apa":"Iyengar, A., Chakraborty Tuhin, S., Goswami, S., Wu, C., & Siddiqi, O. (2010). Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1003856107","mla":"Iyengar, Atulya, et al. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron Coding in Drosophila.” PNAS, vol. 107, no. 21, National Academy of Sciences, 2010, pp. 9855–60, doi:10.1073/pnas.1003856107.","ista":"Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. 2010. Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. PNAS. 107(21), 9855–60.","chicago":"Iyengar, Atulya, Subhra Chakraborty Tuhin, Sarit Goswami, Chun Wu, and Obaid Siddiqi. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron Coding in Drosophila.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1003856107."},"extern":1,"author":[{"full_name":"Iyengar, Atulya","last_name":"Iyengar","first_name":"Atulya"},{"full_name":"Chakraborty Tuhin, Subhra","last_name":"Chakraborty Tuhin","first_name":"Subhra"},{"id":"3A578F32-F248-11E8-B48F-1D18A9856A87","first_name":"Sarit","full_name":"Sarit Goswami","last_name":"Goswami"},{"last_name":"Wu","full_name":"Wu, Chun Fang","first_name":"Chun"},{"first_name":"Obaid","full_name":"Siddiqi, Obaid","last_name":"Siddiqi"}],"publist_id":"3347","title":"Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila","abstract":[{"text":"Olfactory responses of Drosophila undergo pronounced changes after eclosion. The flies develop attraction to odors to which they are exposed and aversion to other odors. Behavioral adaptation is correlated with changes in the firing pattern of olfactory receptor neurons (ORNs). In this article, we present an information-theoretic analysis of the firing pattern of ORNs. Flies reared in a synthetic odorless medium were transferred after eclosion to three different media: (i) a synthetic medium relatively devoid of odor cues, (ii) synthetic medium infused with a single odorant, and (iii) complex cornmeal medium rich in odors. Recordings were made from an identified sensillum (type II), and the Jensen-Shannon divergence (D(JS)) was used to assess quantitatively the differences between ensemble spike responses to different odors. Analysis shows that prolonged exposure to ethyl acetate and several related esters increases sensitivity to these esters but does not improve the ability of the fly to distinguish between them. Flies exposed to cornmeal display varied sensitivity to these odorants and at the same time develop greater capacity to distinguish between odors. Deprivation of odor experience on an odorless synthetic medium leads to a loss of both sensitivity and acuity. Rich olfactory experience thus helps to shape the ORNs response and enhances its discriminative power. The experiments presented here demonstrate an experience-dependent adaptation at the level of the receptor neuron.","lang":"eng"}],"publisher":"National Academy of Sciences","quality_controlled":0,"month":"01","intvolume":" 107","year":"2010","publication_status":"published","day":"01","publication":"PNAS","page":"9855 - 60","volume":107,"issue":"21","date_published":"2010-01-01T00:00:00Z","doi":"10.1073/pnas.1003856107","date_created":"2018-12-11T12:02:31Z"},{"author":[{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publist_id":"3345","article_processing_charge":"No","title":"Animating physical phenomena with embedded surface meshes","supervisor":[{"full_name":"Essa, Irfan","last_name":"Essa","first_name":"Irfan"},{"first_name":"Karen","last_name":"Liu","full_name":"Liu, Karen"},{"last_name":"Mucha","full_name":"Mucha, Peter","first_name":"Peter"},{"first_name":"Jarek","last_name":"Rossignac","full_name":"Rossignac, Jarek"}],"date_updated":"2023-02-23T11:21:00Z","citation":{"chicago":"Wojtan, Chris. “Animating Physical Phenomena with Embedded Surface Meshes.” Georgia Institute of Technology, 2010.","ista":"Wojtan C. 2010. Animating physical phenomena with embedded surface meshes. Georgia Institute of Technology.","mla":"Wojtan, Chris. Animating Physical Phenomena with Embedded Surface Meshes. Georgia Institute of Technology, 2010, pp. 1–175.","apa":"Wojtan, C. (2010). Animating physical phenomena with embedded surface meshes. Georgia Institute of Technology.","ama":"Wojtan C. Animating physical phenomena with embedded surface meshes. 2010:1-175.","short":"C. Wojtan, Animating Physical Phenomena with Embedded Surface Meshes, Georgia Institute of Technology, 2010.","ieee":"C. Wojtan, “Animating physical phenomena with embedded surface meshes,” Georgia Institute of Technology, 2010."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"dissertation","status":"public","_id":"3296","page":"1 - 175","date_published":"2010-11-17T00:00:00Z","date_created":"2018-12-11T12:02:31Z","year":"2010","publication_status":"published","day":"17","language":[{"iso":"eng"}],"publisher":"Georgia Institute of Technology","main_file_link":[{"url":"http://hdl.handle.net/1853/37256"}],"month":"11","abstract":[{"lang":"eng","text":"Accurate computational representations of highly deformable surfaces are indispensable in the fields of computer animation, medical simulation, computer vision, digital modeling, and computational physics. The focus of this dissertation is on the animation of physics-based phenomena with highly detailed deformable surfaces represented by triangle meshes.\r\n \r\nWe first present results from an algorithm that generates continuum mechanics animations with intricate surface features. This method combines a finite element method with a tetrahedral mesh generator and a high resolution surface mesh, and it is orders of magnitude more efficient than previous approaches. Next, we present an efficient solution for the challenging problem of computing topological changes in detailed dynamic surface meshes. We then introduce a new physics-inspired surface tracking algorithm that is capable of preserving arbitrarily thin features and reproducing realistic fine-scale topological changes like Rayleigh-Plateau instabilities. This physics-inspired surface tracking technique also opens the door for a unique coupling between surficial finite element methods and volumetric finite difference methods, in order to simulate liquid surface tension phenomena more efficiently than any previous method. Due to its dramatic increase in computational resolution and efficiency, this method yielded the first computer simulations of a fully developed crown splash with droplet pinch off."}],"oa_version":"None"},{"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/0812.2724","open_access":"1"}],"quality_controlled":0,"publisher":"Institute of Mathematical Statistics","intvolume":" 20","month":"01","abstract":[{"text":"We use methods from combinatorics and algebraic statistics to study analogues of birth-and-death processes that have as their state space a finite subset of the m-dimensional lattice and for which the m matrices that record the transition probabilities in each of the lattice directions commute pairwise. One reason such processes are of interest is that the transition matrix is straightforward to diagonalize, and hence it is easy to compute n step transition probabilities. The set of commuting birth-and-death processes decomposes as a union of toric varieties, with the main component being the closure of all processes whose nearest neighbor transition probabilities are positive. We exhibit an explicit monomial parametrization for this main component, and we explore the boundary components using primary decomposition.","lang":"eng"}],"acknowledgement":"Steven N. Evans was supported in part by NSF Grants DMS-04-05778 and DMS-09-07630. Bernd Sturmfels was supported in part by NSF Grants DMS-04-56960 and DMS-07-57236. Caroline Uhler was supported by an International Fulbright Science and Technology Fellowship.","page":"238 - 266","date_created":"2018-12-11T12:02:35Z","volume":20,"date_published":"2010-01-01T00:00:00Z","doi":"10.1214/09-AAP615","year":"2010","publication_status":"published","publication":"The Annals of Applied Probability","day":"01","type":"journal_article","status":"public","_id":"3306","author":[{"full_name":"Evans, Steven N","last_name":"Evans","first_name":"Steven"},{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Caroline Uhler","last_name":"Uhler"}],"publist_id":"3334","title":"Commuting birth and death processes","citation":{"ama":"Evans S, Sturmfels B, Uhler C. Commuting birth and death processes. The Annals of Applied Probability. 2010;20:238-266. doi:10.1214/09-AAP615","apa":"Evans, S., Sturmfels, B., & Uhler, C. (2010). Commuting birth and death processes. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/09-AAP615","short":"S. Evans, B. Sturmfels, C. Uhler, The Annals of Applied Probability 20 (2010) 238–266.","ieee":"S. Evans, B. Sturmfels, and C. Uhler, “Commuting birth and death processes,” The Annals of Applied Probability, vol. 20. Institute of Mathematical Statistics, pp. 238–266, 2010.","mla":"Evans, Steven, et al. “Commuting Birth and Death Processes.” The Annals of Applied Probability, vol. 20, Institute of Mathematical Statistics, 2010, pp. 238–66, doi:10.1214/09-AAP615.","ista":"Evans S, Sturmfels B, Uhler C. 2010. Commuting birth and death processes. The Annals of Applied Probability. 20, 238–266.","chicago":"Evans, Steven, Bernd Sturmfels, and Caroline Uhler. “Commuting Birth and Death Processes.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/09-AAP615."},"date_updated":"2021-01-12T07:42:32Z","extern":1},{"acknowledgement":"B. Sturmfels is supported in part by NSF grants DMS-0456960 and DMS-0757236. C. Uhler is supported by an International Fulbright Science and Technology Fellowship.","abstract":[{"text":"We study multivariate normal models that are described by linear constraints on the inverse of the covariance matrix. Maximum likelihood estimation for such models leads to the problem of maximizing the determinant function over a spectrahedron, and to the problem of characterizing the image of the positive definite cone under an arbitrary linear projection. These problems at the interface of statistics and optimization are here examined from the perspective of convex algebraic geometry.","lang":"eng"}],"intvolume":" 62","month":"08","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/0906.3529","open_access":"1"}],"quality_controlled":0,"publisher":"Springer","publication":"Annals of the Institute of Statistical Mathematics","day":"01","publication_status":"published","year":"2010","date_created":"2018-12-11T12:02:35Z","volume":62,"doi":"10.1007/s10463-010-0295-4","date_published":"2010-08-01T00:00:00Z","issue":"4","page":"603 - 638","_id":"3308","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T07:42:33Z","citation":{"mla":"Sturmfels, Bernd, and Caroline Uhler. “Multivariate Gaussians, Semidefinite Matrix Completion, and Convex Algebraic Geometry.” Annals of the Institute of Statistical Mathematics, vol. 62, no. 4, Springer, 2010, pp. 603–38, doi:10.1007/s10463-010-0295-4.","ama":"Sturmfels B, Uhler C. Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry. Annals of the Institute of Statistical Mathematics. 2010;62(4):603-638. doi:10.1007/s10463-010-0295-4","apa":"Sturmfels, B., & Uhler, C. (2010). Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry. Annals of the Institute of Statistical Mathematics. Springer. https://doi.org/10.1007/s10463-010-0295-4","short":"B. Sturmfels, C. Uhler, Annals of the Institute of Statistical Mathematics 62 (2010) 603–638.","ieee":"B. Sturmfels and C. Uhler, “Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry,” Annals of the Institute of Statistical Mathematics, vol. 62, no. 4. Springer, pp. 603–638, 2010.","chicago":"Sturmfels, Bernd, and Caroline Uhler. “Multivariate Gaussians, Semidefinite Matrix Completion, and Convex Algebraic Geometry.” Annals of the Institute of Statistical Mathematics. Springer, 2010. https://doi.org/10.1007/s10463-010-0295-4.","ista":"Sturmfels B, Uhler C. 2010. Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry. Annals of the Institute of Statistical Mathematics. 62(4), 603–638."},"title":"Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry","publist_id":"3332","author":[{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Uhler","full_name":"Caroline Uhler","orcid":"0000-0002-7008-0216"}]},{"intvolume":" 22","month":"03","main_file_link":[{"url":"http://infoscience.epfl.ch/record/117513/files/PLDI_paper.pdf","open_access":"0"}],"quality_controlled":0,"publisher":"Springer","acknowledgement":"This research was supported by the Swiss National Science Foundation. This paper is an extended and revised version of our previous work on model checking transactional memories.","abstract":[{"text":"Model checking transactional memories (TMs) is difficult because of the unbounded number, length, and delay of concurrent transactions, as well as the unbounded size of the memory. We show that, under certain conditions satisfied by most TMs we know of, the model checking problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several TMs, including two-phase locking, DSTM, and TL2. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom. Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the TMs mentioned above. In a first step we show that every TM that enjoys certain structural properties either violates a requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step, we use a model checker to prove the requirement for the TM applied to a most general program with two threads and two variables. In the safety case, the model checker checks language inclusion between two finite-state transition systems, a nondeterministic transition system representing the given TM applied to a most general program, and a deterministic transition system representing a most liberal safe TM applied to the same program. The given TM transition system is nondeterministic because a TM can be used with different contention managers, which resolve conflicts differently. In the liveness case, the model checker analyzes fairness conditions on the given TM transition system.","lang":"eng"}],"date_created":"2018-12-11T12:03:08Z","doi":"10.1007/s00446-009-0092-6","volume":22,"issue":"3","date_published":"2010-03-01T00:00:00Z","page":"129 - 145","publication":"Distributed Computing","day":"01","year":"2010","publication_status":"published","pubrep_id":"74","status":"public","type":"journal_article","_id":"3402","title":"Model checking transactional memories","author":[{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"},{"id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu","full_name":"Vasu Singh","last_name":"Singh"}],"publist_id":"3000","extern":1,"citation":{"ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Model checking transactional memories,” Distributed Computing, vol. 22, no. 3. Springer, pp. 129–145, 2010.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, Distributed Computing 22 (2010) 129–145.","ama":"Guerraoui R, Henzinger TA, Singh V. Model checking transactional memories. Distributed Computing. 2010;22(3):129-145. doi:10.1007/s00446-009-0092-6","apa":"Guerraoui, R., Henzinger, T. A., & Singh, V. (2010). Model checking transactional memories. Distributed Computing. Springer. https://doi.org/10.1007/s00446-009-0092-6","mla":"Guerraoui, Rachid, et al. “Model Checking Transactional Memories.” Distributed Computing, vol. 22, no. 3, Springer, 2010, pp. 129–45, doi:10.1007/s00446-009-0092-6.","ista":"Guerraoui R, Henzinger TA, Singh V. 2010. Model checking transactional memories. Distributed Computing. 22(3), 129–145.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Model Checking Transactional Memories.” Distributed Computing. Springer, 2010. https://doi.org/10.1007/s00446-009-0092-6."},"date_updated":"2021-01-12T07:43:14Z"},{"date_created":"2018-12-11T12:03:08Z","issue":"6","volume":68,"date_published":"2010-12-22T00:00:00Z","doi":"10.1016/j.neuron.2010.12.011","page":"1015 - 1016","publication":"Neuron","day":"22","year":"2010","publication_status":"published","intvolume":" 68","month":"12","quality_controlled":0,"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Rate remapping is a conjunctive code that potentially enables hippocampal place cells to jointly represent spatial and nonspatial information. In this issue of Neuron, Rennó-Costa et al. introduce a theoretical model wherein the convergence of the medial and lateral entorhinal excitatory inputs, combined with local inhibition, explains hippocampal rate remapping. © 2010 Elsevier Inc."}],"title":"Rate remapping: When the code goes beyond space (preview)","author":[{"full_name":"Pleydell-Bouverie, Barty","last_name":"Pleydell Bouverie","first_name":"Barty"},{"last_name":"Csicsvari","full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2999","extern":1,"citation":{"short":"B. Pleydell Bouverie, J.L. Csicsvari, Neuron 68 (2010) 1015–1016.","ieee":"B. Pleydell Bouverie and J. L. Csicsvari, “Rate remapping: When the code goes beyond space (preview),” Neuron, vol. 68, no. 6. Elsevier, pp. 1015–1016, 2010.","ama":"Pleydell Bouverie B, Csicsvari JL. Rate remapping: When the code goes beyond space (preview). Neuron. 2010;68(6):1015-1016. doi:10.1016/j.neuron.2010.12.011","apa":"Pleydell Bouverie, B., & Csicsvari, J. L. (2010). Rate remapping: When the code goes beyond space (preview). Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.12.011","mla":"Pleydell Bouverie, Barty, and Jozsef L. Csicsvari. “Rate Remapping: When the Code Goes beyond Space (Preview).” Neuron, vol. 68, no. 6, Elsevier, 2010, pp. 1015–16, doi:10.1016/j.neuron.2010.12.011.","ista":"Pleydell Bouverie B, Csicsvari JL. 2010. Rate remapping: When the code goes beyond space (preview). Neuron. 68(6), 1015–1016.","chicago":"Pleydell Bouverie, Barty, and Jozsef L Csicsvari. “Rate Remapping: When the Code Goes beyond Space (Preview).” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.12.011."},"date_updated":"2019-05-10T12:19:51Z","status":"public","type":"review","_id":"3403"},{"author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik","last_name":"Tkacik"}],"publist_id":"2970","title":"Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics","citation":{"mla":"Tkačik, Gašper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics. Elsevier, 2010.","ieee":"G. Tkačik, “Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, 2010.","short":"G. Tkačik, in:, Elsevier, 2010.","ama":"Tkačik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.","apa":"Tkačik, G. (2010). Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, Elsevier.","chicago":"Tkačik, Gašper. “Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics.” Elsevier, 2010.","ista":"Tkačik G. 2010. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Summer School on Quantitative Evolutionary and Comparative Genomics."},"date_updated":"2021-01-12T07:43:25Z","extern":1,"type":"conference","conference":{"name":"Summer School on Quantitative Evolutionary and Comparative Genomics"},"status":"public","_id":"3430","date_published":"2010-06-22T00:00:00Z","date_created":"2018-12-11T12:03:17Z","year":"2010","publication_status":"published","day":"22","quality_controlled":0,"publisher":"Elsevier","oa":1,"main_file_link":[{"url":"http://arxiv.org/pdf/1006.4291","open_access":"1"}],"month":"06","abstract":[{"lang":"eng","text":"These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes."}]},{"day":"20","language":[{"iso":"eng"}],"publication":"Knee Surgery, Sports Traumatology, Arthroscopy","publication_status":"published","year":"2010","date_published":"2010-08-20T00:00:00Z","doi":"10.1007/s00167-010-1227-9","issue":"12","volume":18,"date_created":"2018-12-11T12:03:39Z","page":"1792 - 1794","oa_version":"None","abstract":[{"text":"Purpose\r\nCalcifying tendinitis is a common condition of the shoulder. In many cases, arthroscopic reduction in the deposit is indicated. The localization of the deposit is sometimes challenging and time-consuming. Pre-operative ultrasound (US)-guided needle placement in the deposit and pre-operative US marking of the deposit at the skin with a ballpoint are described and recommended methods to alleviate the procedure without using ionizing radiation by fluoroscopy.\r\nMethods\r\nIntra-operative sonography of the shoulder is introduced as a new method to localize the calcific deposit with high accuracy. After standard arthroscopic buresectomy, the surgeon performs an ultrasound examination under sterile conditions to localize the deposits. A ventral longitudinal US section is recommended, and the upper arm is rotated until the deposit is visible. Subsequently, perpendicular to the skin at the position of the transducer, a needle is introduced under arthroscopic and ultrasound visualization to puncture the deposit.\r\nResults\r\nThe presence of snow-white crystals at the tip of the needle proves the exact localization. Consecutively, the curettage can be accomplished. Another intra-operative sonography evaluates possible calcific remnants and the tendon structure.\r\nConclusion\r\nThis new technique may alleviate arthroscopic calcific deposit curettage by visualizing the deposit without using ionizing radiation. Additionally, soft tissue damage due to decreased number of punctures to detect the deposit may be achieved. Both factors may contribute to reduced operation time.","lang":"eng"}],"month":"08","intvolume":" 18","scopus_import":1,"publisher":"Springer","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sabeti Aschraf, M., C. Gonano, E. Nemecek, Lisa Cichocki, and C. Schueller Weidekamm. “Intra-Operative Ultrasound Facilitates the Localization of the Calcific Deposit during Arthroscopic Treatment of Calcifying Tendinitis.” Knee Surgery, Sports Traumatology, Arthroscopy. Springer, 2010. https://doi.org/10.1007/s00167-010-1227-9.","ista":"Sabeti Aschraf M, Gonano C, Nemecek E, Cichocki L, Schueller Weidekamm C. 2010. Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis. Knee Surgery, Sports Traumatology, Arthroscopy. 18(12), 1792–1794.","mla":"Sabeti Aschraf, M., et al. “Intra-Operative Ultrasound Facilitates the Localization of the Calcific Deposit during Arthroscopic Treatment of Calcifying Tendinitis.” Knee Surgery, Sports Traumatology, Arthroscopy, vol. 18, no. 12, Springer, 2010, pp. 1792–94, doi:10.1007/s00167-010-1227-9.","apa":"Sabeti Aschraf, M., Gonano, C., Nemecek, E., Cichocki, L., & Schueller Weidekamm, C. (2010). Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis. Knee Surgery, Sports Traumatology, Arthroscopy. Springer. https://doi.org/10.1007/s00167-010-1227-9","ama":"Sabeti Aschraf M, Gonano C, Nemecek E, Cichocki L, Schueller Weidekamm C. Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis. Knee Surgery, Sports Traumatology, Arthroscopy. 2010;18(12):1792-1794. doi:10.1007/s00167-010-1227-9","short":"M. Sabeti Aschraf, C. Gonano, E. Nemecek, L. Cichocki, C. Schueller Weidekamm, Knee Surgery, Sports Traumatology, Arthroscopy 18 (2010) 1792–1794.","ieee":"M. Sabeti Aschraf, C. Gonano, E. Nemecek, L. Cichocki, and C. Schueller Weidekamm, “Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis,” Knee Surgery, Sports Traumatology, Arthroscopy, vol. 18, no. 12. Springer, pp. 1792–1794, 2010."},"date_updated":"2021-01-12T07:43:51Z","title":"Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis","publist_id":"2889","author":[{"last_name":"Sabeti Aschraf","full_name":"Sabeti Aschraf, M.","first_name":"M."},{"first_name":"C.","full_name":"Gonano, C.","last_name":"Gonano"},{"last_name":"Nemecek","full_name":"Nemecek, E.","first_name":"E."},{"full_name":"Cichocki, Lisa","last_name":"Cichocki","first_name":"Lisa","id":"3BC78B60-F248-11E8-B48F-1D18A9856A87"},{"first_name":"C.","full_name":"Schueller Weidekamm, C.","last_name":"Schueller Weidekamm"}],"_id":"3498","status":"public","type":"journal_article"},{"title":"Imaging zebrafish embryos by two-photon excitation time-lapse microscopy","publist_id":"2791","author":[{"last_name":"Carvalho","full_name":"Carvalho, Lara","first_name":"Lara"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Carvalho L, Heisenberg C-PJ. 2010. Imaging zebrafish embryos by two-photon excitation time-lapse microscopy. Methods in Molecular Biology. 546(Part 5), 273–287.","chicago":"Carvalho, Lara, and Carl-Philipp J Heisenberg. “Imaging Zebrafish Embryos by Two-Photon Excitation Time-Lapse Microscopy.” Methods in Molecular Biology. Springer, 2010. https://doi.org/10.1007/978-1-60327-977-2_17.","ieee":"L. Carvalho and C.-P. J. Heisenberg, “Imaging zebrafish embryos by two-photon excitation time-lapse microscopy,” Methods in Molecular Biology, vol. 546, no. Part 5. Springer, pp. 273–287, 2010.","short":"L. Carvalho, C.-P.J. Heisenberg, Methods in Molecular Biology 546 (2010) 273–287.","ama":"Carvalho L, Heisenberg C-PJ. Imaging zebrafish embryos by two-photon excitation time-lapse microscopy. Methods in Molecular Biology. 2010;546(Part 5):273-287. doi:10.1007/978-1-60327-977-2_17","apa":"Carvalho, L., & Heisenberg, C.-P. J. (2010). Imaging zebrafish embryos by two-photon excitation time-lapse microscopy. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-60327-977-2_17","mla":"Carvalho, Lara, and Carl-Philipp J. Heisenberg. “Imaging Zebrafish Embryos by Two-Photon Excitation Time-Lapse Microscopy.” Methods in Molecular Biology, vol. 546, no. Part 5, Springer, 2010, pp. 273–87, doi:10.1007/978-1-60327-977-2_17."},"date_updated":"2021-01-12T07:44:31Z","status":"public","type":"journal_article","_id":"3592","date_published":"2010-01-01T00:00:00Z","doi":"10.1007/978-1-60327-977-2_17","volume":546,"issue":"Part 5","date_created":"2018-12-11T12:04:08Z","page":"273 - 287","day":"01","publication":"Methods in Molecular Biology","language":[{"iso":"eng"}],"year":"2010","publication_status":"published","month":"01","intvolume":" 546","publisher":"Springer","oa_version":"None","abstract":[{"text":"The zebrafish is a favorite model organism to study tissue morphogenesis during development at a subcellular level. This largely results from the fact that zebrafish embryos are transparent and thus accessible to various imaging techniques, such as confocal and two-photon excitation (2PE) microscopy. In particular, 2PE microscopy has been shown to be useful for imaging deep cell layers within the embryo and following tissue morphogenesis over long periods. This chapter describes how to use 2PE microscopy to study morphogenetic movements during early zebrafish embryonic development, providing a general blueprint for its use in zebrafish.","lang":"eng"}]},{"title":"Topic models for semantic video compression","author":[{"full_name":"Wanke,Jörn","last_name":"Wanke","first_name":"Jörn"},{"first_name":"Adrian","full_name":"Ulges, Adrian","last_name":"Ulges"},{"last_name":"Lampert","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Thomas","full_name":"Breuel,Thomas M","last_name":"Breuel"}],"publist_id":"2705","extern":1,"citation":{"chicago":"Wanke, Jörn, Adrian Ulges, Christoph Lampert, and Thomas Breuel. “Topic Models for Semantic Video Compression,” 275–84. ACM, 2010. https://doi.org/10.1145/1743384.1743433.","ista":"Wanke J, Ulges A, Lampert C, Breuel T. 2010. Topic models for semantic video compression. MIR: Multimedia Information Retrieval, 275–284.","mla":"Wanke, Jörn, et al. Topic Models for Semantic Video Compression. ACM, 2010, pp. 275–84, doi:10.1145/1743384.1743433.","short":"J. Wanke, A. Ulges, C. Lampert, T. Breuel, in:, ACM, 2010, pp. 275–284.","ieee":"J. Wanke, A. Ulges, C. Lampert, and T. Breuel, “Topic models for semantic video compression,” presented at the MIR: Multimedia Information Retrieval, 2010, pp. 275–284.","apa":"Wanke, J., Ulges, A., Lampert, C., & Breuel, T. (2010). Topic models for semantic video compression (pp. 275–284). Presented at the MIR: Multimedia Information Retrieval, ACM. https://doi.org/10.1145/1743384.1743433","ama":"Wanke J, Ulges A, Lampert C, Breuel T. Topic models for semantic video compression. In: ACM; 2010:275-284. doi:10.1145/1743384.1743433"},"date_updated":"2021-01-12T07:45:04Z","status":"public","conference":{"name":"MIR: Multimedia Information Retrieval"},"type":"conference","_id":"3676","date_created":"2018-12-11T12:04:34Z","doi":"10.1145/1743384.1743433","date_published":"2010-03-31T00:00:00Z","page":"275 - 284","day":"31","publication_status":"published","year":"2010","month":"03","main_file_link":[{"url":"http://pub.ist.ac.at/~chl/papers/wanke-mir2010.pdf","open_access":"0"}],"publisher":"ACM","quality_controlled":0,"abstract":[{"text":"Most state-of-the-art systems for content-based video understanding tasks require video content to be represented as collections of many low-level descriptors, e.g. as histograms of the color, texture or motion in local image regions.\n\nIn order to preserve as much of the information contained in the original video as possible, these representations are typically high-dimensional, which conflicts with the aim for compact descriptors that would allow better efficiency and lower storage requirements.\nIn this paper, we address the problem of semantic com- pression of video, i.e. the reduction of low-level descriptors to a small number of dimensions while preserving most of the semantic information. For this, we adapt topic models – which have previously been used as compact representations of still images – to take into account the temporal structure of a video, as well as multi-modal components such as motion information.\n\nExperiments on a large-scale collection of YouTube videos show that we can achieve a compression ratio of 20 : 1 compared to ordinary histogram representations and at least 2 : 1 compared to other dimensionality reduction techniques without significant loss of prediction accuracy. Also, improvements are demonstrated for our video-specific extensions modeling temporal structure and multiple modalities.","lang":"eng"}]},{"intvolume":" 88","month":"06","quality_controlled":0,"publisher":"Springer","acknowledgement":"The authors acknowledge support from the EU projects CLASS (IST project 027978), PerAct (IST project 504321) and the EU Network of Excellence PASCAL2.","abstract":[{"text":"The goal of this paper is to evaluate and compare models and methods for learning to recognize basic entities in images in an unsupervised setting. In other words, we want to discover the objects present in the images by analyzing unlabeled data and searching for re-occurring patterns. We experiment with various baseline methods, methods based on latent variable models, as well as spectral clustering methods. The results are presented and compared both on subsets of Caltech256 and MSRC2, data sets that are larger and more challenging and that include more object classes than what has previously been reported in the literature. A rigorous framework for evaluating unsupervised object discovery methods is proposed.","lang":"eng"}],"date_created":"2018-12-11T12:04:40Z","volume":88,"issue":"2","date_published":"2010-06-01T00:00:00Z","doi":"10.1007/s11263-009-0271-8","page":"284 - 302","publication":"International Journal of Computer Vision","day":"01","year":"2010","publication_status":"published","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","_id":"3697","title":"Unsupervised object discovery: A comparison","author":[{"last_name":"Tuytelaars","full_name":"Tuytelaars,Tinne","first_name":"Tinne"},{"last_name":"Lampert","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Matthew","last_name":"Blaschko","full_name":"Blaschko,Matthew B"},{"first_name":"Wray","last_name":"Buntine","full_name":"Buntine,Wray"}],"publist_id":"2664","extern":1,"date_updated":"2021-01-12T07:49:02Z","citation":{"ista":"Tuytelaars T, Lampert C, Blaschko M, Buntine W. 2010. Unsupervised object discovery: A comparison. International Journal of Computer Vision. 88(2), 284–302.","chicago":"Tuytelaars, Tinne, Christoph Lampert, Matthew Blaschko, and Wray Buntine. “Unsupervised Object Discovery: A Comparison.” International Journal of Computer Vision. Springer, 2010. https://doi.org/10.1007/s11263-009-0271-8.","ieee":"T. Tuytelaars, C. Lampert, M. Blaschko, and W. Buntine, “Unsupervised object discovery: A comparison,” International Journal of Computer Vision, vol. 88, no. 2. Springer, pp. 284–302, 2010.","short":"T. Tuytelaars, C. Lampert, M. Blaschko, W. Buntine, International Journal of Computer Vision 88 (2010) 284–302.","apa":"Tuytelaars, T., Lampert, C., Blaschko, M., & Buntine, W. (2010). Unsupervised object discovery: A comparison. International Journal of Computer Vision. Springer. https://doi.org/10.1007/s11263-009-0271-8","ama":"Tuytelaars T, Lampert C, Blaschko M, Buntine W. Unsupervised object discovery: A comparison. International Journal of Computer Vision. 2010;88(2):284-302. doi:10.1007/s11263-009-0271-8","mla":"Tuytelaars, Tinne, et al. “Unsupervised Object Discovery: A Comparison.” International Journal of Computer Vision, vol. 88, no. 2, Springer, 2010, pp. 284–302, doi:10.1007/s11263-009-0271-8."}},{"page":"1022 - 1029","date_published":"2010-06-18T00:00:00Z","doi":"10.1109/CVPR.2010.5540107","date_created":"2018-12-11T12:04:46Z","year":"2010","publication_status":"published","day":"18","publisher":"IEEE","quality_controlled":0,"month":"06","abstract":[{"text":"We introduce a method to accelerate the evaluation of object detection cascades with the help of a divide-and-conquer procedure in the space of candidate regions. Compared to the exhaustive procedure that thus far is the state-of-the-art for cascade evaluation, the proposed method requires fewer evaluations of the classifier functions, thereby speeding up the search. Furthermore, we show how the recently developed efficient subwindow search (ESS) procedure [11] can be integrated into the last stage of our method. This allows us to use our method to act not only as a faster procedure for cascade evaluation, but also as a tool to perform efficient branch-and-bound object detection with nonlinear quality functions, in particular kernelized support vector machines. Experiments on the PASCAL VOC 2006 dataset show an acceleration of more than 50% by our method compared to standard cascade evaluation.","lang":"eng"}],"acknowledgement":"Conference Information URL:\n\nhttp://cvl.umiacs.umd.edu/conferences/cvpr2010/","publist_id":"2643","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Christoph Lampert"}],"title":"An efficient divide-and-conquer cascade for nonlinear object detection","citation":{"chicago":"Lampert, Christoph. “An Efficient Divide-and-Conquer Cascade for Nonlinear Object Detection,” 1022–29. IEEE, 2010. https://doi.org/10.1109/CVPR.2010.5540107.","ista":"Lampert C. 2010. An efficient divide-and-conquer cascade for nonlinear object detection. CVPR: Computer Vision and Pattern Recognition, 1022–1029.","mla":"Lampert, Christoph. An Efficient Divide-and-Conquer Cascade for Nonlinear Object Detection. IEEE, 2010, pp. 1022–29, doi:10.1109/CVPR.2010.5540107.","ama":"Lampert C. An efficient divide-and-conquer cascade for nonlinear object detection. In: IEEE; 2010:1022-1029. doi:10.1109/CVPR.2010.5540107","apa":"Lampert, C. (2010). An efficient divide-and-conquer cascade for nonlinear object detection (pp. 1022–1029). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2010.5540107","ieee":"C. Lampert, “An efficient divide-and-conquer cascade for nonlinear object detection,” presented at the CVPR: Computer Vision and Pattern Recognition, 2010, pp. 1022–1029.","short":"C. Lampert, in:, IEEE, 2010, pp. 1022–1029."},"date_updated":"2021-01-12T07:51:40Z","extern":1,"type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"status":"public","_id":"3713"},{"abstract":[{"text":"These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1006.4291v1","open_access":"1"}],"publisher":"ArXiv","quality_controlled":0,"month":"06","publication_status":"published","year":"2010","publication":"ArXiv","day":"22","page":"1 - 52","date_created":"2018-12-11T12:04:55Z","date_published":"2010-06-22T00:00:00Z","volume":"q-bio.MN","_id":"3743","type":"preprint","status":"public","date_updated":"2021-01-12T07:51:53Z","citation":{"mla":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010, pp. 1–52.","ama":"Tkačik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.","apa":"Tkačik, G. (2010). From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. ArXiv.","ieee":"G. Tkačik, “From statistical mechanics to information theory: understanding biophysical information-processing systems,” ArXiv, vol. q-MN. ArXiv, pp. 1–52, 2010.","short":"G. Tkačik, ArXiv q-MN (2010) 1–52.","chicago":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv. ArXiv, 2010.","ista":"Tkačik G. 2010. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv, q-MN, 1–52, ."},"extern":1,"publist_id":"2487","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik"}],"title":"From statistical mechanics to information theory: understanding biophysical information-processing systems"},{"publisher":"IEEE","month":"01","intvolume":" 16","abstract":[{"text":"We present an algorithm for creating realistic animations of characters that are swimming through fluids. Our approach combines dynamic simulation with data-driven kinematic motions (motion capture data) to produce realistic animation in a fluid. The interaction of the articulated body with the fluid is performed by incorporating joint constraints with rigid animation and by extending a solid/fluid coupling method to handle articulated chains. Our solver takes as input the current state of the simulation and calculates the angular and linear accelerations of the connected bodies needed to match a particular motion sequence for the articulated body. These accelerations are used to estimate the forces and torques that are then applied to each joint. Based on this approach, we demonstrate simulated swimming results for a variety of different strokes, including crawl, backstroke, breaststroke, and butterfly. The ability to have articulated bodies interact with fluids also allows us to generate simulations of simple water creatures that are driven by simple controllers.","lang":"eng"}],"oa_version":"None","page":"70 - 80","date_published":"2010-01-01T00:00:00Z","issue":"1","doi":"10.1109/TVCG.2009.66","volume":16,"date_created":"2018-12-11T12:05:01Z","year":"2010","publication_status":"published","day":"01","publication":"IEEE Transactions on Visualization and Computer Graphics","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"3761","author":[{"last_name":"Kwatra","full_name":"Kwatra, Nipun","first_name":"Nipun"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"},{"full_name":"Carlson, Mark","last_name":"Carlson","first_name":"Mark"},{"last_name":"Essa","full_name":"Essa, Irfan","first_name":"Irfan"},{"last_name":"Mucha","full_name":"Mucha, Peter","first_name":"Peter"},{"first_name":"Greg","last_name":"Turk","full_name":"Turk, Greg"}],"publist_id":"2468","article_processing_charge":"No","title":"Fluid simulation with articulated bodies","date_updated":"2023-02-23T11:41:31Z","citation":{"chicago":"Kwatra, Nipun, Chris Wojtan, Mark Carlson, Irfan Essa, Peter Mucha, and Greg Turk. “Fluid Simulation with Articulated Bodies.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2010. https://doi.org/10.1109/TVCG.2009.66.","ista":"Kwatra N, Wojtan C, Carlson M, Essa I, Mucha P, Turk G. 2010. Fluid simulation with articulated bodies. IEEE Transactions on Visualization and Computer Graphics. 16(1), 70–80.","mla":"Kwatra, Nipun, et al. “Fluid Simulation with Articulated Bodies.” IEEE Transactions on Visualization and Computer Graphics, vol. 16, no. 1, IEEE, 2010, pp. 70–80, doi:10.1109/TVCG.2009.66.","ieee":"N. Kwatra, C. Wojtan, M. Carlson, I. Essa, P. Mucha, and G. Turk, “Fluid simulation with articulated bodies,” IEEE Transactions on Visualization and Computer Graphics, vol. 16, no. 1. IEEE, pp. 70–80, 2010.","short":"N. Kwatra, C. Wojtan, M. Carlson, I. Essa, P. Mucha, G. Turk, IEEE Transactions on Visualization and Computer Graphics 16 (2010) 70–80.","ama":"Kwatra N, Wojtan C, Carlson M, Essa I, Mucha P, Turk G. Fluid simulation with articulated bodies. IEEE Transactions on Visualization and Computer Graphics. 2010;16(1):70-80. doi:10.1109/TVCG.2009.66","apa":"Kwatra, N., Wojtan, C., Carlson, M., Essa, I., Mucha, P., & Turk, G. (2010). Fluid simulation with articulated bodies. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2009.66"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"3759","type":"journal_article","status":"public","citation":{"mla":"Wojtan, Chris, et al. “Physics-Inspired Topology Changes for Thin Fluid Features.” ACM Transactions on Graphics, vol. 29, no. 4, ACM, 2010, doi:10.1145/1778765.1778787.","short":"C. Wojtan, N. Thürey, M. Gross, G. Turk, ACM Transactions on Graphics 29 (2010).","ieee":"C. Wojtan, N. Thürey, M. Gross, and G. Turk, “Physics-inspired topology changes for thin fluid features,” ACM Transactions on Graphics, vol. 29, no. 4. ACM, 2010.","ama":"Wojtan C, Thürey N, Gross M, Turk G. Physics-inspired topology changes for thin fluid features. ACM Transactions on Graphics. 2010;29(4). doi:10.1145/1778765.1778787","apa":"Wojtan, C., Thürey, N., Gross, M., & Turk, G. (2010). Physics-inspired topology changes for thin fluid features. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1778765.1778787","chicago":"Wojtan, Chris, Nils Thürey, Markus Gross, and Greg Turk. “Physics-Inspired Topology Changes for Thin Fluid Features.” ACM Transactions on Graphics. ACM, 2010. https://doi.org/10.1145/1778765.1778787.","ista":"Wojtan C, Thürey N, Gross M, Turk G. 2010. Physics-inspired topology changes for thin fluid features. ACM Transactions on Graphics. 29(4)."},"date_updated":"2023-02-23T11:41:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nils","full_name":"Thürey, Nils","last_name":"Thürey"},{"full_name":"Gross, Markus","last_name":"Gross","first_name":"Markus"},{"first_name":"Greg","last_name":"Turk","full_name":"Turk, Greg"}],"publist_id":"2470","title":"Physics-inspired topology changes for thin fluid features","abstract":[{"lang":"eng","text":"We propose a mesh-based surface tracking method for fluid animation that both preserves fine surface details and robustly adjusts the topology of the surface in the presence of arbitrarily thin features like sheets and strands. We replace traditional re-sampling methods with a convex hull method for connecting surface features during topological changes. This technique permits arbitrarily thin fluid features with minimal re-sampling errors by reusing points from the original surface. We further reduce re-sampling artifacts with a subdivision-based mesh-stitching algorithm, and we use a higher order interpolating subdivision scheme to determine the location of any newly-created vertices. The resulting algorithm efficiently produces detailed fluid surfaces with arbitrarily thin features while maintaining a consistent topology with the underlying fluid simulation."}],"oa_version":"None","main_file_link":[{"url":"http://kucg.korea.ac.kr/seminar/2010/src/paper-2010-09-02.pdf"}],"publisher":"ACM","intvolume":" 29","month":"01","year":"2010","publication_status":"published","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","day":"01","date_created":"2018-12-11T12:05:00Z","doi":"10.1145/1778765.1778787","date_published":"2010-01-01T00:00:00Z","issue":"4","volume":29},{"volume":365,"issue":"1552","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5093","checksum":"4d8aade10db030124ab158b622e337e0","creator":"system","file_size":250255,"date_updated":"2020-07-14T12:46:15Z","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","date_created":"2018-12-12T10:14:40Z"}],"publication_status":"published","intvolume":" 365","month":"08","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps."}],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:15Z","ddc":["570"],"date_updated":"2021-01-12T07:52:07Z","pubrep_id":"555","status":"public","type":"journal_article","_id":"3776","date_created":"2018-12-11T12:05:06Z","doi":"10.1098/rstb.2010.0106","date_published":"2010-08-27T00:00:00Z","page":"2559 - 2569","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","day":"27","year":"2010","has_accepted_license":"1","oa":1,"publisher":"Royal Society","quality_controlled":"1","acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","title":"Genetic linkage and natural selection","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"2450","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.","chicago":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569.","ieee":"N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010.","apa":"Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0106","ama":"Barton NH. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569. doi:10.1098/rstb.2010.0106","mla":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106."}},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284","open_access":"1"}],"scopus_import":1,"intvolume":" 365","month":"06","abstract":[{"lang":"eng","text":"If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry."}],"pmid":1,"oa_version":"Submitted Version","volume":365,"issue":"1547","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"3773","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:06Z","oa":1,"publisher":"Royal Society","quality_controlled":"1","acknowledgement":"The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n","page":"1825 - 1840","date_created":"2018-12-11T12:05:05Z","doi":"10.1098/rstb.2010.0001","date_published":"2010-06-12T00:00:00Z","year":"2010","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","day":"12","external_id":{"pmid":["20439284"]},"publist_id":"2455","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"title":"What role does natural selection play in speciation?","citation":{"ista":"Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840.","chicago":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840.","ieee":"N. H. Barton, “What role does natural selection play in speciation?,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.","ama":"Barton NH. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001","apa":"Barton, N. H. (2010). What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001","mla":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model."}],"intvolume":" 365","month":"04","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","issue":"1544","volume":365,"_id":"3777","status":"public","type":"journal_article","date_updated":"2021-01-12T07:52:07Z","department":[{"_id":"NiBa"}],"acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","oa":1,"publisher":"Royal Society","quality_controlled":"1","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","day":"27","year":"2010","date_created":"2018-12-11T12:05:07Z","doi":"10.1098/rstb.2009.0320","date_published":"2010-04-27T00:00:00Z","page":"1281 - 1294","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.","apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2009.0320","ama":"Barton NH. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294. doi:10.1098/rstb.2009.0320","ieee":"N. H. Barton, “Mutation and the evolution of recombination,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294.","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.","ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294."},"title":"Mutation and the evolution of recombination","external_id":{"pmid":["20308104"]},"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"2451"},{"publication":"Journal of Animal Ecology","day":"01","year":"2010","date_created":"2018-12-11T12:05:06Z","date_published":"2010-03-01T00:00:00Z","doi":"10.1111/j.1365-2656.2009.01633.x","page":"414 - 425","acknowledgement":"This project was funded through a NERC studentship to HVS which was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission Scotland rangers for all their help with providing the larder data for and samples from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice and Steve Albon for helpful comments on the manuscript.","quality_controlled":"1","publisher":"Wiley-Blackwell","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x.","ista":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 79(2), 414–425.","mla":"Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell, 2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x.","ama":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x","apa":"Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010). Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x","ieee":"H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic correlates of hybridisation between red and sika deer (genus Cervus),” Journal of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.","short":"H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 414–425."},"title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","external_id":{"pmid":["20002231"]},"author":[{"full_name":"Senn, Helen","last_name":"Senn","first_name":"Helen"},{"first_name":"Graeme","last_name":"Swanson","full_name":"Swanson, Graeme"},{"last_name":"Goodman","full_name":"Goodman, Simon","first_name":"Simon"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Pemberton","full_name":"Pemberton, Josephine","first_name":"Josephine"}],"publist_id":"2453","language":[{"iso":"eng"}],"publication_status":"published","issue":"2","volume":79,"oa_version":"None","pmid":1,"abstract":[{"text":"1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict.","lang":"eng"}],"intvolume":" 79","month":"03","scopus_import":1,"date_updated":"2021-01-12T07:52:06Z","department":[{"_id":"NiBa"}],"_id":"3774","status":"public","type":"journal_article"},{"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"date_published":"2010-06-17T00:00:00Z","doi":"10.1371/journal.pgen.1000987","date_created":"2018-12-11T12:05:05Z","has_accepted_license":"1","year":"2010","day":"17","publication":"PLoS Genetics","article_number":"e1000987","publist_id":"2454","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"Understanding adaptation in large populations","citation":{"ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987.","chicago":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.","ieee":"N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics, vol. 6, no. 6. Public Library of Science, 2010.","short":"N.H. Barton, PLoS Genetics 6 (2010).","ama":"Barton NH. Understanding adaptation in large populations. PLoS Genetics. 2010;6(6). doi:10.1371/journal.pgen.1000987","apa":"Barton, N. H. (2010). Understanding adaptation in large populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987","mla":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"06","intvolume":" 6","oa_version":"Published Version","issue":"6","volume":6,"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:46:15Z","file_size":349965,"date_created":"2018-12-12T10:14:24Z","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5075","checksum":"5c14de2680ab483cb835096c99ee734d"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"524","_id":"3772","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:15Z","date_updated":"2021-01-12T07:52:05Z","ddc":["570","576"]},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz, L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans, M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for help and advice at various stages of this project and to J. Helenius for help with programming. This work was supported by grants from the Boehringer Ingelheim Fonds to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n","date_created":"2018-12-11T12:05:11Z","doi":"10.1371/journal.pbio.1000544","date_published":"2010-11-30T00:00:00Z","year":"2010","has_accepted_license":"1","publication":"PLoS Biology","day":"30","article_number":"e1000544","author":[{"full_name":"Diz Muñoz, Alba","last_name":"Diz Muñoz","first_name":"Alba"},{"first_name":"Michael","last_name":"Krieg","full_name":"Krieg, Michael"},{"first_name":"Martin","last_name":"Bergert","full_name":"Bergert, Martin"},{"full_name":"Ibarlucea Benitez, Itziar","last_name":"Ibarlucea Benitez","first_name":"Itziar"},{"full_name":"Müller, Daniel","last_name":"Müller","first_name":"Daniel"},{"first_name":"Ewa","last_name":"Paluch","full_name":"Paluch, Ewa"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2437","title":"Control of directed cell migration in vivo by membrane-to-cortex attachment","citation":{"ista":"Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E, Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. 8(11), e1000544.","chicago":"Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez, Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000544.","ieee":"A. Diz Muñoz et al., “Control of directed cell migration in vivo by membrane-to-cortex attachment,” PLoS Biology, vol. 8, no. 11. Public Library of Science, 2010.","short":"A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch, C.-P.J. Heisenberg, PLoS Biology 8 (2010).","apa":"Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch, E., & Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000544","ama":"Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. 2010;8(11). doi:10.1371/journal.pbio.1000544","mla":"Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology, vol. 8, no. 11, e1000544, Public Library of Science, 2010, doi:10.1371/journal.pbio.1000544."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 8","month":"11","abstract":[{"lang":"eng","text":"Cell shape and motility are primarily controlled by cellular mechanics. The attachment of the plasma membrane to the underlying actomyosin cortex has been proposed to be important for cellular processes involving membrane deformation. However, little is known about the actual function of membrane-to-cortex attachment (MCA) in cell protrusion formation and migration, in particular in the context of the developing embryo. Here, we use a multidisciplinary approach to study MCA in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells, which migrate using a combination of different protrusion types, namely, lamellipodia, filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity of molecules linking the cortex to the membrane and measuring resulting changes in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors increases the proportion of cellular blebs and reduces the directionality of cell migration. We propose that MCA is a key parameter controlling the relative proportions of different cell protrusion types in mesendoderm progenitors, and thus is key in controlling directed migration during gastrulation."}],"oa_version":"Published Version","volume":8,"issue":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"52d18c90ca6b02234cea5e8b399b7f46","file_id":"4685","creator":"system","file_size":799506,"date_updated":"2020-07-14T12:46:16Z","file_name":"IST-2015-365-v1+1_journal.pbio.1000544.pdf","date_created":"2018-12-12T10:08:24Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"365","status":"public","_id":"3790","file_date_updated":"2020-07-14T12:46:16Z","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T07:52:13Z","ddc":["576"]},{"date_published":"2010-11-04T00:00:00Z","doi":"10.1007/978-3-642-15567-3_8","date_created":"2018-12-11T12:05:12Z","page":"98 - 111","day":"04","has_accepted_license":"1","year":"2010","publisher":"Springer","quality_controlled":"1","oa":1,"title":"On parameter learning in CRF-based approaches to object class image segmentation","author":[{"first_name":"Sebastian","last_name":"Nowozin","full_name":"Nowozin, Sebastian"},{"first_name":"Peter","last_name":"Gehler","full_name":"Gehler, Peter"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"publist_id":"2431","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Nowozin, Sebastian, et al. On Parameter Learning in CRF-Based Approaches to Object Class Image Segmentation. Vol. 6316, Springer, 2010, pp. 98–111, doi:10.1007/978-3-642-15567-3_8.","short":"S. Nowozin, P. Gehler, C. Lampert, in:, Springer, 2010, pp. 98–111.","ieee":"S. Nowozin, P. Gehler, and C. Lampert, “On parameter learning in CRF-based approaches to object class image segmentation,” presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6316, pp. 98–111.","apa":"Nowozin, S., Gehler, P., & Lampert, C. (2010). On parameter learning in CRF-based approaches to object class image segmentation (Vol. 6316, pp. 98–111). Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece: Springer. https://doi.org/10.1007/978-3-642-15567-3_8","ama":"Nowozin S, Gehler P, Lampert C. On parameter learning in CRF-based approaches to object class image segmentation. In: Vol 6316. Springer; 2010:98-111. doi:10.1007/978-3-642-15567-3_8","chicago":"Nowozin, Sebastian, Peter Gehler, and Christoph Lampert. “On Parameter Learning in CRF-Based Approaches to Object Class Image Segmentation,” 6316:98–111. Springer, 2010. https://doi.org/10.1007/978-3-642-15567-3_8.","ista":"Nowozin S, Gehler P, Lampert C. 2010. On parameter learning in CRF-based approaches to object class image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 6316, 98–111."},"volume":6316,"file":[{"date_created":"2020-05-19T16:27:34Z","file_name":"2010_ECCV_Nowozin.pdf","date_updated":"2020-07-14T12:46:16Z","file_size":4087332,"creator":"dernst","file_id":"7871","checksum":"3716e10e161f7c714fd17ec193a223c3","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"11","intvolume":" 6316","alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Recent progress in per-pixel object class labeling of natural images can be attributed to the use of multiple types of image features and sound statistical learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently used for their ability to represent interactions between random variables. Despite their popularity in computer vision, parameter learning for CRFs has remained difficult, popular approaches being cross-validation and piecewise training.\r\nIn this work, we propose a simple yet expressive tree-structured CRF based on a recent hierarchical image segmentation method. Our model combines and weights multiple image features within a hierarchical representation and allows simple and efficient globally-optimal learning of ≈ 105 parameters. The tractability of our model allows us to pose and answer some of the open questions regarding parameter learning applying to CRF-based approaches. The key findings for learning CRF models are, from the obvious to the surprising, i) multiple image features always help, ii) the limiting dimension with respect to current models is the amount of training data, iii) piecewise training is competitive, iv) current methods for max-margin training fail for models with many parameters.\r\n"}],"department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:46:16Z","ddc":["000"],"date_updated":"2021-01-12T07:52:14Z","status":"public","type":"conference","conference":{"end_date":"2010-09-11","location":"Heraklion, Crete, Greece","start_date":"2010-09-05","name":"ECCV: European Conference on Computer Vision"},"_id":"3793"},{"acknowledgement":"This work was supported by grants from the Fundacion Caja Madrid to E.Q.H. and the Institute of Science and Technology Austria, the Max-Planck-Society, and the Deutsche Forschungsgemeinschaft to C.P.H.\r\nWe are grateful to Jon Clarke, Andy Oates, and Garrett Greenan for reading earlier versions of this manuscript. We thank J. Peychl, H. Ibarra, and P. Pitrone for excellent assistance and advice in multi-photon microscopy and D. White for assistance during the image-processing steps. We also thank D. Panhans for technical assistance, the whole Heisenberg laboratory for useful comments and discussions, and E. Lehmann, J. Hückmann, and G. Junghans for excellent fish care. ","oa_version":"None","abstract":[{"lang":"eng","text":"The development of multicellular organisms is dependent on the tight coordination between tissue growth and morphogenesis. The stereotypical orientation of cell divisions has been proposed to be a fundamental mechanism by which proliferating and growing tissues take shape. However, the actual contribution of stereotypical division orientation (SDO) to tissue morphogenesis is unclear. In zebrafish, cell divisions with stereotypical orientation have been implicated in both body-axis elongation and neural rod formation [1, 2], although there is little direct evidence for a critical function of SDO in either of these processes. Here we show that SDO is required for formation of the neural rod midline during neurulation but dispensable for elongation of the body axis during gastrulation. Our data indicate that SDO during both gastrulation and neurulation is dependent on the noncanonical Wnt receptor Frizzled 7 (Fz7) and that interfering with cell division orientation leads to severe defects in neural rod midline formation but not body-axis elongation. These findings suggest a novel function for Fz7-controlled cell division orientation in neural rod midline formation during neurulation. "}],"intvolume":" 20","month":"11","publisher":"Cell Press","quality_controlled":"1","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Current Biology","day":"09","publication_status":"published","year":"2010","date_created":"2018-12-11T12:05:11Z","issue":"21","date_published":"2010-11-09T00:00:00Z","volume":20,"doi":"10.1016/j.cub.2010.10.009","page":"1966 - 1972","_id":"3789","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Quesada-Hernández, Elena, et al. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” Current Biology, vol. 20, no. 21, Cell Press, 2010, pp. 1966–72, doi:10.1016/j.cub.2010.10.009.","short":"E. Quesada-Hernández, L. Caneparo, S. Schneider, S. Winkler, M. Liebling, S. Fraser, C.-P.J. Heisenberg, Current Biology 20 (2010) 1966–1972.","ieee":"E. Quesada-Hernández et al., “Stereotypical cell division orientation controls neural rod midline formation in zebrafish,” Current Biology, vol. 20, no. 21. Cell Press, pp. 1966–1972, 2010.","ama":"Quesada-Hernández E, Caneparo L, Schneider S, et al. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. 2010;20(21):1966-1972. doi:10.1016/j.cub.2010.10.009","apa":"Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling, M., Fraser, S., & Heisenberg, C.-P. J. (2010). Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2010.10.009","chicago":"Quesada-Hernández, Elena, Luca Caneparo, Sylvia Schneider, Sylke Winkler, Michael Liebling, Scott Fraser, and Carl-Philipp J Heisenberg. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” Current Biology. Cell Press, 2010. https://doi.org/10.1016/j.cub.2010.10.009.","ista":"Quesada-Hernández E, Caneparo L, Schneider S, Winkler S, Liebling M, Fraser S, Heisenberg C-PJ. 2010. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. 20(21), 1966–1972."},"date_updated":"2021-01-12T07:52:12Z","title":"Stereotypical cell division orientation controls neural rod midline formation in zebrafish","department":[{"_id":"CaHe"}],"publist_id":"2438","author":[{"last_name":"Quesada-Hernández","full_name":"Quesada-Hernández, Elena","first_name":"Elena","id":"EA35229E-E909-11E9-8DF8-C90C5D5AF86E"},{"full_name":"Caneparo, Luca","last_name":"Caneparo","first_name":"Luca"},{"last_name":"Schneider","full_name":"Schneider, Sylvia","id":"1FAC36B0-E90A-11E9-9D2F-EF31CE0C9C2F","first_name":"Sylvia"},{"full_name":"Winkler, Sylke","last_name":"Winkler","first_name":"Sylke"},{"full_name":"Liebling, Michael","last_name":"Liebling","first_name":"Michael"},{"first_name":"Scott","full_name":"Fraser, Scott","last_name":"Fraser"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}]},{"quality_controlled":"1","publisher":"Consejo Superior de Investigaciones Científicas","oa":1,"acknowledgement":"The authors would like to thank two anonymous reviewers for their remarks, which helped to improve the manuscript. This project was supported by the Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS Project http://www.synthesys. info/ which is financed by European Community Research Infrastructure Action under the FP6 “Structuring the European Research Area” Programme. Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical point drying, P.Crabb for helping with the UV-light photography setting and our colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology NHM \r\n\r\n","date_published":"2010-09-01T00:00:00Z","doi":"10.3989/scimar.2010.74n3465","date_created":"2018-12-11T12:05:10Z","page":"465 - 470","day":"01","publication":"Scientia Marina","year":"2010","title":"DNA extraction from formalin-fixed tissue: new light from the deep sea","publist_id":"2440","author":[{"first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran","last_name":"Palero"},{"full_name":"Hall, Sally","last_name":"Hall","first_name":"Sally"},{"last_name":"Clark","full_name":"Clark, Paul","first_name":"Paul"},{"first_name":"David","last_name":"Johnston","full_name":"Johnston, David"},{"last_name":"Mackenzie Dodds","full_name":"Mackenzie Dodds, Jackie","first_name":"Jackie"},{"first_name":"Sven","full_name":"Thatje, Sven","last_name":"Thatje"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 465–470.","ieee":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje, “DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp. 465–470, 2010.","apa":"Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., & Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas. https://doi.org/10.3989/scimar.2010.74n3465","ama":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465","mla":"Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.","ista":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 74(3), 465–470.","chicago":"Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465."},"month":"09","intvolume":" 74","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://eprints.soton.ac.uk/68731/"}],"oa_version":"Submitted Version","abstract":[{"text":"DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided.","lang":"eng"}],"volume":74,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"3787","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:11Z"},{"_id":"3788","type":"journal_article","status":"public","citation":{"mla":"Klopper, Abigail, et al. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” The European Physical Journal E: Soft Matter and Biological Physics, vol. 33, no. 2, Springer, 2010, pp. 99–103, doi:10.1140/epje/i2010-10642-y.","apa":"Klopper, A., Krens, G., Grill, S., & Heisenberg, C.-P. J. (2010). Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. Springer. https://doi.org/10.1140/epje/i2010-10642-y","ama":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. 2010;33(2):99-103. doi:10.1140/epje/i2010-10642-y","ieee":"A. Klopper, G. Krens, S. Grill, and C.-P. J. Heisenberg, “Finite-size corrections to scaling behavior in sorted cell aggregates,” The European Physical Journal E: Soft Matter and Biological Physics, vol. 33, no. 2. Springer, pp. 99–103, 2010.","short":"A. Klopper, G. Krens, S. Grill, C.-P.J. Heisenberg, The European Physical Journal E: Soft Matter and Biological Physics 33 (2010) 99–103.","chicago":"Klopper, Abigail, Gabriel Krens, Stephan Grill, and Carl-Philipp J Heisenberg. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” The European Physical Journal E: Soft Matter and Biological Physics. Springer, 2010. https://doi.org/10.1140/epje/i2010-10642-y.","ista":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. 2010. Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. 33(2), 99–103."},"date_updated":"2021-01-12T07:52:12Z","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","publist_id":"2439","author":[{"full_name":"Klopper, Abigail","last_name":"Klopper","first_name":"Abigail"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grill, Stephan","last_name":"Grill","first_name":"Stephan"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"Finite-size corrections to scaling behavior in sorted cell aggregates","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","text":"Cell sorting is a widespread phenomenon pivotal to the early development of multicellular organisms. In vitro cell sorting studies have been instrumental in revealing the cellular properties driving this process. However, these studies have as yet been limited to two-dimensional analysis of three-dimensional cell sorting events. Here we describe a method to record the sorting of primary zebrafish ectoderm and mesoderm germ layer progenitor cells in three dimensions over time, and quantitatively analyze their sorting behavior using an order parameter related to heterotypic interface length. We investigate the cell population size dependence of sorted aggregates and find that the germ layer progenitor cells engulfed in the final configuration display a relationship between total interfacial length and system size according to a simple geometrical argument, subject to a finite-size effect."}],"oa_version":"None","publisher":"Springer","scopus_import":1,"intvolume":" 33","month":"09","year":"2010","publication_status":"published","language":[{"iso":"eng"}],"publication":"The European Physical Journal E: Soft Matter and Biological Physics","day":"18","page":"99 - 103","date_created":"2018-12-11T12:05:10Z","volume":33,"doi":"10.1140/epje/i2010-10642-y","issue":"2","date_published":"2010-09-18T00:00:00Z"},{"year":"2010","publication_status":"published","day":"19","language":[{"iso":"eng"}],"publication":"Zootaxa","page":"42 - 58","volume":2403,"date_published":"2010-03-19T00:00:00Z","doi":"10.11646/zootaxa.2403.1.4","issue":"1","date_created":"2018-12-11T12:05:10Z","abstract":[{"text":"Four rare palinurid phyllosoma larvae, one mid-stage and three final stage, were found among the unclassified collections in the Crustacea Section, Natural History Museum, London. Detailed morphological analysis of the larvae indicated that they belong to several Palinustus species given the presence of incipient blunt-horns, length of antennula, length ratio of segments of antennular peduncle, distribution of pereiopod spines, and shape of uropods and telson. Moreover, the size of the final-stage larvae agrees with that expected given the size of the recently described puerulus stage of Palinustus mossambicus. This constitutes the first description of a complete phyllosoma assigned to Palinustus species. The phyllosoma described in the present study include the largest Palinuridae larva ever found.","lang":"eng"}],"oa_version":"None","scopus_import":"1","quality_controlled":"1","publisher":"Magnolia Press","month":"03","intvolume":" 2403","citation":{"ista":"Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2403(1), 42–58.","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press, 2010. https://doi.org/10.11646/zootaxa.2403.1.4.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press, pp. 42–58, 2010.","apa":"Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4","ama":"Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4","mla":"Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4."},"date_updated":"2022-03-21T08:22:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Palero","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran","first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guillermo","last_name":"Guerao","full_name":"Guerao, Guillermo"},{"full_name":"Clark, Paul","last_name":"Clark","first_name":"Paul"},{"last_name":"Abello","full_name":"Abello, Pere","first_name":"Pere"}],"publist_id":"2441","article_processing_charge":"No","title":"Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description","department":[{"_id":"NiBa"}],"_id":"3786","type":"journal_article","article_type":"original","status":"public"},{"publication":"Trends in Cell Biology","language":[{"iso":"eng"}],"day":"01","year":"2010","publication_status":"published","date_created":"2018-12-11T12:05:12Z","date_published":"2010-10-01T00:00:00Z","doi":"10.1016/j.tcb.2010.06.009","volume":20,"issue":"10","page":"586 - 592","acknowledgement":"We are grateful to Valerie Virta and Jennifer Regan for reading earlier versions of the review.\r\n","oa_version":"None","abstract":[{"lang":"eng","text":"The yolk syncytial layer (YSL) plays crucial roles in early zebrafish development. The YSL is a transient extra-embryonic syncytial tissue that forms during early cleavage stages and persists until larval stages. During gastrulation, the YSL undergoes highly dynamic movements, which are tightly coordinated with the movements of the overlying germ layer progenitor cells, and has critical functions in cell fate specification and morphogenesis of the early germ layers. Movement coordination between the YSL and blastoderm cells is dependent on contact between these tissues, and is probably required for the patterning and morphogenetic function of the YSL. In this review, we will discuss recent advances in elucidating the molecular and cellular mechanisms underlying the YSL morphogenesis and movement coordination between the YSL and blastoderm during early development."}],"intvolume":" 20","month":"10","quality_controlled":"1","scopus_import":"1","publisher":"Cell Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Carvalho, Lara, and Carl-Philipp J Heisenberg. “The Yolk Syncytial Layer in Early, Zebrafish Development.” Trends in Cell Biology. Cell Press, 2010. https://doi.org/10.1016/j.tcb.2010.06.009.","ista":"Carvalho L, Heisenberg C-PJ. 2010. The yolk syncytial layer in early, zebrafish development. Trends in Cell Biology. 20(10), 586–592.","mla":"Carvalho, Lara, and Carl-Philipp J. Heisenberg. “The Yolk Syncytial Layer in Early, Zebrafish Development.” Trends in Cell Biology, vol. 20, no. 10, Cell Press, 2010, pp. 586–92, doi:10.1016/j.tcb.2010.06.009.","short":"L. Carvalho, C.-P.J. Heisenberg, Trends in Cell Biology 20 (2010) 586–592.","ieee":"L. Carvalho and C.-P. J. Heisenberg, “The yolk syncytial layer in early, zebrafish development,” Trends in Cell Biology, vol. 20, no. 10. Cell Press, pp. 586–592, 2010.","apa":"Carvalho, L., & Heisenberg, C.-P. J. (2010). The yolk syncytial layer in early, zebrafish development. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2010.06.009","ama":"Carvalho L, Heisenberg C-PJ. The yolk syncytial layer in early, zebrafish development. Trends in Cell Biology. 2010;20(10):586-592. doi:10.1016/j.tcb.2010.06.009"},"date_updated":"2022-08-25T15:00:19Z","title":"The yolk syncytial layer in early, zebrafish development","article_processing_charge":"No","author":[{"last_name":"Carvalho","full_name":"Carvalho, Lara","first_name":"Lara"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"publist_id":"2435","_id":"3792","status":"public","type":"journal_article"},{"oa_version":"Published Version","abstract":[{"text":"Background\r\n\r\nThe chemical master equation (CME) is a system of ordinary differential equations that describes the evolution of a network of chemical reactions as a stochastic process. Its solution yields the probability density vector of the system at each point in time. Solving the CME numerically is in many cases computationally expensive or even infeasible as the number of reachable states can be very large or infinite. We introduce the sliding window method, which computes an approximate solution of the CME by performing a sequence of local analysis steps. In each step, only a manageable subset of states is considered, representing a "window" into the state space. In subsequent steps, the window follows the direction in which the probability mass moves, until the time period of interest has elapsed. We construct the window based on a deterministic approximation of the future behavior of the system by estimating upper and lower bounds on the populations of the chemical species.\r\nResults\r\n\r\nIn order to show the effectiveness of our approach, we apply it to several examples previously described in the literature. The experimental results show that the proposed method speeds up the analysis considerably, compared to a global analysis, while still providing high accuracy.\r\n\r\n\r\nConclusions\r\n\r\nThe sliding window method is a novel approach to address the performance problems of numerical algorithms for the solution of the chemical master equation. The method efficiently approximates the probability distributions at the time points of interest for a variety of chemically reacting systems, including systems for which no upper bound on the population sizes of the chemical species is known a priori.","lang":"eng"}],"month":"04","intvolume":" 4","scopus_import":1,"file":[{"creator":"system","file_size":1919130,"date_updated":"2020-07-14T12:46:16Z","file_name":"IST-2012-72-v1+1_Solving_the_chemical_master_equation_using_sliding_windows.pdf","date_created":"2018-12-12T10:16:29Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"220239fae76f7b03c4d7f05d74ef426f","file_id":"5217"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"42","volume":4,"_id":"3834","status":"public","pubrep_id":"72","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["005"],"date_updated":"2021-01-12T07:52:32Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:16Z","acknowledgement":"This research has been partially funded by the Swiss National Science Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal Computing and Interaction at Saarland University.","publisher":"BioMed Central","quality_controlled":"1","oa":1,"day":"08","publication":"BMC Systems Biology","has_accepted_license":"1","year":"2010","doi":"10.1186/1752-0509-4-42","date_published":"2010-04-08T00:00:00Z","date_created":"2018-12-11T12:05:25Z","page":"1 - 19","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wolf, Verena, et al. “Solving the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology, vol. 4, no. 42, BioMed Central, 2010, pp. 1–19, doi:10.1186/1752-0509-4-42.","short":"V. Wolf, R. Goel, M. Mateescu, T.A. Henzinger, BMC Systems Biology 4 (2010) 1–19.","ieee":"V. Wolf, R. Goel, M. Mateescu, and T. A. Henzinger, “Solving the chemical master equation using sliding windows,” BMC Systems Biology, vol. 4, no. 42. BioMed Central, pp. 1–19, 2010.","apa":"Wolf, V., Goel, R., Mateescu, M., & Henzinger, T. A. (2010). Solving the chemical master equation using sliding windows. BMC Systems Biology. BioMed Central. https://doi.org/10.1186/1752-0509-4-42","ama":"Wolf V, Goel R, Mateescu M, Henzinger TA. Solving the chemical master equation using sliding windows. BMC Systems Biology. 2010;4(42):1-19. doi:10.1186/1752-0509-4-42","chicago":"Wolf, Verena, Rushil Goel, Maria Mateescu, and Thomas A Henzinger. “Solving the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology. BioMed Central, 2010. https://doi.org/10.1186/1752-0509-4-42.","ista":"Wolf V, Goel R, Mateescu M, Henzinger TA. 2010. Solving the chemical master equation using sliding windows. BMC Systems Biology. 4(42), 1–19."},"title":"Solving the chemical master equation using sliding windows","publist_id":"2374","author":[{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"},{"full_name":"Goel, Rushil","last_name":"Goel","first_name":"Rushil"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}]},{"year":"2010","publication_status":"published","language":[{"iso":"eng"}],"day":"17","page":"157 - 158","date_created":"2018-12-11T12:05:27Z","issue":"1","doi":"10.1145/1706299.1706319","volume":45,"date_published":"2010-01-17T00:00:00Z","abstract":[{"lang":"eng","text":"Classical formalizations of systems and properties are boolean: given a system and a property, the property is either true or false of the system. Correspondingly, classical methods for system analysis determine the truth value of a property, preferably giving a proof if the property is true, and a counterexample if the property is false; classical methods for system synthesis construct a system for which a property is true; classical methods for system transformation, composition, and abstraction aim to preserve the truth of properties. The boolean view is prevalent even if the system, the property, or both refer to numerical quantities, such as the times or probabilities of events. For example, a timed automaton either satisfies or violates a formula of a real-time logic; a stochastic process either satisfies or violates a formula of a probabilistic logic. The classical black-and-white view partitions the world into \"correct\" and \"incorrect\" systems, offering few nuances. In reality, of several systems that satisfy a property in the boolean sense, often some are more desirable than others, and of the many systems that violate a property, usually some are less objectionable than others. For instance, among the systems that satisfy the response property that every request be granted, we may prefer systems that grant requests quickly (the quicker, the better), or we may prefer systems that issue few unnecessary grants (the fewer, the better); and among the systems that violate the response property, we may prefer systems that serve many initial requests (the more, the better), or we may prefer systems that serve many requests in the long run (the greater the fraction of served to unserved requests, the better). Formally, while a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a directed metric on systems and properties, where the distance between a system and a property provides a measure of \"fit\" or \"desirability.\" There are many ways how such distances can be defined. In a linear-time framework, one assigns numerical values to individual behaviors before assigning values to systems and properties, which are sets of behaviors. For example, the value of a single behavior may be a discounted value, which is largely determined by a prefix of the behavior, e.g., by the number of requests that are granted before the first request that is not granted; or a limit value, which is independent of any finite prefix. A limit value may be an average, such as the average response time over an infinite sequence of requests and grants, or a supremum, such as the worst-case response time. Similarly, the value of a set of behaviors may be an extremum or an average across the values of all behaviors in the set: in this way one can measure the worst of all possible average-case response times, or the average of all possible worst-case response times, etc. Accordingly, the distance between two sets of behaviors may be defined as the worst or average difference between the values of corresponding behaviors. In summary, we propagate replacing boolean specifications for the correctness of systems with quantitative measures for the desirability of systems. In quantitative analysis, the aim is to compute the distance between a system and a property (or between two systems, or two properties); in quantitative synthesis, the objective is to construct a system that has minimal distance from a given property. Multiple quantitative measures can be prioritized (e.g., combined lexicographically into a single measure) or studied along the Pareto curve. Quantitative transformations, compositions, and abstractions of systems are useful if they allow us to bound the induced change in distance from a property. We present some initial results in some of these directions. We also give some potential applications, which not only generalize tradiditional correctness concerns in the functional, timed, and probabilistic domains, but also capture such system measures as resource use, performance, cost, reliability, and robustness."}],"acknowledgement":"This talk surveys joint work with Roderick Bloem, Krishnendu Chatterjee, Laurent Doyen, and Barbara Jobstmann.","oa_version":"None","publisher":"ACM","quality_controlled":"1","scopus_import":1,"intvolume":" 45","month":"01","citation":{"mla":"Henzinger, Thomas A. From Boolean to Quantitative Notions of Correctness. Vol. 45, no. 1, ACM, 2010, pp. 157–58, doi:10.1145/1706299.1706319.","ieee":"T. A. Henzinger, “From boolean to quantitative notions of correctness,” presented at the POPL: Principles of Programming Languages, Madrid, Spain, 2010, vol. 45, no. 1, pp. 157–158.","short":"T.A. Henzinger, in:, ACM, 2010, pp. 157–158.","ama":"Henzinger TA. From boolean to quantitative notions of correctness. In: Vol 45. ACM; 2010:157-158. doi:10.1145/1706299.1706319","apa":"Henzinger, T. A. (2010). From boolean to quantitative notions of correctness (Vol. 45, pp. 157–158). Presented at the POPL: Principles of Programming Languages, Madrid, Spain: ACM. https://doi.org/10.1145/1706299.1706319","chicago":"Henzinger, Thomas A. “From Boolean to Quantitative Notions of Correctness,” 45:157–58. ACM, 2010. https://doi.org/10.1145/1706299.1706319.","ista":"Henzinger TA. 2010. From boolean to quantitative notions of correctness. POPL: Principles of Programming Languages vol. 45, 157–158."},"date_updated":"2021-01-12T07:52:34Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"2354","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"title":"From boolean to quantitative notions of correctness","department":[{"_id":"ToHe"}],"_id":"3840","conference":{"location":"Madrid, Spain","end_date":"2010-01-23","start_date":"2010-01-17","name":"POPL: Principles of Programming Languages"},"type":"conference","status":"public"},{"publist_id":"2357","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Thibaud","full_name":"Hottelier, Thibaud","last_name":"Hottelier"},{"first_name":"Laura","full_name":"Kovács, Laura","last_name":"Kovács"},{"first_name":"Andrei","full_name":"Voronkov, Andrei","last_name":"Voronkov"}],"title":"Invariant and type inference for matrices","citation":{"chicago":"Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrei Voronkov. “Invariant and Type Inference for Matrices,” 5944:163–79. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_14.","ista":"Henzinger TA, Hottelier T, Kovács L, Voronkov A. 2010. Invariant and type inference for matrices. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 5944, 163–179.","mla":"Henzinger, Thomas A., et al. Invariant and Type Inference for Matrices. Vol. 5944, Springer, 2010, pp. 163–79, doi:10.1007/978-3-642-11319-2_14.","ieee":"T. A. Henzinger, T. Hottelier, L. Kovács, and A. Voronkov, “Invariant and type inference for matrices,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 163–179.","short":"T.A. Henzinger, T. Hottelier, L. Kovács, A. Voronkov, in:, Springer, 2010, pp. 163–179.","apa":"Henzinger, T. A., Hottelier, T., Kovács, L., & Voronkov, A. (2010). Invariant and type inference for matrices (Vol. 5944, pp. 163–179). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-642-11319-2_14","ama":"Henzinger TA, Hottelier T, Kovács L, Voronkov A. Invariant and type inference for matrices. In: Vol 5944. Springer; 2010:163-179. doi:10.1007/978-3-642-11319-2_14"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"163 - 179","date_created":"2018-12-11T12:05:27Z","doi":"10.1007/978-3-642-11319-2_14","date_published":"2010-01-01T00:00:00Z","year":"2010","has_accepted_license":"1","day":"01","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"The research was supported by the Swiss NSF.","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:16Z","date_updated":"2021-01-12T07:52:33Z","ddc":["005"],"conference":{"end_date":"2010-01-19","location":"Madrid, Spain","start_date":"2010-01-17","name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"type":"conference","pubrep_id":"69","status":"public","_id":"3839","volume":5944,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"da69b13a2d9a7a316c909e09c1090cef","file_id":"4989","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:09Z","file_name":"IST-2012-69-v1+1_Invariant_and_type_inference_for_matrices.pdf","creator":"system","date_updated":"2020-07-14T12:46:16Z","file_size":251265}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 5944","month":"01","abstract":[{"text":"We present a loop property generation method for loops iterating over multi-dimensional arrays. When used on matrices, our method is able to infer their shapes (also called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties, we first transform a nested loop iterating over a multi- dimensional array into an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants for each unnested loop using a generalization of a recurrence-based invariant generation technique. These loop invariants give us conditions on matrices from which we can derive matrix types automatically us- ing theorem provers. Invariant generation is implemented in the software package Aligator and types are derived by theorem provers and SMT solvers, including Vampire and Z3. When run on the Java matrix package JAMA, our tool was able to infer automatically all matrix types describing the matrix shapes guaranteed by JAMA’s API.","lang":"eng"}],"oa_version":"Submitted Version"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Henzinger, Thomas A, Maria Mateescu, Linar Mikeev, and Verena Wolf. “Hybrid Numerical Solution of the Chemical Master Equation,” 55–65. Springer, 2010. https://doi.org/10.1145/1839764.1839772.","ista":"Henzinger TA, Mateescu M, Mikeev L, Wolf V. 2010. Hybrid numerical solution of the chemical master equation. CMSB: Computational Methods in Systems Biology, 55–65.","mla":"Henzinger, Thomas A., et al. Hybrid Numerical Solution of the Chemical Master Equation. Springer, 2010, pp. 55–65, doi:10.1145/1839764.1839772.","apa":"Henzinger, T. A., Mateescu, M., Mikeev, L., & Wolf, V. (2010). Hybrid numerical solution of the chemical master equation (pp. 55–65). Presented at the CMSB: Computational Methods in Systems Biology, Trento, Italy: Springer. https://doi.org/10.1145/1839764.1839772","ama":"Henzinger TA, Mateescu M, Mikeev L, Wolf V. Hybrid numerical solution of the chemical master equation. In: Springer; 2010:55-65. doi:10.1145/1839764.1839772","short":"T.A. Henzinger, M. Mateescu, L. Mikeev, V. Wolf, in:, Springer, 2010, pp. 55–65.","ieee":"T. A. Henzinger, M. Mateescu, L. Mikeev, and V. Wolf, “Hybrid numerical solution of the chemical master equation,” presented at the CMSB: Computational Methods in Systems Biology, Trento, Italy, 2010, pp. 55–65."},"title":"Hybrid numerical solution of the chemical master equation","publist_id":"2356","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria"},{"first_name":"Linar","full_name":"Mikeev, Linar","last_name":"Mikeev"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}],"day":"29","year":"2010","has_accepted_license":"1","date_created":"2018-12-11T12:05:27Z","date_published":"2010-09-29T00:00:00Z","doi":"10.1145/1839764.1839772","page":"55 - 65","oa":1,"publisher":"Springer","quality_controlled":"1","ddc":["004"],"date_updated":"2021-01-12T07:52:33Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:16Z","_id":"3838","pubrep_id":"68","status":"public","conference":{"name":"CMSB: Computational Methods in Systems Biology","end_date":"2010-10-01","location":"Trento, Italy","start_date":"2010-09-29"},"type":"conference","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5179","checksum":"81cb6f0babd97151b171d1ce86582831","creator":"system","date_updated":"2020-07-14T12:46:16Z","file_size":671790,"date_created":"2018-12-12T10:15:55Z","file_name":"IST-2012-68-v1+1_Hybrid_Numerical_Solution_of_the_Chemical_Master_Equation.pdf"}],"publication_status":"published","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe net- works of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is based on the construction of a stochastic hybrid model in which certain discrete random variables of the original Markov chain are approximated by continuous deterministic variables. We compute the solution of the stochastic hybrid model using a numerical algorithm that discretizes time and in each step performs a mutual update of the transient prob- ability distribution of the discrete stochastic variables and the values of the continuous deterministic variables. We im- plemented the algorithm and we demonstrate its usefulness and efficiency on several case studies from systems biology."}],"month":"09","scopus_import":1},{"day":"18","has_accepted_license":"1","year":"2010","doi":"10.1007/978-3-642-15375-4_19","date_published":"2010-11-18T00:00:00Z","date_created":"2018-12-11T12:05:31Z","page":"269 - 283","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. Mean-Payoff Automaton Expressions. Vol. 6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 269–83, doi:10.1007/978-3-642-15375-4_19.","ama":"Chatterjee K, Doyen L, Edelsbrunner H, Henzinger TA, Rannou P. Mean-payoff automaton expressions. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:269-283. doi:10.1007/978-3-642-15375-4_19","apa":"Chatterjee, K., Doyen, L., Edelsbrunner, H., Henzinger, T. A., & Rannou, P. (2010). Mean-payoff automaton expressions (Vol. 6269, pp. 269–283). Presented at the CONCUR: Concurrency Theory, Paris, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-15375-4_19","ieee":"K. Chatterjee, L. Doyen, H. Edelsbrunner, T. A. Henzinger, and P. Rannou, “Mean-payoff automaton expressions,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 269–283.","short":"K. Chatterjee, L. Doyen, H. Edelsbrunner, T.A. Henzinger, P. Rannou, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 269–283.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Herbert Edelsbrunner, Thomas A Henzinger, and Philippe Rannou. “Mean-Payoff Automaton Expressions,” 6269:269–83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.1007/978-3-642-15375-4_19.","ista":"Chatterjee K, Doyen L, Edelsbrunner H, Henzinger TA, Rannou P. 2010. Mean-payoff automaton expressions. CONCUR: Concurrency Theory, LNCS, vol. 6269, 269–283."},"title":"Mean-payoff automaton expressions","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"full_name":"Rannou, Philippe","last_name":"Rannou","first_name":"Philippe"}],"publist_id":"2328","project":[{"name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5163","checksum":"4f753ae99d076553fb8733e2c8b390e2","creator":"system","file_size":233260,"date_updated":"2020-07-14T12:46:17Z","file_name":"IST-2012-62-v1+1_Mean-payoff_automaton_expressions.pdf","date_created":"2018-12-12T10:15:41Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6269,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"Quantitative languages are an extension of boolean languages that assign to each word a real number. Mean-payoff automata are finite automata with numerical weights on transitions that assign to each infinite path the long-run average of the transition weights. When the mode of branching of the automaton is deterministic, nondeterministic, or alternating, the corresponding class of quantitative languages is not robust as it is not closed under the pointwise operations of max, min, sum, and numerical complement. Nondeterministic and alternating mean-payoff automata are not decidable either, as the quantitative generalization of the problems of universality and language inclusion is undecidable. We introduce a new class of quantitative languages, defined by mean-payoff automaton expressions, which is robust and decidable: it is closed under the four pointwise operations, and we show that all decision problems are decidable for this class. Mean-payoff automaton expressions subsume deterministic meanpayoff automata, and we show that they have expressive power incomparable to nondeterministic and alternating mean-payoff automata. We also present for the first time an algorithm to compute distance between two quantitative languages, and in our case the quantitative languages are given as mean-payoff automaton expressions.","lang":"eng"}],"month":"11","intvolume":" 6269","scopus_import":1,"alternative_title":["LNCS"],"ddc":["000","005"],"date_updated":"2021-01-12T07:52:40Z","department":[{"_id":"KrCh"},{"_id":"HeEd"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:17Z","_id":"3853","status":"public","pubrep_id":"62","type":"conference","conference":{"start_date":"2010-08-31","location":"Paris, France","end_date":"2010-09-03","name":"CONCUR: Concurrency Theory"}},{"volume":6281,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-537-v1+1_2010-P-05-NonuniformError.pdf","date_created":"2018-12-12T10:13:13Z","file_size":142357,"date_updated":"2020-07-14T12:46:17Z","creator":"system","checksum":"af61e1c2bb42f3d556179d4692caeb1b","file_id":"4994","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 6281","month":"08","abstract":[{"text":"Using ideas from persistent homology, the robustness of a level set of a real-valued function is defined in terms of the magnitude of the perturbation necessary to kill the classes. Prior work has shown that the homology and robustness information can be read off the extended persistence diagram of the function. This paper extends these results to a non-uniform error model in which perturbations vary in their magnitude across the domain.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:17Z","date_updated":"2021-01-12T07:52:38Z","ddc":["000"],"conference":{"start_date":"2010-08-23","end_date":"2010-08-27","location":"Brno, Czech Republic","name":"MFCS: Mathematical Foundations of Computer Science"},"type":"conference","pubrep_id":"537","status":"public","_id":"3849","page":"12 - 23","date_created":"2018-12-11T12:05:30Z","date_published":"2010-08-10T00:00:00Z","doi":"10.1007/978-3-642-15155-2_2","year":"2010","has_accepted_license":"1","day":"10","oa":1,"quality_controlled":"1","publisher":"Springer","publist_id":"2333","author":[{"last_name":"Bendich","full_name":"Bendich, Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","last_name":"Kerber"},{"last_name":"Patel","full_name":"Patel, Amit","first_name":"Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87"}],"title":"Persistent homology under non-uniform error","citation":{"ista":"Bendich P, Edelsbrunner H, Kerber M, Patel A. 2010. Persistent homology under non-uniform error. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6281, 12–23.","chicago":"Bendich, Paul, Herbert Edelsbrunner, Michael Kerber, and Amit Patel. “Persistent Homology under Non-Uniform Error,” 6281:12–23. Springer, 2010. https://doi.org/10.1007/978-3-642-15155-2_2.","short":"P. Bendich, H. Edelsbrunner, M. Kerber, A. Patel, in:, Springer, 2010, pp. 12–23.","ieee":"P. Bendich, H. Edelsbrunner, M. Kerber, and A. Patel, “Persistent homology under non-uniform error,” presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic, 2010, vol. 6281, pp. 12–23.","ama":"Bendich P, Edelsbrunner H, Kerber M, Patel A. Persistent homology under non-uniform error. In: Vol 6281. Springer; 2010:12-23. doi:10.1007/978-3-642-15155-2_2","apa":"Bendich, P., Edelsbrunner, H., Kerber, M., & Patel, A. (2010). Persistent homology under non-uniform error (Vol. 6281, pp. 12–23). Presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-15155-2_2","mla":"Bendich, Paul, et al. Persistent Homology under Non-Uniform Error. Vol. 6281, Springer, 2010, pp. 12–23, doi:10.1007/978-3-642-15155-2_2."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"title":"Obliging games","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Horn","full_name":"Horn, Florian","first_name":"Florian","id":"37327ACE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Löding, Christof","last_name":"Löding","first_name":"Christof"}],"publist_id":"2327","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. Obliging Games. Vol. 6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 284–96, doi:10.1007/978-3-642-15375-4_20.","ama":"Chatterjee K, Horn F, Löding C. Obliging games. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:284-296. doi:10.1007/978-3-642-15375-4_20","apa":"Chatterjee, K., Horn, F., & Löding, C. (2010). Obliging games (Vol. 6269, pp. 284–296). Presented at the CONCUR: Concurrency Theory, Paris, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-15375-4_20","ieee":"K. Chatterjee, F. Horn, and C. Löding, “Obliging games,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 284–296.","short":"K. Chatterjee, F. Horn, C. Löding, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 284–296.","chicago":"Chatterjee, Krishnendu, Florian Horn, and Christof Löding. “Obliging Games,” 6269:284–96. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.1007/978-3-642-15375-4_20.","ista":"Chatterjee K, Horn F, Löding C. 2010. Obliging games. CONCUR: Concurrency Theory, LNCS, vol. 6269, 284–296."},"date_updated":"2021-01-12T07:52:41Z","status":"public","type":"conference","conference":{"start_date":"2010-08-31","end_date":"2010-09-03","location":"Paris, France","name":"CONCUR: Concurrency Theory"},"_id":"3854","doi":"10.1007/978-3-642-15375-4_20","date_published":"2010-09-08T00:00:00Z","volume":6269,"date_created":"2018-12-11T12:05:32Z","page":"284 - 296","day":"08","language":[{"iso":"eng"}],"publication_status":"published","year":"2010","month":"09","intvolume":" 6269","scopus_import":1,"alternative_title":["LNCS"],"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa_version":"None","abstract":[{"lang":"eng","text":"Graph games of infinite length provide a natural model for open reactive systems: one player (Eve) represents the controller and the other player (Adam) represents the environment. The evolution of the system depends on the decisions of both players. The specification for the system is usually given as an ω-regular language L over paths and Eve’s goal is to ensure that the play belongs to L irrespective of Adam’s behaviour. The classical notion of winning strategies fails to capture several interesting scenarios. For example, strong fairness (Streett) conditions are specified by a number of request-grant pairs and require every pair that is requested infinitely often to be granted infinitely often: Eve might win just by preventing Adam from making any new request, but a “better” strategy would allow Adam to make as many requests as possible and still ensure fairness. To address such questions, we introduce the notion of obliging games, where Eve has to ensure a strong condition Φ, while always allowing Adam to satisfy a weak condition Ψ. We present a linear time reduction of obliging games with two Muller conditions Φ and Ψ to classical Muller games. We consider obliging Streett games and show they are co-NP complete, and show a natural quantitative optimisation problem for obliging Streett games is in FNP. We also show how obliging games can provide new and interesting semantics for multi-player games."}]},{"date_published":"2010-09-10T00:00:00Z","doi":"10.1007/978-3-642-14162-1_50","date_created":"2018-12-11T12:05:31Z","page":"599 - 610","day":"10","year":"2010","quality_controlled":"1","publisher":"Springer","oa":1,"title":"Energy parity games","publist_id":"2330","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"external_id":{"arxiv":["1001.5183"]},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. Energy Parity Games. Vol. 6199, Springer, 2010, pp. 599–610, doi:10.1007/978-3-642-14162-1_50.","apa":"Chatterjee, K., & Doyen, L. (2010). Energy parity games (Vol. 6199, pp. 599–610). Presented at the ICALP: Automata, Languages and Programming, 37th International Colloquium, Bordeaux, France: Springer. https://doi.org/10.1007/978-3-642-14162-1_50","ama":"Chatterjee K, Doyen L. Energy parity games. In: Vol 6199. Springer; 2010:599-610. doi:10.1007/978-3-642-14162-1_50","ieee":"K. Chatterjee and L. Doyen, “Energy parity games,” presented at the ICALP: Automata, Languages and Programming, 37th International Colloquium, Bordeaux, France, 2010, vol. 6199, pp. 599–610.","short":"K. Chatterjee, L. Doyen, in:, Springer, 2010, pp. 599–610.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games,” 6199:599–610. Springer, 2010. https://doi.org/10.1007/978-3-642-14162-1_50.","ista":"Chatterjee K, Doyen L. 2010. Energy parity games. ICALP: Automata, Languages and Programming, 37th International Colloquium, LNCS, vol. 6199, 599–610."},"related_material":{"record":[{"status":"public","id":"2972","relation":"later_version"}]},"volume":6199,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 6199","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1001.5183","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objective. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is polynomially equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games.","lang":"eng"}],"department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T11:06:35Z","status":"public","type":"conference","conference":{"name":" ICALP: Automata, Languages and Programming, 37th International Colloquium","location":"Bordeaux, France","end_date":"2010-07-10","start_date":"2010-07-06"},"_id":"3851"},{"publication_status":"published","year":"2010","day":"04","language":[{"iso":"eng"}],"publication":"Physical Review Letters","volume":104,"doi":"10.1103/PhysRevLett.104.016401","date_published":"2010-01-04T00:00:00Z","issue":"1","date_created":"2018-12-11T11:46:10Z","abstract":[{"text":"Scanning tunneling spectroscopy studies on high-quality Bi2Te3 crystals exhibit perfect correspondence to angle-resolved photoemission spectroscopy data, hence enabling identification of different regimes measured in the local density of states (LDOS). Oscillations of LDOS near a step are analyzed. Within the main part of the surface band oscillations are strongly damped, supporting the hypothesis of topological protection. At higher energies, as the surface band becomes concave, oscillations appear, dispersing with a wave vector that may result from a hexagonal warping term. ","lang":"eng"}],"oa_version":"None","publisher":"American Physical Society","oa":1,"main_file_link":[{"url":"https://arxiv.org/pdf/0908.0371.pdf","open_access":"1"}],"month":"01","intvolume":" 104","date_updated":"2021-01-12T07:52:39Z","citation":{"ista":"Alpichshev Z, Analytis J, Chu J, Fisher I, Chen Y, Shen Z, Fang A, Kapitulnik A. 2010. STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects. Physical Review Letters. 104(1).","chicago":"Alpichshev, Zhanybek, James Analytis, Jiunhaw Chu, Ian Fisher, Yulin Chen, Zhixun Shen, Aiping Fang, and Aharon Kapitulnik. “STM Imaging of Electronic Waves on the Surface of Bi2Te3 Topologically Protected Surface States and Hexagonal Warping Effects.” Physical Review Letters. American Physical Society, 2010. https://doi.org/10.1103/PhysRevLett.104.016401.","apa":"Alpichshev, Z., Analytis, J., Chu, J., Fisher, I., Chen, Y., Shen, Z., … Kapitulnik, A. (2010). STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.104.016401","ama":"Alpichshev Z, Analytis J, Chu J, et al. STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects. Physical Review Letters. 2010;104(1). doi:10.1103/PhysRevLett.104.016401","ieee":"Z. Alpichshev et al., “STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects,” Physical Review Letters, vol. 104, no. 1. American Physical Society, 2010.","short":"Z. Alpichshev, J. Analytis, J. Chu, I. Fisher, Y. Chen, Z. Shen, A. Fang, A. Kapitulnik, Physical Review Letters 104 (2010).","mla":"Alpichshev, Zhanybek, et al. “STM Imaging of Electronic Waves on the Surface of Bi2Te3 Topologically Protected Surface States and Hexagonal Warping Effects.” Physical Review Letters, vol. 104, no. 1, American Physical Society, 2010, doi:10.1103/PhysRevLett.104.016401."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek"},{"first_name":"James","full_name":"Analytis, James","last_name":"Analytis"},{"first_name":"Jiunhaw","full_name":"Chu, Jiunhaw","last_name":"Chu"},{"full_name":"Fisher, Ian","last_name":"Fisher","first_name":"Ian"},{"last_name":"Chen","full_name":"Chen, Yulin","first_name":"Yulin"},{"full_name":"Shen, Zhixun","last_name":"Shen","first_name":"Zhixun"},{"full_name":"Fang, Aiping","last_name":"Fang","first_name":"Aiping"},{"full_name":"Kapitulnik, Aharon","last_name":"Kapitulnik","first_name":"Aharon"}],"publist_id":"7444","title":"STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects","_id":"385","type":"journal_article","status":"public"},{"year":"2010","publication_status":"published","language":[{"iso":"eng"}],"day":"01","page":"12 - 23","date_created":"2018-12-11T12:05:30Z","date_published":"2010-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape with a disk of fixed radius? If it does, we also seek a preferably simple solution shape P;P’s offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give a decision algorithm for fixed radius in O(nlogn) time that handles any polygonal shape. For convex shapes, the complexity drops to O(n), which is also the time required to compute a solution shape P with at most one more vertex than a vertex-minimal one."}],"oa_version":"None","publisher":"TU Dortmund","quality_controlled":"1","month":"01","date_updated":"2021-01-12T07:52:39Z","citation":{"mla":"Berberich, Eric, et al. Polygonal Reconstruction from Approximate Offsets. TU Dortmund, 2010, pp. 12–23.","ama":"Berberich E, Halperin D, Kerber M, Pogalnikova R. Polygonal reconstruction from approximate offsets. In: TU Dortmund; 2010:12-23.","apa":"Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2010). Polygonal reconstruction from approximate offsets (pp. 12–23). Presented at the EuroCG: European Workshop on Computational Geometry, Dortmund, Germany: TU Dortmund.","ieee":"E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Polygonal reconstruction from approximate offsets,” presented at the EuroCG: European Workshop on Computational Geometry, Dortmund, Germany, 2010, pp. 12–23.","short":"E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, in:, TU Dortmund, 2010, pp. 12–23.","chicago":"Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Polygonal Reconstruction from Approximate Offsets,” 12–23. TU Dortmund, 2010.","ista":"Berberich E, Halperin D, Kerber M, Pogalnikova R. 2010. Polygonal reconstruction from approximate offsets. EuroCG: European Workshop on Computational Geometry, 12–23."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Berberich, Eric","last_name":"Berberich","first_name":"Eric"},{"full_name":"Halperin, Dan","last_name":"Halperin","first_name":"Dan"},{"orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"last_name":"Pogalnikova","full_name":"Pogalnikova, Roza","first_name":"Roza"}],"publist_id":"2334","department":[{"_id":"HeEd"}],"title":"Polygonal reconstruction from approximate offsets","_id":"3850","conference":{"end_date":"2010-03-24","location":"Dortmund, Germany","start_date":"2010-03-22","name":"EuroCG: European Workshop on Computational Geometry"},"type":"conference","status":"public"},{"citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Generalized Mean-Payoff and Energy Games,” 8:505–16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.505.","ista":"Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2010. Generalized mean-payoff and energy games. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 8, 505–516.","mla":"Chatterjee, Krishnendu, et al. Generalized Mean-Payoff and Energy Games. Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 505–16, doi:10.4230/LIPIcs.FSTTCS.2010.505.","ama":"Chatterjee K, Doyen L, Henzinger TA, Raskin J. Generalized mean-payoff and energy games. In: Vol 8. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:505-516. doi:10.4230/LIPIcs.FSTTCS.2010.505","apa":"Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2010). Generalized mean-payoff and energy games (Vol. 8, pp. 505–516). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.505","ieee":"K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Generalized mean-payoff and energy games,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India, 2010, vol. 8, pp. 505–516.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 505–516."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2321","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Jean","last_name":"Raskin","full_name":"Raskin, Jean"}],"article_processing_charge":"No","title":"Generalized mean-payoff and energy games","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2010","day":"13","page":"505 - 516","doi":"10.4230/LIPIcs.FSTTCS.2010.505","date_published":"2010-12-13T00:00:00Z","date_created":"2018-12-11T12:05:34Z","_id":"3860","type":"conference","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"conference":{"location":"Chennai, India","end_date":"2010-12-18","start_date":"2010-12-15","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"status":"public","pubrep_id":"59","date_updated":"2021-01-12T07:52:44Z","ddc":["005"],"file_date_updated":"2020-07-14T12:46:18Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"text":"In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Generalized mean-payoff and energy games replace individual weights by tuples, and the limit average (resp. running sum) of each coordinate must be (resp. remain) nonnegative. These games have applications in the synthesis of resource-bounded processes with multiple resources. We prove the finite-memory determinacy of generalized energy games and show the inter- reducibility of generalized mean-payoff and energy games for finite-memory strategies. We also improve the computational complexity for solving both classes of games with finite-memory strategies: while the previously best known upper bound was EXPSPACE, and no lower bound was known, we give an optimal coNP-complete bound. For memoryless strategies, we show that the problem of deciding the existence of a winning strategy for the protagonist is NP-complete.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LIPIcs"],"month":"12","intvolume":" 8","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1caabd6319b979927208117a41192637","file_id":"5147","file_size":178278,"date_updated":"2020-07-14T12:46:18Z","creator":"system","file_name":"IST-2012-59-v1+1_Generalized_mean-payoff_and_energy_games.pdf","date_created":"2018-12-12T10:15:27Z"},{"file_name":"IST-2016-59-v2+1_2_1_.pdf","date_created":"2018-12-12T10:15:28Z","creator":"system","file_size":477976,"date_updated":"2020-07-14T12:46:18Z","file_id":"5148","checksum":"3a59759ceeacdb5b578f3803d5e6769b","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":8,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"_id":"3862","status":"public","pubrep_id":"57","type":"journal_article","extern":"1","ddc":["004"],"date_updated":"2022-03-21T08:20:03Z","file_date_updated":"2020-07-14T12:46:18Z","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Quantitative generalizations of classical languages, which assign to each word a real number instead of a Boolean value, have applications in modeling resource-constrained computation. We use weighted automata (finite automata with transition weights) to define several natural classes of quantitative languages over finite and infinite words; in particular, the real value of an infinite run is computed as the maximum, limsup, liminf, limit average, or discounted sum of the transition weights. We define the classical decision problems of automata theory (emptiness, universality, language inclusion, and language equivalence) in the quantitative setting and study their computational complexity. As the decidability of the language-inclusion problem remains open for some classes of weighted automata, we introduce a notion of quantitative simulation that is decidable and implies language inclusion. We also give a complete characterization of the expressive power of the various classes of weighted automata. In particular, we show that most classes of weighted automata cannot be determinized."}],"month":"07","intvolume":" 11","scopus_import":"1","file":[{"file_id":"5230","checksum":"f2e50bbd6871fba0aec30bd9625a1ee7","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:41Z","file_name":"IST-2012-57-v1+1_Quantitative_languages.pdf","date_updated":"2020-07-14T12:46:18Z","file_size":169136,"creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":11,"ec_funded":1,"article_number":"23","project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Quantitative Languages.” ACM Transactions on Computational Logic (TOCL). ACM, 2010. https://doi.org/10.1145/1805950.1805953.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2010. Quantitative languages. ACM Transactions on Computational Logic (TOCL). 11(4), 23.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Languages.” ACM Transactions on Computational Logic (TOCL), vol. 11, no. 4, 23, ACM, 2010, doi:10.1145/1805950.1805953.","ama":"Chatterjee K, Doyen L, Henzinger TA. Quantitative languages. ACM Transactions on Computational Logic (TOCL). 2010;11(4). doi:10.1145/1805950.1805953","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2010). Quantitative languages. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/1805950.1805953","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Quantitative languages,” ACM Transactions on Computational Logic (TOCL), vol. 11, no. 4. ACM, 2010.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, ACM Transactions on Computational Logic (TOCL) 11 (2010)."},"title":"Quantitative languages","publist_id":"2318","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"article_processing_charge":"No","publisher":"ACM","quality_controlled":"1","oa":1,"day":"01","publication":"ACM Transactions on Computational Logic (TOCL)","has_accepted_license":"1","year":"2010","doi":"10.1145/1805950.1805953","date_published":"2010-07-01T00:00:00Z","date_created":"2018-12-11T12:05:34Z"},{"_id":"3864","status":"public","conference":{"location":"Edinburgh, United Kingdom","end_date":"2010-07-19","start_date":"201-07-15","name":"CAV: Computer Aided Verification"},"type":"conference","date_updated":"2023-02-23T10:17:28Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Often one has a preference order among the different systems that satisfy a given specification. Under a probabilistic assumption about the possible inputs, such a preference order is naturally expressed by a weighted automaton, which assigns to each word a value, such that a system is preferred if it generates a higher expected value. We solve the following optimal-synthesis problem: given an omega-regular specification, a Markov chain that describes the distribution of inputs, and a weighted automaton that measures how well a system satisfies the given specification tinder the given input assumption, synthesize a system that optimizes the measured value. For safety specifications and measures that are defined by mean-payoff automata, the optimal-synthesis problem amounts to finding a strategy in a Markov decision process (MDP) that is optimal for a long-run average reward objective, which can be done in polynomial time. For general omega-regular specifications, the solution rests on a new, polynomial-time algorithm for computing optimal strategies in MDPs with mean-payoff parity objectives. We present some experimental results showing optimal systems that were automatically generated in this way."}],"intvolume":" 6174","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1004.0739"}],"alternative_title":["LNCS"],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"1856"}]},"volume":6174,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “Measuring and Synthesizing Systems in Probabilistic Environments,” 6174:380–95. Springer, 2010. https://doi.org/10.1007/978-3-642-14295-6_34.","ista":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2010. Measuring and synthesizing systems in probabilistic environments. CAV: Computer Aided Verification, LNCS, vol. 6174, 380–395.","mla":"Chatterjee, Krishnendu, et al. Measuring and Synthesizing Systems in Probabilistic Environments. Vol. 6174, Springer, 2010, pp. 380–95, doi:10.1007/978-3-642-14295-6_34.","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Singh, R. (2010). Measuring and synthesizing systems in probabilistic environments (Vol. 6174, pp. 380–395). Presented at the CAV: Computer Aided Verification, Edinburgh, United Kingdom: Springer. https://doi.org/10.1007/978-3-642-14295-6_34","ama":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. Measuring and synthesizing systems in probabilistic environments. In: Vol 6174. Springer; 2010:380-395. doi:10.1007/978-3-642-14295-6_34","short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, in:, Springer, 2010, pp. 380–395.","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “Measuring and synthesizing systems in probabilistic environments,” presented at the CAV: Computer Aided Verification, Edinburgh, United Kingdom, 2010, vol. 6174, pp. 380–395."},"title":"Measuring and synthesizing systems in probabilistic environments","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Jobstmann","full_name":"Jobstmann, Barbara","first_name":"Barbara"},{"first_name":"Rohit","last_name":"Singh","full_name":"Singh, Rohit"}],"publist_id":"2313","acknowledgement":"This research was supported by the European Union project COMBEST and the European Network of Excellence ArtistDesign.","oa":1,"quality_controlled":"1","publisher":"Springer","day":"09","year":"2010","date_created":"2018-12-11T12:05:35Z","date_published":"2010-07-09T00:00:00Z","doi":"10.1007/978-3-642-14295-6_34","page":"380 - 395"},{"department":[{"_id":"KrCh"}],"editor":[{"first_name":"David","last_name":"Rosenblum","full_name":"Rosenblum, David"},{"first_name":"Gabriele","last_name":"Taenzer","full_name":"Taenzer, Gabriele"}],"title":"Analyzing the impact of change in multi-threaded programs","publist_id":"2315","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"De Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"full_name":"Raman, Vishwanath","last_name":"Raman","first_name":"Vishwanath"},{"full_name":"Sánchez, César","last_name":"Sánchez","first_name":"César"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:52:47Z","citation":{"mla":"Chatterjee, Krishnendu, et al. Analyzing the Impact of Change in Multi-Threaded Programs. Edited by David Rosenblum and Gabriele Taenzer, vol. 6013, Springer, 2010, pp. 293–307, doi:10.1007/978-3-642-12029-9_21.","ama":"Chatterjee K, De Alfaro L, Raman V, Sánchez C. Analyzing the impact of change in multi-threaded programs. In: Rosenblum D, Taenzer G, eds. Vol 6013. Springer; 2010:293-307. doi:10.1007/978-3-642-12029-9_21","apa":"Chatterjee, K., De Alfaro, L., Raman, V., & Sánchez, C. (2010). Analyzing the impact of change in multi-threaded programs. In D. Rosenblum & G. Taenzer (Eds.) (Vol. 6013, pp. 293–307). Presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus: Springer. https://doi.org/10.1007/978-3-642-12029-9_21","ieee":"K. Chatterjee, L. De Alfaro, V. Raman, and C. Sánchez, “Analyzing the impact of change in multi-threaded programs,” presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 293–307.","short":"K. Chatterjee, L. De Alfaro, V. Raman, C. Sánchez, in:, D. Rosenblum, G. Taenzer (Eds.), Springer, 2010, pp. 293–307.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Vishwanath Raman, and César Sánchez. “Analyzing the Impact of Change in Multi-Threaded Programs.” edited by David Rosenblum and Gabriele Taenzer, 6013:293–307. Springer, 2010. https://doi.org/10.1007/978-3-642-12029-9_21.","ista":"Chatterjee K, De Alfaro L, Raman V, Sánchez C. 2010. Analyzing the impact of change in multi-threaded programs. FASE: Fundamental Approaches To Software Engineering, LNCS, vol. 6013, 293–307."},"status":"public","conference":{"start_date":"2010-03-20","location":"Paphos, Cyprus","end_date":"2010-03-28","name":"FASE: Fundamental Approaches To Software Engineering"},"type":"conference","_id":"3865","date_created":"2018-12-11T12:05:35Z","doi":"10.1007/978-3-642-12029-9_21","volume":6013,"date_published":"2010-04-21T00:00:00Z","page":"293 - 307","language":[{"iso":"eng"}],"day":"21","publication_status":"published","year":"2010","intvolume":" 6013","month":"04","alternative_title":["LNCS"],"publisher":"Springer","quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"We introduce a technique for debugging multi-threaded C programs and analyzing the impact of source code changes, and its implementation in the prototype tool DIRECT. Our approach uses a combination of source code instrumentation and runtime management. The source code along with a test harness is instrumented to monitor Operating System (OS) and user defined function calls. DIRECT tracks all concurrency control primitives and, optionally, data from the program. DIRECT maintains an abstract global state that combines information from every thread, including the sequence of function calls and concurrency primitives executed. The runtime manager can insert delays, provoking thread inter-leavings that may exhibit bugs that are difficult to reach otherwise. The runtime manager collects an approximation of the reachable state space and uses this approximation to assess the impact of change in a new version of the program."}]},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"page":"1206 - 1220","doi":"10.1016/j.ic.2009.09.006","date_published":"2010-10-01T00:00:00Z","date_created":"2018-12-11T12:05:35Z","has_accepted_license":"1","year":"2010","day":"01","publication":"Information and Computation","project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"}],"publist_id":"2319","author":[{"last_name":"Berwanger","full_name":"Berwanger, Dietmar","first_name":"Dietmar"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"De Wulf","full_name":"De Wulf, Martin"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"title":"Strategy construction for parity games with imperfect information","citation":{"short":"D. Berwanger, K. Chatterjee, M. De Wulf, L. Doyen, T.A. Henzinger, Information and Computation 208 (2010) 1206–1220.","ieee":"D. Berwanger, K. Chatterjee, M. De Wulf, L. Doyen, and T. A. Henzinger, “Strategy construction for parity games with imperfect information,” Information and Computation, vol. 208, no. 10. Elsevier, pp. 1206–1220, 2010.","apa":"Berwanger, D., Chatterjee, K., De Wulf, M., Doyen, L., & Henzinger, T. A. (2010). Strategy construction for parity games with imperfect information. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2009.09.006","ama":"Berwanger D, Chatterjee K, De Wulf M, Doyen L, Henzinger TA. Strategy construction for parity games with imperfect information. Information and Computation. 2010;208(10):1206-1220. doi:10.1016/j.ic.2009.09.006","mla":"Berwanger, Dietmar, et al. “Strategy Construction for Parity Games with Imperfect Information.” Information and Computation, vol. 208, no. 10, Elsevier, 2010, pp. 1206–20, doi:10.1016/j.ic.2009.09.006.","ista":"Berwanger D, Chatterjee K, De Wulf M, Doyen L, Henzinger TA. 2010. Strategy construction for parity games with imperfect information. Information and Computation. 208(10), 1206–1220.","chicago":"Berwanger, Dietmar, Krishnendu Chatterjee, Martin De Wulf, Laurent Doyen, and Thomas A Henzinger. “Strategy Construction for Parity Games with Imperfect Information.” Information and Computation. Elsevier, 2010. https://doi.org/10.1016/j.ic.2009.09.006."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"10","intvolume":" 208","abstract":[{"lang":"eng","text":"We consider two-player parity games with imperfect information in which strategies rely on observations that provide imperfect information about the history of a play. To solve such games, i.e., to determine the winning regions of players and corresponding winning strategies, one can use the subset construction to build an equivalent perfect-information game. Recently, an algorithm that avoids the inefficient subset construction has been proposed. The algorithm performs a fixed-point computation in a lattice of antichains, thus maintaining a succinct representation of state sets. However, this representation does not allow to recover winning strategies. In this paper, we build on the antichain approach to develop an algorithm for constructing the winning strategies in parity games of imperfect information. One major obstacle in adapting the classical procedure is that the complementation of attractor sets would break the invariant of downward-closedness on which the antichain representation relies. We overcome this difficulty by decomposing problem instances recursively into games with a combination of reachability, safety, and simpler parity conditions. We also report on an experimental implementation of our algorithm: to our knowledge, this is the first implementation of a procedure for solving imperfect-information parity games on graphs."}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"earlier_version","id":"3880","status":"public"}]},"issue":"10","volume":208,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-12T10:17:44Z","file_name":"IST-2012-58-v1+1_Strategy_construction_for_parity_games_with_imperfect_information.pdf","creator":"system","date_updated":"2020-07-14T12:46:18Z","file_size":287496,"file_id":"5300","checksum":"29d146e4f8049dbb7f80bbf7ea3700ed","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","pubrep_id":"58","_id":"3863","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:18Z","date_updated":"2023-02-23T11:46:47Z","ddc":["005"]},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2018-12-11T12:05:34Z","date_published":"2010-06-01T00:00:00Z","doi":"10.1016/j.ic.2009.07.004","page":"677 - 693","publication":"Information and Computation","day":"01","year":"2010","has_accepted_license":"1","title":"Strategy logic","publist_id":"2317","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Piterman, Nir","last_name":"Piterman","first_name":"Nir"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and N. Piterman, “Strategy logic,” Information and Computation, vol. 208, no. 6. Elsevier, pp. 677–693, 2010.","short":"K. Chatterjee, T.A. Henzinger, N. Piterman, Information and Computation 208 (2010) 677–693.","ama":"Chatterjee K, Henzinger TA, Piterman N. Strategy logic. Information and Computation. 2010;208(6):677-693. doi:10.1016/j.ic.2009.07.004","apa":"Chatterjee, K., Henzinger, T. A., & Piterman, N. (2010). Strategy logic. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2009.07.004","mla":"Chatterjee, Krishnendu, et al. “Strategy Logic.” Information and Computation, vol. 208, no. 6, Elsevier, 2010, pp. 677–93, doi:10.1016/j.ic.2009.07.004.","ista":"Chatterjee K, Henzinger TA, Piterman N. 2010. Strategy logic. Information and Computation. 208(6), 677–693.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Strategy Logic.” Information and Computation. Elsevier, 2010. https://doi.org/10.1016/j.ic.2009.07.004."},"intvolume":" 208","month":"06","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We introduce strategy logic, a logic that treats strategies in two-player games as explicit first-order objects. The explicit treatment of strategies allows us to specify properties of nonzero-sum games in a simple and natural way. We show that the one-alternation fragment of strategy logic is strong enough to express the existence of Nash equilibria and secure equilibria, and subsumes other logics that were introduced to reason about games, such as ATL, ATL*, and game logic. We show that strategy logic is decidable, by constructing tree automata that recognize sets of strategies. While for the general logic, our decision procedure is nonelementary, for the simple fragment that is used above we show that the complexity is polynomial in the size of the game graph and optimal in the size of the formula (ranging from polynomial to 2EXPTIME depending on the form of the formula)."}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3884"}]},"issue":"6","volume":208,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:11:54Z","file_name":"IST-2012-56-v1+1_Strategy_logic.pdf","creator":"system","date_updated":"2020-07-14T12:46:18Z","file_size":189120,"file_id":"4911","checksum":"13bff93f3c2a014e2908145a4517f177","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","pubrep_id":"56","status":"public","type":"journal_article","_id":"3861","file_date_updated":"2020-07-14T12:46:18Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["000","004"],"date_updated":"2023-02-23T11:46:57Z"},{"doi":"10.1109/TVCG.2010.139","date_published":"2010-10-28T00:00:00Z","date_created":"2018-12-11T12:05:47Z","page":"1251 - 1260","day":"28","publication":"IEEE Transactions of Visualization and Computer Graphics","has_accepted_license":"1","year":"2010","quality_controlled":"1","publisher":"IEEE","oa":1,"title":"Computing robustness and persistence for images","author":[{"last_name":"Bendich","full_name":"Bendich, Paul","first_name":"Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299"}],"publist_id":"2253","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bendich, Paul, Herbert Edelsbrunner, and Michael Kerber. “Computing Robustness and Persistence for Images.” IEEE Transactions of Visualization and Computer Graphics. IEEE, 2010. https://doi.org/10.1109/TVCG.2010.139.","ista":"Bendich P, Edelsbrunner H, Kerber M. 2010. Computing robustness and persistence for images. IEEE Transactions of Visualization and Computer Graphics. 16(6), 1251–1260.","mla":"Bendich, Paul, et al. “Computing Robustness and Persistence for Images.” IEEE Transactions of Visualization and Computer Graphics, vol. 16, no. 6, IEEE, 2010, pp. 1251–60, doi:10.1109/TVCG.2010.139.","apa":"Bendich, P., Edelsbrunner, H., & Kerber, M. (2010). Computing robustness and persistence for images. IEEE Transactions of Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2010.139","ama":"Bendich P, Edelsbrunner H, Kerber M. Computing robustness and persistence for images. IEEE Transactions of Visualization and Computer Graphics. 2010;16(6):1251-1260. doi:10.1109/TVCG.2010.139","ieee":"P. Bendich, H. Edelsbrunner, and M. Kerber, “Computing robustness and persistence for images,” IEEE Transactions of Visualization and Computer Graphics, vol. 16, no. 6. IEEE, pp. 1251–1260, 2010.","short":"P. Bendich, H. Edelsbrunner, M. Kerber, IEEE Transactions of Visualization and Computer Graphics 16 (2010) 1251–1260."},"volume":16,"issue":"6","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5262","checksum":"f6d813c04f4b46023cec6b9a17f15472","creator":"system","file_size":721994,"date_updated":"2020-07-14T12:46:21Z","file_name":"IST-2016-536-v1+1_2010-J-02-PersistenceforImages.pdf","date_created":"2018-12-12T10:17:10Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 16","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"We are interested in 3-dimensional images given as arrays of voxels with intensity values. Extending these values to acontinuous function, we study the robustness of homology classes in its level and interlevel sets, that is, the amount of perturbationneeded to destroy these classes. The structure of the homology classes and their robustness, over all level and interlevel sets, can bevisualized by a triangular diagram of dots obtained by computing the extended persistence of the function. We give a fast hierarchicalalgorithm using the dual complexes of oct-tree approximations of the function. In addition, we show that for balanced oct-trees, thedual complexes are geometrically realized in $R^3$ and can thus be used to construct level and interlevel sets. We apply these tools tostudy 3-dimensional images of plant root systems.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:21Z","department":[{"_id":"HeEd"}],"ddc":["000"],"date_updated":"2021-01-12T07:53:04Z","status":"public","pubrep_id":"536","type":"journal_article","_id":"3901"},{"language":[{"iso":"eng"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"05","year":"2010","publication_status":"published","date_created":"2018-12-11T12:05:48Z","date_published":"2010-05-05T00:00:00Z","doi":"10.1098/rspb.2010.0644","issue":"1695","volume":277,"page":"2821 - 2828","oa_version":"None","abstract":[{"lang":"eng","text":"Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by gen- etic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony."}],"intvolume":" 277","month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981995/"}],"publisher":"Royal Society, The","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T07:53:05Z","citation":{"ista":"Ugelvig LV, Kronauer D, Schrempf A, Heinze J, Cremer S. 2010. Rapid anti-pathogen response in ant societies relies on high genetic diversity. Proceedings of the Royal Society of London Series B Biological Sciences. 277(1695), 2821–2828.","chicago":"Ugelvig, Line V, Daniel Kronauer, Alexandra Schrempf, Jürgen Heinze, and Sylvia Cremer. “Rapid Anti-Pathogen Response in Ant Societies Relies on High Genetic Diversity.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2010. https://doi.org/10.1098/rspb.2010.0644.","ieee":"L. V. Ugelvig, D. Kronauer, A. Schrempf, J. Heinze, and S. Cremer, “Rapid anti-pathogen response in ant societies relies on high genetic diversity,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 277, no. 1695. Royal Society, The, pp. 2821–2828, 2010.","short":"L.V. Ugelvig, D. Kronauer, A. Schrempf, J. Heinze, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 277 (2010) 2821–2828.","ama":"Ugelvig LV, Kronauer D, Schrempf A, Heinze J, Cremer S. Rapid anti-pathogen response in ant societies relies on high genetic diversity. Proceedings of the Royal Society of London Series B Biological Sciences. 2010;277(1695):2821-2828. doi:10.1098/rspb.2010.0644","apa":"Ugelvig, L. V., Kronauer, D., Schrempf, A., Heinze, J., & Cremer, S. (2010). Rapid anti-pathogen response in ant societies relies on high genetic diversity. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2010.0644","mla":"Ugelvig, Line V., et al. “Rapid Anti-Pathogen Response in Ant Societies Relies on High Genetic Diversity.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 277, no. 1695, Royal Society, The, 2010, pp. 2821–28, doi:10.1098/rspb.2010.0644."},"title":"Rapid anti-pathogen response in ant societies relies on high genetic diversity","publist_id":"2251","author":[{"orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"first_name":"Daniel","full_name":"Kronauer, Daniel","last_name":"Kronauer"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"_id":"3904","status":"public","type":"journal_article"},{"page":"366 - 378","date_created":"2018-12-11T12:06:06Z","volume":11,"issue":"5","doi":"10.1038/nrm2889","date_published":"2010-05-01T00:00:00Z","year":"2010","publication_status":"published","publication":"Nature Reviews Molecular Cell Biology","day":"01","publisher":"Nature Publishing Group","quality_controlled":0,"intvolume":" 11","month":"05","abstract":[{"lang":"eng","text":"The shuttling of leukocytes between the bloodstream and interstitial tissues involves different locomotion strategies that are governed by locally presented soluble and cell-bound signals. Recent studies have furthered our understanding of the rapidly advancing field of leukocyte migration, particularly regarding cellular and subcellular events at the level of the venular wall. Furthermore, emerging cellular models are now addressing the transition from an adherent mode to a non-adherent state, incorporating mechanisms that support an efficient migratory profile of leukocytes in the interstitial tissue beyond the venular wall."}],"publist_id":"2170","author":[{"first_name":"Sussan","last_name":"Nourshargh","full_name":"Nourshargh, Sussan"},{"first_name":"Peter","full_name":"Hordijk, Peter L","last_name":"Hordijk"},{"last_name":"Sixt","full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"title":"Breaching multiple barriers: leukocyte motility through venular walls and the interstitium","date_updated":"2021-01-12T07:53:27Z","citation":{"apa":"Nourshargh, S., Hordijk, P., & Sixt, M. K. (2010). Breaching multiple barriers: leukocyte motility through venular walls and the interstitium. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm2889","ama":"Nourshargh S, Hordijk P, Sixt MK. Breaching multiple barriers: leukocyte motility through venular walls and the interstitium. Nature Reviews Molecular Cell Biology. 2010;11(5):366-378. doi:10.1038/nrm2889","ieee":"S. Nourshargh, P. Hordijk, and M. K. Sixt, “Breaching multiple barriers: leukocyte motility through venular walls and the interstitium,” Nature Reviews Molecular Cell Biology, vol. 11, no. 5. Nature Publishing Group, pp. 366–378, 2010.","short":"S. Nourshargh, P. Hordijk, M.K. Sixt, Nature Reviews Molecular Cell Biology 11 (2010) 366–378.","mla":"Nourshargh, Sussan, et al. “Breaching Multiple Barriers: Leukocyte Motility through Venular Walls and the Interstitium.” Nature Reviews Molecular Cell Biology, vol. 11, no. 5, Nature Publishing Group, 2010, pp. 366–78, doi:10.1038/nrm2889.","ista":"Nourshargh S, Hordijk P, Sixt MK. 2010. Breaching multiple barriers: leukocyte motility through venular walls and the interstitium. Nature Reviews Molecular Cell Biology. 11(5), 366–378.","chicago":"Nourshargh, Sussan, Peter Hordijk, and Michael K Sixt. “Breaching Multiple Barriers: Leukocyte Motility through Venular Walls and the Interstitium.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2010. https://doi.org/10.1038/nrm2889."},"extern":1,"type":"journal_article","status":"public","_id":"3956"},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924654/","open_access":"1"}],"scopus_import":1,"intvolume":" 29","month":"08","abstract":[{"lang":"eng","text":"Integrin- and cadherin-mediated adhesion is central for cell and tissue morphogenesis, allowing cells and tissues to change shape without loosing integrity. Studies predominantly in cell culture showed that mechanosensation through adhesion structures is achieved by force-mediated modulation of their molecular composition. The specific molecular composition of adhesion sites in turn determines their signalling activity and dynamic reorganization. Here, we will review how adhesion sites respond to mecanical stimuli, and how spatially and temporally regulated signalling from different adhesion sites controls cell migration and tissue morphogenesis."}],"acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"oa_version":"Submitted Version","issue":"16","volume":29,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"4157","department":[{"_id":"Bio"},{"_id":"CaHe"}],"date_updated":"2021-01-12T07:54:55Z","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","page":"2753 - 2768","date_created":"2018-12-11T12:07:17Z","doi":"10.1038/emboj.2010.182","date_published":"2010-08-18T00:00:00Z","year":"2010","publication":"EMBO Journal","day":"18","external_id":{"pmid":["20717145"]},"publist_id":"1962","author":[{"full_name":"Papusheva, Ekaterina","last_name":"Papusheva","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"title":"Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis","citation":{"mla":"Papusheva, Ekaterina, and Carl-Philipp J. Heisenberg. “Spatial Organization of Adhesion: Force-Dependent Regulation and Function in Tissue Morphogenesis.” EMBO Journal, vol. 29, no. 16, Wiley-Blackwell, 2010, pp. 2753–68, doi:10.1038/emboj.2010.182.","apa":"Papusheva, E., & Heisenberg, C.-P. J. (2010). Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2010.182","ama":"Papusheva E, Heisenberg C-PJ. Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis. EMBO Journal. 2010;29(16):2753-2768. doi:10.1038/emboj.2010.182","ieee":"E. Papusheva and C.-P. J. Heisenberg, “Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis,” EMBO Journal, vol. 29, no. 16. Wiley-Blackwell, pp. 2753–2768, 2010.","short":"E. Papusheva, C.-P.J. Heisenberg, EMBO Journal 29 (2010) 2753–2768.","chicago":"Papusheva, Ekaterina, and Carl-Philipp J Heisenberg. “Spatial Organization of Adhesion: Force-Dependent Regulation and Function in Tissue Morphogenesis.” EMBO Journal. Wiley-Blackwell, 2010. https://doi.org/10.1038/emboj.2010.182.","ista":"Papusheva E, Heisenberg C-PJ. 2010. Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis. EMBO Journal. 29(16), 2753–2768."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Nature Publishing Group","quality_controlled":0,"month":"01","intvolume":" 12","abstract":[{"text":"Cell migration is central to embryonic development, homeostasis and disease(1), processes in which cells move as part of a group or individually. Whereas the mechanisms controlling single-cell migration in vitro are relatively well understood(2-4), less is known about the mechanisms promoting the motility of individual cells in vivo. In particular, it is not clear how cells that form blebs in their migration use those protrusions to bring about movement in the context of the three-dimensional cellular environment(5,6). Here we show that the motility of chemokine-guided germ cells within the zebrafish embryo requires the function of the small Rho GTPases Rac1 and RhoA, as well as E-cadherin-mediated cell-cell adhesion. Using fluorescence resonance energy transfer we demonstrate that Rac1 and RhoA are activated in the cell front. At this location, Rac1 is responsible for the formation of actin-rich structures, and RhoA promotes retrograde actin flow. We propose that these actin-rich structures undergoing retrograde flow are essential for the generation of E-cadherin-mediated traction forces between the germ cells and the surrounding tissue and are therefore crucial for cell motility in vivo.","lang":"eng"}],"page":"47 - 53","volume":12,"issue":"1","doi":"10.1038/ncb2003","date_published":"2010-01-01T00:00:00Z","date_created":"2018-12-11T12:07:28Z","year":"2010","publication_status":"published","day":"01","publication":"Nature Cell Biology","type":"journal_article","status":"public","_id":"4187","publist_id":"1932","author":[{"first_name":"Elena","last_name":"Kardash","full_name":"Kardash, Elena"},{"last_name":"Reichman Fried","full_name":"Reichman-Fried, Michal","first_name":"Michal"},{"last_name":"Maître","full_name":"Maître, Jean-Léon","first_name":"Jean"},{"first_name":"Bijan","last_name":"Boldajipour","full_name":"Boldajipour, Bijan"},{"full_name":"Ekaterina Papusheva","last_name":"Papusheva","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Messerschmidt, Esther-Maria","last_name":"Messerschmidt","first_name":"Esther"},{"full_name":"Heisenberg, Carl-Philipp","last_name":"Heisenberg","first_name":"Carl"},{"last_name":"Raz","full_name":"Raz, Erez","first_name":"Erez"}],"title":"A role for Rho GTPases and cell-cell adhesion in single-cell motility in vivo","date_updated":"2021-01-12T07:55:09Z","citation":{"ista":"Kardash E, Reichman Fried M, Maître J, Boldajipour B, Papusheva E, Messerschmidt E, Heisenberg C, Raz E. 2010. A role for Rho GTPases and cell-cell adhesion in single-cell motility in vivo. Nature Cell Biology. 12(1), 47–53.","chicago":"Kardash, Elena, Michal Reichman Fried, Jean Maître, Bijan Boldajipour, Ekaterina Papusheva, Esther Messerschmidt, Carl Heisenberg, and Erez Raz. “A Role for Rho GTPases and Cell-Cell Adhesion in Single-Cell Motility in Vivo.” Nature Cell Biology. Nature Publishing Group, 2010. https://doi.org/10.1038/ncb2003.","short":"E. Kardash, M. Reichman Fried, J. Maître, B. Boldajipour, E. Papusheva, E. Messerschmidt, C. Heisenberg, E. Raz, Nature Cell Biology 12 (2010) 47–53.","ieee":"E. Kardash et al., “A role for Rho GTPases and cell-cell adhesion in single-cell motility in vivo,” Nature Cell Biology, vol. 12, no. 1. Nature Publishing Group, pp. 47–53, 2010.","apa":"Kardash, E., Reichman Fried, M., Maître, J., Boldajipour, B., Papusheva, E., Messerschmidt, E., … Raz, E. (2010). A role for Rho GTPases and cell-cell adhesion in single-cell motility in vivo. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2003","ama":"Kardash E, Reichman Fried M, Maître J, et al. A role for Rho GTPases and cell-cell adhesion in single-cell motility in vivo. Nature Cell Biology. 2010;12(1):47-53. doi:10.1038/ncb2003","mla":"Kardash, Elena, et al. “A Role for Rho GTPases and Cell-Cell Adhesion in Single-Cell Motility in Vivo.” Nature Cell Biology, vol. 12, no. 1, Nature Publishing Group, 2010, pp. 47–53, doi:10.1038/ncb2003."},"extern":1},{"day":"26","publication":"Current Biology","language":[{"iso":"eng"}],"publication_status":"published","year":"2010","doi":"10.1016/j.cub.2009.11.036","date_published":"2010-01-26T00:00:00Z","volume":20,"issue":"2","date_created":"2018-12-11T12:07:40Z","page":"161 - 169","oa_version":"None","abstract":[{"lang":"eng","text":"Collective cell migration, the simultaneous movement of multiple cells that are connected by cell-cell adhesion, is ubiquitous in development, tissue repair, and tumor metastasis [1, 2]. It has been hypothesized that the directionality of cell movement during collective migration emerges as a collective property [3, 4]. Here we determine how movement directionality is established in collective mesendoderm migration during zebrafish gastrulation. By interfering with two key features of collective migration, (1) having neighboring cells and (2) adhering to them, we show that individual mesendoderm cells are capable of normal directed migration when moving as single cells but require cell-cell adhesion to participate in coordinated and directed migration when moving as part of a group. We conclude that movement directionality is not a de novo collective property of mesendoderm cells but rather a property of single mesendoderm cells that requires cell-cell adhesion during collective migration."}],"month":"01","intvolume":" 20","publisher":"Cell Press","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:55:25Z","citation":{"ista":"Arboleda Estudillo Y, Krieg M, Stuehmer J, Licata N, Mueller D, Heisenberg C-PJ. 2010. Movement directionality in collective migration of germ layer progenitors. Current Biology. 20(2), 161–169.","chicago":"Arboleda Estudillo, Yohanna, Michael Krieg, Jan Stuehmer, Nicholas Licata, Daniel Mueller, and Carl-Philipp J Heisenberg. “Movement Directionality in Collective Migration of Germ Layer Progenitors.” Current Biology. Cell Press, 2010. https://doi.org/10.1016/j.cub.2009.11.036.","apa":"Arboleda Estudillo, Y., Krieg, M., Stuehmer, J., Licata, N., Mueller, D., & Heisenberg, C.-P. J. (2010). Movement directionality in collective migration of germ layer progenitors. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2009.11.036","ama":"Arboleda Estudillo Y, Krieg M, Stuehmer J, Licata N, Mueller D, Heisenberg C-PJ. Movement directionality in collective migration of germ layer progenitors. Current Biology. 2010;20(2):161-169. doi:10.1016/j.cub.2009.11.036","short":"Y. Arboleda Estudillo, M. Krieg, J. Stuehmer, N. Licata, D. Mueller, C.-P.J. Heisenberg, Current Biology 20 (2010) 161–169.","ieee":"Y. Arboleda Estudillo, M. Krieg, J. Stuehmer, N. Licata, D. Mueller, and C.-P. J. Heisenberg, “Movement directionality in collective migration of germ layer progenitors,” Current Biology, vol. 20, no. 2. Cell Press, pp. 161–169, 2010.","mla":"Arboleda Estudillo, Yohanna, et al. “Movement Directionality in Collective Migration of Germ Layer Progenitors.” Current Biology, vol. 20, no. 2, Cell Press, 2010, pp. 161–69, doi:10.1016/j.cub.2009.11.036."},"title":"Movement directionality in collective migration of germ layer progenitors","author":[{"first_name":"Yohanna","full_name":"Arboleda Estudillo, Yohanna","last_name":"Arboleda Estudillo"},{"first_name":"Michael","last_name":"Krieg","full_name":"Krieg, Michael"},{"first_name":"Jan","full_name":"Stuehmer, Jan","last_name":"Stuehmer"},{"first_name":"Nicholas","last_name":"Licata","full_name":"Licata, Nicholas"},{"full_name":"Mueller, Daniel","last_name":"Mueller","first_name":"Daniel"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"1897","article_processing_charge":"No","_id":"4221","status":"public","type":"journal_article"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bergmann, Julia, and Patrick Danowski. “Ist Bibliothek 2.0 Überhaupt Noch Relevant? – Eine Einleitung in Das Handbuch.” Handbuch Bibliothek 2.0, edited by Julia Bergmann and Patrick Danowski, De Gruyter, 2010, pp. 5–20, doi:10.1515/9783110232103.","ieee":"J. Bergmann and P. Danowski, “Ist Bibliothek 2.0 überhaupt noch relevant? – Eine Einleitung in das Handbuch,” in Handbuch Bibliothek 2.0, J. Bergmann and P. Danowski, Eds. De Gruyter, 2010, pp. 5–20.","short":"J. Bergmann, P. Danowski, in:, J. Bergmann, P. Danowski (Eds.), Handbuch Bibliothek 2.0, De Gruyter, 2010, pp. 5–20.","apa":"Bergmann, J., & Danowski, P. (2010). Ist Bibliothek 2.0 überhaupt noch relevant? – Eine Einleitung in das Handbuch. In J. Bergmann & P. Danowski (Eds.), Handbuch Bibliothek 2.0 (pp. 5–20). De Gruyter. https://doi.org/10.1515/9783110232103","ama":"Bergmann J, Danowski P. Ist Bibliothek 2.0 überhaupt noch relevant? – Eine Einleitung in das Handbuch. In: Bergmann J, Danowski P, eds. Handbuch Bibliothek 2.0. Bibliotheks- und Informationspraxis 41. De Gruyter; 2010:5-20. doi:10.1515/9783110232103","chicago":"Bergmann, Julia, and Patrick Danowski. “Ist Bibliothek 2.0 Überhaupt Noch Relevant? – Eine Einleitung in Das Handbuch.” In Handbuch Bibliothek 2.0, edited by Julia Bergmann and Patrick Danowski, 5–20. Bibliotheks- Und Informationspraxis 41. De Gruyter, 2010. https://doi.org/10.1515/9783110232103.","ista":"Bergmann J, Danowski P. 2010.Ist Bibliothek 2.0 überhaupt noch relevant? – Eine Einleitung in das Handbuch. In: Handbuch Bibliothek 2.0. , 5–20."},"title":"Ist Bibliothek 2.0 überhaupt noch relevant? – Eine Einleitung in das Handbuch","editor":[{"last_name":"Bergmann","full_name":"Bergmann, Julia","first_name":"Julia"},{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","last_name":"Danowski","orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick"}],"author":[{"first_name":"Julia","last_name":"Bergmann","full_name":"Bergmann, Julia"},{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","last_name":"Danowski"}],"publist_id":"1235","quality_controlled":"1","publisher":"De Gruyter","oa":1,"day":"23","publication":"Handbuch Bibliothek 2.0","has_accepted_license":"1","year":"2010","doi":"10.1515/9783110232103","date_published":"2010-09-23T00:00:00Z","date_created":"2018-12-11T12:08:21Z","page":"5 - 20","series_title":"Bibliotheks- und Informationspraxis 41","_id":"4339","status":"public","pubrep_id":"12","type":"book_chapter","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["020"],"date_updated":"2021-01-12T07:56:15Z","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:46:27Z","oa_version":"Published Version","abstract":[{"text":"Mit diesem Buch möchten wir einen Überblick der aktuellen Diskussion zum Thema Bibliothek 2.0 geben und den Stand der tatsächlichen Umsetzung der Web 2.0-Ansätze in deutschsprachigen Bibliotheken beleuchten. An dieser Stelle ist die Frage erlaubt, warum es zu einer Zeit, in der es bereits die ersten \"Web 3.0\"- Konferenzen gibt, eines Handbuches der Bibliothek 2.0 noch bedarf. Und warum es überhaupt ein deutschsprachiges Handbuch zur Bibliothek 2.0 braucht, wo es doch bereits verschiedenste Publikationen zu diesem Thema aus anderen Ländern, insbesondere des angloamerikanischen Raums gibt. Ist dazu nicht bereits alles gesagt?","lang":"ger"}],"month":"09","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5123","checksum":"d42cedd48fffa85d75046f396a309fc3","creator":"system","file_size":567580,"date_updated":"2020-07-14T12:46:27Z","file_name":"IST-2012-12-v1+1_9783110232103.5.pdf","date_created":"2018-12-12T10:15:06Z"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"_id":"4358","type":"journal_article","status":"public","date_updated":"2021-01-12T07:56:23Z","citation":{"ama":"Guinane C, Ben Zakour N, Tormo Mas M, et al. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution. 2010;2:454-466. doi:10.1093/gbe/evq031","apa":"Guinane, C., Ben Zakour, N., Tormo Mas, M., Weinert, L., Lowder, B., Cartwright, R., … Fitzgerald, J. R. (2010). Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evq031","ieee":"C. Guinane et al., “Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation,” Genome Biology and Evolution, vol. 2. Oxford University Press, pp. 454–466, 2010.","short":"C. Guinane, N. Ben Zakour, M. Tormo Mas, L. Weinert, B. Lowder, R. Cartwright, D. Smyth, C. Smyth, J. Lindsay, K. Gould, A. Witney, J. Hinds, J.P. Bollback, A. Rambaut, J. Penades, J.R. Fitzgerald, Genome Biology and Evolution 2 (2010) 454–466.","mla":"Guinane, Caitriona, et al. “Evolutionary Genomics of Staphylococcus Aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation.” Genome Biology and Evolution, vol. 2, Oxford University Press, 2010, pp. 454–66, doi:10.1093/gbe/evq031.","ista":"Guinane C, Ben Zakour N, Tormo Mas M, Weinert L, Lowder B, Cartwright R, Smyth D, Smyth C, Lindsay J, Gould K, Witney A, Hinds J, Bollback JP, Rambaut A, Penades J, Fitzgerald JR. 2010. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution. 2, 454–466.","chicago":"Guinane, Caitriona, Nouri Ben Zakour, Maria Tormo Mas, Lucy Weinert, Bethan Lowder, Robyn Cartwright, Davida Smyth, et al. “Evolutionary Genomics of Staphylococcus Aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation.” Genome Biology and Evolution. Oxford University Press, 2010. https://doi.org/10.1093/gbe/evq031."},"extern":1,"publist_id":"1100","author":[{"last_name":"Guinane","full_name":"Guinane, Caitriona M","first_name":"Caitriona"},{"first_name":"Nouri","last_name":"Ben Zakour","full_name":"Ben Zakour, Nouri L"},{"last_name":"Tormo Mas","full_name":"Tormo-Mas, Maria A","first_name":"Maria"},{"first_name":"Lucy","last_name":"Weinert","full_name":"Weinert, Lucy A"},{"first_name":"Bethan","last_name":"Lowder","full_name":"Lowder, Bethan V"},{"first_name":"Robyn","last_name":"Cartwright","full_name":"Cartwright, Robyn A"},{"first_name":"Davida","full_name":"Smyth, Davida S","last_name":"Smyth"},{"last_name":"Smyth","full_name":"Smyth, Cyril J","first_name":"Cyril"},{"full_name":"Lindsay, Jodi A","last_name":"Lindsay","first_name":"Jodi"},{"last_name":"Gould","full_name":"Gould, Katherine A","first_name":"Katherine"},{"first_name":"Adam","full_name":"Witney, Adam","last_name":"Witney"},{"full_name":"Hinds, Jason","last_name":"Hinds","first_name":"Jason"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Jonathan Bollback"},{"last_name":"Rambaut","full_name":"Rambaut, Andrew","first_name":"Andrew"},{"full_name":"Penades, Jose R","last_name":"Penades","first_name":"Jose"},{"first_name":"J Ross","last_name":"Fitzgerald","full_name":"Fitzgerald, J Ross"}],"title":"Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation","abstract":[{"lang":"eng","text":"Phenotypic biotyping has traditionally been used to differentiate bacteria occupying distinct ecological niches such as host species. For example, the capacity of Staphylococcus aureus from sheep to coagulate ruminant plasma, reported over 60 years ago, led to the description of small ruminant and bovine S. aureus ecovars. The great majority of small ruminant isolates are represented by a single, widespread clonal complex (CC133) of S. aureus, but its evolutionary origin and the molecular basis for its host tropism remain unknown. Here, we provide evidence that the CC133 clone evolved as the result of a human to ruminant host jump followed by adaptive genome diversification. Comparative whole-genome sequencing revealed molecular evidence for host adaptation including gene decay and diversification of proteins involved in host-pathogen interactions. Importantly, several novel mobile genetic elements encoding virulence proteins with attenuated or enhanced activity in ruminants were widely distributed in CC133 isolates, suggesting a key role in its host-specific interactions. To investigate this further, we examined the activity of a novel staphylococcal pathogenicity island (SaPIov2) found in the great majority of CC133 isolates which encodes a variant of the chromosomally encoded von Willebrand-binding protein (vWbp(Sov2)), previously demonstrated to have coagulase activity for human plasma. Remarkably, we discovered that SaPIov2 confers the ability to coagulate ruminant plasma suggesting an important role in ruminant disease pathogenesis and revealing the origin of a defining phenotype of the classical S. aureus biotyping scheme. Taken together, these data provide broad new insights into the origin and molecular basis of S. aureus ruminant host specificity."}],"quality_controlled":0,"publisher":"Oxford University Press","intvolume":" 2","month":"06","year":"2010","publication_status":"published","publication":"Genome Biology and Evolution","day":"09","page":"454 - 466","date_created":"2018-12-11T12:08:27Z","volume":2,"date_published":"2010-06-09T00:00:00Z","doi":"10.1093/gbe/evq031"},{"_id":"4362","type":"conference","conference":{"location":"St. Julians, Malta","end_date":"2010-11-04","start_date":"2010-11-01","name":"RV: International Conference on Runtime Verification"},"status":"public","date_updated":"2021-01-12T07:56:25Z","citation":{"ista":"Singh V. 2010. Runtime verification for software transactional memories. RV: International Conference on Runtime Verification, LNCS, vol. 6418, 421–435.","chicago":"Singh, Vasu. “Runtime Verification for Software Transactional Memories.” edited by Oleg Sokolsky, Grigore Rosu, Nikolai Tilmann, Howard Barringer, Ylies Falcone, Bernd Finkbeiner, Klaus Havelund, Insup Lee, and Gordon Pace, 6418:421–35. Springer, 2010. https://doi.org/10.1007/978-3-642-16612-9_32.","ama":"Singh V. Runtime verification for software transactional memories. In: Sokolsky O, Rosu G, Tilmann N, et al., eds. Vol 6418. Springer; 2010:421-435. doi:10.1007/978-3-642-16612-9_32","apa":"Singh, V. (2010). Runtime verification for software transactional memories. In O. Sokolsky, G. Rosu, N. Tilmann, H. Barringer, Y. Falcone, B. Finkbeiner, … G. Pace (Eds.) (Vol. 6418, pp. 421–435). Presented at the RV: International Conference on Runtime Verification, St. Julians, Malta: Springer. https://doi.org/10.1007/978-3-642-16612-9_32","ieee":"V. Singh, “Runtime verification for software transactional memories,” presented at the RV: International Conference on Runtime Verification, St. Julians, Malta, 2010, vol. 6418, pp. 421–435.","short":"V. Singh, in:, O. Sokolsky, G. Rosu, N. Tilmann, H. Barringer, Y. Falcone, B. Finkbeiner, K. Havelund, I. Lee, G. Pace (Eds.), Springer, 2010, pp. 421–435.","mla":"Singh, Vasu. Runtime Verification for Software Transactional Memories. Edited by Oleg Sokolsky et al., vol. 6418, Springer, 2010, pp. 421–35, doi:10.1007/978-3-642-16612-9_32."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"1096","author":[{"first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","last_name":"Singh","full_name":"Singh, Vasu"}],"editor":[{"first_name":"Oleg","last_name":"Sokolsky","full_name":"Sokolsky, Oleg"},{"first_name":"Grigore","last_name":"Rosu","full_name":"Rosu, Grigore"},{"full_name":"Tilmann, Nikolai","last_name":"Tilmann","first_name":"Nikolai"},{"full_name":"Barringer, Howard","last_name":"Barringer","first_name":"Howard"},{"first_name":"Ylies","full_name":"Falcone, Ylies","last_name":"Falcone"},{"last_name":"Finkbeiner","full_name":"Finkbeiner, Bernd","first_name":"Bernd"},{"first_name":"Klaus","full_name":"Havelund, Klaus","last_name":"Havelund"},{"last_name":"Lee","full_name":"Lee, Insup","first_name":"Insup"},{"full_name":"Pace, Gordon","last_name":"Pace","first_name":"Gordon"}],"title":"Runtime verification for software transactional memories","department":[{"_id":"ToHe"}],"abstract":[{"text":"Software transactional memories (STMs) promise simple and efficient concurrent programming. Several correctness properties have been proposed for STMs. Based on a bounded conflict graph algorithm for verifying correctness of STMs, we develop TRACER, a tool for runtime verification of STM implementations. The novelty of TRACER lies in the way it combines coarse and precise runtime analyses to guarantee sound and complete verification in an efficient manner. We implement TRACER in the TL2 STM implementation. We evaluate the performance of TRACER on STAMP benchmarks. While a precise runtime verification technique based on conflict graphs results in an average slowdown of 60x, the two-level approach of TRACER performs complete verification with an average slowdown of around 25x across different benchmarks.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"Springer","scopus_import":1,"alternative_title":["LNCS"],"month":"01","intvolume":" 6418","publication_status":"published","year":"2010","day":"01","language":[{"iso":"eng"}],"page":"421 - 435","date_published":"2010-01-01T00:00:00Z","doi":"10.1007/978-3-642-16612-9_32","volume":6418,"date_created":"2018-12-11T12:08:28Z"},{"intvolume":" 5944","month":"01","main_file_link":[{"open_access":"1","url":"https://infoscience.epfl.ch/record/161290/"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"Techniques such as verification condition generation, predicate abstraction, and expressive type systems reduce software verification to proving formulas in expressive logics. Programs and their specifications often make use of data structures such as sets, multisets, algebraic data types, or graphs. Consequently, formulas generated from verification also involve such data structures. To automate the proofs of such formulas we propose a logic (a “calculus”) of such data structures. We build the calculus by starting from decidable logics of individual data structures, and connecting them through functions and sets, in ways that go beyond the frameworks such as Nelson-Oppen. The result are new decidable logics that can simultaneously specify properties of different kinds of data structures and overcome the limitations of the individual logics. Several of our decidable logics include abstraction functions that map a data structure into its more abstract view (a tree into a multiset, a multiset into a set), into a numerical quantity (the size or the height), or into the truth value of a candidate data structure invariant (sortedness, or the heap property). For algebraic data types, we identify an asymptotic many-to-one condition on the abstraction function that guarantees the existence of a decision procedure. In addition to the combination based on abstraction functions, we can combine multiple data structure theories if they all reduce to the same data structure logic. As an instance of this approach, we describe a decidable logic whose formulas are propositional combinations of formulas in: weak monadic second-order logic of two successors, two-variable logic with counting, multiset algebra with Presburger arithmetic, the Bernays-Schönfinkel-Ramsey class of first-order logic, and the logic of algebraic data types with the set content function. The subformulas in this combination can share common variables that refer to sets of objects along with the common set algebra operations. Such sound and complete combination is possible because the relations on sets definable in the component logics are all expressible in Boolean Algebra with Presburger Arithmetic. Presburger arithmetic and its new extensions play an important role in our decidability results. In several cases, when we combine logics that belong to NP, we can prove the satisfiability for the combined logic is still in NP.","lang":"eng"}],"volume":5944,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2010-01-17","location":"Madrid, Spain","end_date":"2010-01-19"},"type":"conference","_id":"4378","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:56:31Z","oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T12:08:33Z","date_published":"2010-01-01T00:00:00Z","doi":"10.1007/978-3-642-11319-2_6","page":"26 - 44","day":"01","year":"2010","title":"Building a calculus of data structures","editor":[{"first_name":"Gilles","last_name":"Barthe","full_name":"Barthe, Gilles"},{"full_name":"Hermenegildo, Manuel","last_name":"Hermenegildo","first_name":"Manuel"}],"publist_id":"1081","author":[{"full_name":"Kuncak, Viktor","last_name":"Kuncak","first_name":"Viktor"},{"first_name":"Ruzica","last_name":"Piskac","full_name":"Piskac, Ruzica"},{"first_name":"Philippe","full_name":"Suter, Philippe","last_name":"Suter"},{"last_name":"Wies","full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kuncak, Viktor, Ruzica Piskac, Philippe Suter, and Thomas Wies. “Building a Calculus of Data Structures.” edited by Gilles Barthe and Manuel Hermenegildo, 5944:26–44. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_6.","ista":"Kuncak V, Piskac R, Suter P, Wies T. 2010. Building a calculus of data structures. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 5944, 26–44.","mla":"Kuncak, Viktor, et al. Building a Calculus of Data Structures. Edited by Gilles Barthe and Manuel Hermenegildo, vol. 5944, Springer, 2010, pp. 26–44, doi:10.1007/978-3-642-11319-2_6.","short":"V. Kuncak, R. Piskac, P. Suter, T. Wies, in:, G. Barthe, M. Hermenegildo (Eds.), Springer, 2010, pp. 26–44.","ieee":"V. Kuncak, R. Piskac, P. Suter, and T. Wies, “Building a calculus of data structures,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 26–44.","ama":"Kuncak V, Piskac R, Suter P, Wies T. Building a calculus of data structures. In: Barthe G, Hermenegildo M, eds. Vol 5944. Springer; 2010:26-44. doi:10.1007/978-3-642-11319-2_6","apa":"Kuncak, V., Piskac, R., Suter, P., & Wies, T. (2010). Building a calculus of data structures. In G. Barthe & M. Hermenegildo (Eds.) (Vol. 5944, pp. 26–44). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-642-11319-2_6"}},{"extern":1,"date_updated":"2021-01-12T07:56:31Z","citation":{"mla":"Jones, Kevin, et al. “Analog Property Checkers: A DDR2 Case Study.” Formal Methods in System Design, vol. 36, no. 2, Springer, 2010, pp. 114–30, doi:10.1007/s10703-009-0085-x.","short":"K. Jones, V. Konrad, D. Nickovic, Formal Methods in System Design 36 (2010) 114–130.","ieee":"K. Jones, V. Konrad, and D. Nickovic, “Analog property checkers: a DDR2 case study,” Formal Methods in System Design, vol. 36, no. 2. Springer, pp. 114–130, 2010.","apa":"Jones, K., Konrad, V., & Nickovic, D. (2010). Analog property checkers: a DDR2 case study. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-009-0085-x","ama":"Jones K, Konrad V, Nickovic D. Analog property checkers: a DDR2 case study. Formal Methods in System Design. 2010;36(2):114-130. doi:10.1007/s10703-009-0085-x","chicago":"Jones, Kevin, Victor Konrad, and Dejan Nickovic. “Analog Property Checkers: A DDR2 Case Study.” Formal Methods in System Design. Springer, 2010. https://doi.org/10.1007/s10703-009-0085-x.","ista":"Jones K, Konrad V, Nickovic D. 2010. Analog property checkers: a DDR2 case study. Formal Methods in System Design. 36(2), 114–130."},"title":"Analog property checkers: a DDR2 case study","publist_id":"1080","author":[{"first_name":"Kevin","last_name":"Jones","full_name":"Jones, Kevin D"},{"full_name":"Konrad,Victor","last_name":"Konrad","first_name":"Victor"},{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Dejan Nickovic"}],"_id":"4379","status":"public","type":"journal_article","day":"01","publication":"Formal Methods in System Design","year":"2010","publication_status":"published","date_published":"2010-06-01T00:00:00Z","volume":36,"issue":"2","doi":"10.1007/s10703-009-0085-x","date_created":"2018-12-11T12:08:33Z","page":"114 - 130","acknowledgement":"We would like to thank Tom Giovannini from Rambus, Inc. for his detailed explana- tions of the DDR2 specification and for providing us with simulation traces. We would also like to thank Oded Maler from Verimag for discussions on the STL/PSL language and its extensions.","abstract":[{"lang":"eng","text":"The formal specification component of verification can be exported to simulation through the idea of property checkers. The essence of this approach is the automatic construction of an observer from the specification in the form of a program that can be interfaced with a simulator and alert the user if the property is violated by a simulation trace. Although not complete, this lighter approach to formal verification has been effectively used in software and digital hardware to detect errors. Recently, the idea of property checkers has been extended to analog and mixed-signal systems.\n\nIn this paper, we apply the property-based checking methodology to an industrial and realistic example of a DDR2 memory interface. The properties describing the DDR2 analog behavior are expressed in the formal specification language stl/psl in form of assertions. The simulation traces generated from an actual DDR2 interface design are checked with respect to the stl/psl assertions using the amt tool. The focus of this paper is on the translation of the official (informal and descriptive) specification of two non-trivial DDR2 properties into stl/psl assertions. We study both the benefits and the current limits of such approach.\n"}],"month":"06","intvolume":" 36","quality_controlled":0,"publisher":"Springer","main_file_link":[{"url":"http://openaccess.city.ac.uk/1066/","open_access":"1"}],"oa":1},{"citation":{"apa":"Henzinger, T. A., Tomar, A., Singh, V., Wies, T., & Zufferey, D. (2010). FlexPRICE: Flexible provisioning of resources in a cloud environment (pp. 83–90). Presented at the CLOUD: Cloud Computing, Miami, USA: IEEE. https://doi.org/10.1109/CLOUD.2010.71","ama":"Henzinger TA, Tomar A, Singh V, Wies T, Zufferey D. FlexPRICE: Flexible provisioning of resources in a cloud environment. In: IEEE; 2010:83-90. doi:10.1109/CLOUD.2010.71","short":"T.A. Henzinger, A. Tomar, V. Singh, T. Wies, D. Zufferey, in:, IEEE, 2010, pp. 83–90.","ieee":"T. A. Henzinger, A. Tomar, V. Singh, T. Wies, and D. Zufferey, “FlexPRICE: Flexible provisioning of resources in a cloud environment,” presented at the CLOUD: Cloud Computing, Miami, USA, 2010, pp. 83–90.","mla":"Henzinger, Thomas A., et al. FlexPRICE: Flexible Provisioning of Resources in a Cloud Environment. IEEE, 2010, pp. 83–90, doi:10.1109/CLOUD.2010.71.","ista":"Henzinger TA, Tomar A, Singh V, Wies T, Zufferey D. 2010. FlexPRICE: Flexible provisioning of resources in a cloud environment. CLOUD: Cloud Computing, 83–90.","chicago":"Henzinger, Thomas A, Anmol Tomar, Vasu Singh, Thomas Wies, and Damien Zufferey. “FlexPRICE: Flexible Provisioning of Resources in a Cloud Environment,” 83–90. IEEE, 2010. https://doi.org/10.1109/CLOUD.2010.71."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"1077","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Tomar, Anmol","last_name":"Tomar","id":"3D8D36B6-F248-11E8-B48F-1D18A9856A87","first_name":"Anmol"},{"last_name":"Singh","full_name":"Singh, Vasu","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Wies, Thomas"},{"first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","last_name":"Zufferey"}],"article_processing_charge":"No","title":"FlexPRICE: Flexible provisioning of resources in a cloud environment","quality_controlled":"1","publisher":"IEEE","oa":1,"has_accepted_license":"1","year":"2010","day":"26","page":"83 - 90","date_published":"2010-08-26T00:00:00Z","doi":"10.1109/CLOUD.2010.71","date_created":"2018-12-11T12:08:33Z","_id":"4381","type":"conference","conference":{"name":"CLOUD: Cloud Computing","start_date":"2010-07-05","location":"Miami, USA","end_date":"2010-07-10"},"status":"public","pubrep_id":"47","date_updated":"2021-01-12T07:56:33Z","ddc":["004"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:28Z","abstract":[{"lang":"eng","text":"Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We claim that, in order to realize the full potential of cloud computing, the user must be presented with a pricing model that offers flexibility at the requirements level, such as a choice between different degrees of execution speed and the cloud provider must be presented with a programming model that offers flexibility at the execution level, such as a choice between different scheduling policies. In such a flexible framework, with each job, the user purchases a virtual computer with the desired speed and cost characteristics, and the cloud provider can optimize the utilization of resources across a stream of jobs from different users. We designed a flexible framework to test our hypothesis, which is called FlexPRICE (Flexible Provisioning of Resources in a Cloud Environment) and works as follows. A user presents a job to the cloud. The cloud finds different schedules to execute the job and presents a set of quotes to the user in terms of price and duration for the execution. The user then chooses a particular quote and the cloud is obliged to execute the job according to the chosen quote. FlexPRICE thus hides the complexity of the actual scheduling decisions from the user, but still provides enough flexibility to meet the users actual demands. We implemented FlexPRICE in a simulator called PRICES that allows us to experiment with our framework. We observe that FlexPRICE provides a wide range of execution options-from fast and expensive to slow and cheap-- for the whole spectrum of data-intensive and computation-intensive jobs. We also observe that the set of quotes computed by FlexPRICE do not vary as the number of simultaneous jobs increases."}],"oa_version":"Submitted Version","scopus_import":1,"month":"08","publication_status":"published","file":[{"creator":"system","file_size":467436,"date_updated":"2020-07-14T12:46:28Z","file_name":"IST-2012-47-v1+1_FlexPRICE-_Flexible_provisioning_of_resources_in_a_cloud_environment.pdf","date_created":"2018-12-12T10:16:03Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5188","checksum":"98e534675339a8e2beca08890d048145"}],"language":[{"iso":"eng"}]},{"has_accepted_license":"1","year":"2010","publication_status":"published","file":[{"file_id":"5080","checksum":"f2ad6c00a6304da34bf21bcdcfd36c4b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2012-46-v1+1_Transactions_in_the_jungle.pdf","date_created":"2018-12-12T10:14:28Z","creator":"system","file_size":246409,"date_updated":"2020-07-14T12:46:28Z"}],"day":"13","language":[{"iso":"eng"}],"page":"263 - 272","date_published":"2010-06-13T00:00:00Z","doi":"10.1145/1810479.1810529","date_created":"2018-12-11T12:08:34Z","abstract":[{"lang":"eng","text":"Transactional memory (TM) has shown potential to simplify the task of writing concurrent programs. Inspired by classical work on databases, formal definitions of the semantics of TM executions have been proposed. Many of these definitions assumed that accesses to shared data are solely performed through transactions. In practice, due to legacy code and concurrency libraries, transactions in a TM have to share data with non-transactional operations. The semantics of such interaction, while widely discussed by practitioners, lacks a clear formal specification. Those interactions can vary, sometimes in subtle ways, between TM implementations and underlying memory models. We propose a correctness condition for TMs, parametrized opacity, to formally capture the now folklore notion of strong atomicity by stipulating the two following intuitive requirements: first, every transaction appears as if it is executed instantaneously with respect to other transactions and non-transactional operations, and second, non-transactional operations conform to the given underlying memory model. We investigate the inherent cost of implementing parametrized opacity. We first prove that parametrized opacity requires either instrumenting non-transactional operations (for most memory models) or writing to memory by transactions using potentially expensive read-modify-write instructions (such as compare-and-swap). Then, we show that for a class of practical relaxed memory models, parametrized opacity can indeed be implemented with constant-time instrumentation of non-transactional writes and no instrumentation of non-transactional reads. We show that, in practice, parametrizing the notion of correctness allows developing more efficient TM implementations."}],"oa_version":"Submitted Version","quality_controlled":"1","publisher":"ACM","oa":1,"month":"06","date_updated":"2021-01-12T07:56:33Z","citation":{"short":"R. Guerraoui, T.A. Henzinger, M. Kapalka, V. Singh, in:, ACM, 2010, pp. 263–272.","ieee":"R. Guerraoui, T. A. Henzinger, M. Kapalka, and V. Singh, “Transactions in the jungle,” presented at the SPAA: ACM Symposium on Parallel Algorithms and Architectures, Santorini, Greece, 2010, pp. 263–272.","ama":"Guerraoui R, Henzinger TA, Kapalka M, Singh V. Transactions in the jungle. In: ACM; 2010:263-272. doi:10.1145/1810479.1810529","apa":"Guerraoui, R., Henzinger, T. A., Kapalka, M., & Singh, V. (2010). Transactions in the jungle (pp. 263–272). Presented at the SPAA: ACM Symposium on Parallel Algorithms and Architectures, Santorini, Greece: ACM. https://doi.org/10.1145/1810479.1810529","mla":"Guerraoui, Rachid, et al. Transactions in the Jungle. ACM, 2010, pp. 263–72, doi:10.1145/1810479.1810529.","ista":"Guerraoui R, Henzinger TA, Kapalka M, Singh V. 2010. Transactions in the jungle. SPAA: ACM Symposium on Parallel Algorithms and Architectures, 263–272.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, Michal Kapalka, and Vasu Singh. “Transactions in the Jungle,” 263–72. ACM, 2010. https://doi.org/10.1145/1810479.1810529."},"ddc":["005"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Michal","last_name":"Kapalka","full_name":"Kapalka, Michal"},{"id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu","last_name":"Singh","full_name":"Singh, Vasu"}],"publist_id":"1076","file_date_updated":"2020-07-14T12:46:28Z","department":[{"_id":"ToHe"}],"title":"Transactions in the jungle","_id":"4382","type":"conference","conference":{"end_date":"2010-06-15","location":"Santorini, Greece","start_date":"2010-06-13","name":"SPAA: ACM Symposium on Parallel Algorithms and Architectures"},"status":"public","pubrep_id":"46"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":222626,"date_updated":"2020-07-14T12:46:28Z","creator":"system","file_name":"IST-2012-48-v1+1_A_marketplace_for_cloud_resources.pdf","date_created":"2018-12-12T10:09:42Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7680dd24016810710f7c977bc94f85e9","file_id":"4767"}],"abstract":[{"text":"Cloud computing is an emerging paradigm aimed to offer users pay-per-use computing resources, while leaving the burden of managing the computing infrastructure to the cloud provider. We present a new programming and pricing model that gives the cloud user the flexibility of trading execution speed and price on a per-job basis. We discuss the scheduling and resource management challenges for the cloud provider that arise in the implementation of this model. We argue that techniques from real-time and embedded software can be useful in this context.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"10","date_updated":"2021-01-12T07:56:32Z","ddc":["005"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:28Z","_id":"4380","conference":{"start_date":"2010-10-24","end_date":"2010-10-29","location":"Arizona, USA","name":"EMSOFT: Embedded Software "},"type":"conference","pubrep_id":"48","status":"public","year":"2010","has_accepted_license":"1","day":"24","page":"1 - 8","date_created":"2018-12-11T12:08:33Z","doi":"10.1145/1879021.1879022","date_published":"2010-10-24T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","citation":{"chicago":"Henzinger, Thomas A, Anmol Tomar, Vasu Singh, Thomas Wies, and Damien Zufferey. “A Marketplace for Cloud Resources,” 1–8. ACM, 2010. https://doi.org/10.1145/1879021.1879022.","ista":"Henzinger TA, Tomar A, Singh V, Wies T, Zufferey D. 2010. A marketplace for cloud resources. EMSOFT: Embedded Software , 1–8.","mla":"Henzinger, Thomas A., et al. A Marketplace for Cloud Resources. ACM, 2010, pp. 1–8, doi:10.1145/1879021.1879022.","ama":"Henzinger TA, Tomar A, Singh V, Wies T, Zufferey D. A marketplace for cloud resources. In: ACM; 2010:1-8. doi:10.1145/1879021.1879022","apa":"Henzinger, T. A., Tomar, A., Singh, V., Wies, T., & Zufferey, D. (2010). A marketplace for cloud resources (pp. 1–8). Presented at the EMSOFT: Embedded Software , Arizona, USA: ACM. https://doi.org/10.1145/1879021.1879022","short":"T.A. Henzinger, A. Tomar, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2010, pp. 1–8.","ieee":"T. A. Henzinger, A. Tomar, V. Singh, T. Wies, and D. Zufferey, “A marketplace for cloud resources,” presented at the EMSOFT: Embedded Software , Arizona, USA, 2010, pp. 1–8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tomar, Anmol","last_name":"Tomar","first_name":"Anmol","id":"3D8D36B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","full_name":"Singh, Vasu","last_name":"Singh"},{"full_name":"Wies, Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Zufferey","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"1078","title":"A marketplace for cloud resources"},{"status":"public","pubrep_id":"44","type":"conference","conference":{"name":"ACSD: Application of Concurrency to System Design"},"_id":"4389","file_date_updated":"2020-07-14T12:46:28Z","department":[{"_id":"ToHe"}],"ddc":["004"],"date_updated":"2021-01-12T07:56:36Z","month":"08","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Digital components play a central role in the design of complex embedded systems. These components are interconnected with other, possibly analog, devices and the physical environment. This environment cannot be entirely captured and can provide inaccurate input data to the component. It is thus important for digital components to have a robust behavior, i.e. the presence of a small change in the input sequences should not result in a drastic change in the output sequences. In this paper, we study a notion of robustness for sequential circuits. However, since sequential circuits may have parts that are naturally discontinuous (e.g., digital controllers with switching behavior), we need a flexible framework that accommodates this fact and leaves discontinuous parts of the circuit out from the robustness analysis. As a consequence, we consider sequential circuits that have their input variables partitioned into two disjoint sets: control and disturbance variables. Our contributions are (1) a definition of robustness for sequential circuits as a form of continuity with respect to disturbance variables, (2) the characterization of the exact class of sequential circuits that are robust according to our definition, (3) an algorithm to decide whether a sequential circuit is robust or not."}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4733","checksum":"42b2952bfc6b6974617bd554842b904a","creator":"system","date_updated":"2020-07-14T12:46:28Z","file_size":159920,"date_created":"2018-12-12T10:09:10Z","file_name":"IST-2012-44-v1+1_Robustness_of_sequential_circuits.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"Robustness of sequential circuits","author":[{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Legay","full_name":"Legay, Axel","first_name":"Axel"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"publist_id":"1069","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Doyen, Laurent, et al. Robustness of Sequential Circuits. IEEE, 2010, pp. 77–84, doi:10.1109/ACSD.2010.26.","ieee":"L. Doyen, T. A. Henzinger, A. Legay, and D. Nickovic, “Robustness of sequential circuits,” presented at the ACSD: Application of Concurrency to System Design, 2010, pp. 77–84.","short":"L. Doyen, T.A. Henzinger, A. Legay, D. Nickovic, in:, IEEE, 2010, pp. 77–84.","apa":"Doyen, L., Henzinger, T. A., Legay, A., & Nickovic, D. (2010). Robustness of sequential circuits (pp. 77–84). Presented at the ACSD: Application of Concurrency to System Design, IEEE. https://doi.org/10.1109/ACSD.2010.26","ama":"Doyen L, Henzinger TA, Legay A, Nickovic D. Robustness of sequential circuits. In: IEEE; 2010:77-84. doi:10.1109/ACSD.2010.26","chicago":"Doyen, Laurent, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Robustness of Sequential Circuits,” 77–84. IEEE, 2010. https://doi.org/10.1109/ACSD.2010.26.","ista":"Doyen L, Henzinger TA, Legay A, Nickovic D. 2010. Robustness of sequential circuits. ACSD: Application of Concurrency to System Design, 77–84."},"quality_controlled":"1","publisher":"IEEE","oa":1,"doi":"10.1109/ACSD.2010.26","date_published":"2010-08-23T00:00:00Z","date_created":"2018-12-11T12:08:36Z","page":"77 - 84","day":"23","has_accepted_license":"1","year":"2010"},{"author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","last_name":"Cerny"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"}],"publist_id":"1064","editor":[{"full_name":"Manna, Zohar","last_name":"Manna","first_name":"Zohar"},{"last_name":"Peled","full_name":"Peled, Doron","first_name":"Doron"}],"title":"Quantitative Simulation Games","citation":{"ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010.Quantitative Simulation Games. In: Time For Verification: Essays in Memory of Amir Pnueli. LNCS, vol. 6200, 42–60.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative Simulation Games.” In Time For Verification: Essays in Memory of Amir Pnueli, edited by Zohar Manna and Doron Peled, 6200:42–60. Essays in Memory of Amir Pnueli. Springer, 2010. https://doi.org/10.1007/978-3-642-13754-9_3.","apa":"Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Quantitative Simulation Games. In Z. Manna & D. Peled (Eds.), Time For Verification: Essays in Memory of Amir Pnueli (Vol. 6200, pp. 42–60). Springer. https://doi.org/10.1007/978-3-642-13754-9_3","ama":"Cerny P, Henzinger TA, Radhakrishna A. Quantitative Simulation Games. In: Manna Z, Peled D, eds. Time For Verification: Essays in Memory of Amir Pnueli. Vol 6200. Essays in Memory of Amir Pnueli. Springer; 2010:42-60. doi:10.1007/978-3-642-13754-9_3","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative Simulation Games,” in Time For Verification: Essays in Memory of Amir Pnueli, vol. 6200, Z. Manna and D. Peled, Eds. Springer, 2010, pp. 42–60.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Z. Manna, D. Peled (Eds.), Time For Verification: Essays in Memory of Amir Pnueli, Springer, 2010, pp. 42–60.","mla":"Cerny, Pavol, et al. “Quantitative Simulation Games.” Time For Verification: Essays in Memory of Amir Pnueli, edited by Zohar Manna and Doron Peled, vol. 6200, Springer, 2010, pp. 42–60, doi:10.1007/978-3-642-13754-9_3."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"214373","name":"Design for Embedded Systems"}],"page":"42 - 60","date_published":"2010-07-29T00:00:00Z","doi":"10.1007/978-3-642-13754-9_3","date_created":"2018-12-11T12:08:37Z","year":"2010","day":"29","publication":"Time For Verification: Essays in Memory of Amir Pnueli","publisher":"Springer","quality_controlled":"1","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:56:38Z","type":"book_chapter","status":"public","series_title":"Essays in Memory of Amir Pnueli","_id":"4392","volume":6200,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["LNCS"],"month":"07","intvolume":" 6200","abstract":[{"lang":"eng","text":"While a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a distance function on systems and properties, where the distance between a system and a property provides a measure of “fit” or “desirability.” In this article, we explore several ways how the simulation preorder can be generalized to a distance function. This is done by equipping the classical simulation game between a system and a property with quantitative objectives. In particular, for systems that satisfy a property, a quantitative simulation game can measure the “robustness” of the satisfaction, that is, how much the system can deviate from its nominal behavior while still satisfying the property. For systems that violate a property, a quantitative simulation game can measure the “seriousness” of the violation, that is, how much the property has to be modified so that it is satisfied by the system. These distances can be computed in polynomial time, since the computation reduces to the value problem in limit average games with constant weights. Finally, we demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes. "}],"oa_version":"None"},{"volume":6013,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":312147,"date_updated":"2020-07-14T12:46:29Z","creator":"system","file_name":"IST-2012-41-v1+1_Shape_refinement_through_explicit_heap_analysis.pdf","date_created":"2018-12-12T10:18:13Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5332","checksum":"7d26e59a9681487d7283eba337292b2c"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 6013","month":"04","abstract":[{"text":"Shape analysis is a promising technique to prove program properties about recursive data structures. The challenge is to automatically determine the data-structure type, and to supply the shape analysis with the necessary information about the data structure. We present a stepwise approach to the selection of instrumentation predicates for a TVLA-based shape analysis, which takes us a step closer towards the fully automatic verification of data structures. The approach uses two techniques to guide the refinement of shape abstractions: (1) during program exploration, an explicit heap analysis collects sample instances of the heap structures, which are used to identify the data structures that are manipulated by the program; and (2) during abstraction refinement along an infeasible error path, we consider different possible heap abstractions and choose the coarsest one that eliminates the infeasible path. We have implemented this combined approach for automatic shape refinement as an extension of the software model checker BLAST. Example programs from a data-structure library that manipulate doubly-linked lists and trees were successfully verified by our tool.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:29Z","date_updated":"2021-01-12T07:56:40Z","ddc":["004"],"conference":{"name":"FASE: Fundamental Approaches To Software Engineering","start_date":"2010-03-20","end_date":"2010-03-28","location":"Paphos, Cyprus"},"type":"conference","pubrep_id":"41","status":"public","_id":"4396","page":"263 - 277","date_created":"2018-12-11T12:08:38Z","date_published":"2010-04-21T00:00:00Z","doi":"10.1007/978-3-642-12029-9_19","year":"2010","has_accepted_license":"1","day":"21","oa":1,"quality_controlled":"1","publisher":"Springer","author":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Théoduloz, Grégory","last_name":"Théoduloz","first_name":"Grégory"},{"last_name":"Zufferey","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien"}],"publist_id":"1061","editor":[{"full_name":"Rosenblum, David","last_name":"Rosenblum","first_name":"David"},{"first_name":"Gabriele","full_name":"Taenzer, Gabriele","last_name":"Taenzer"}],"title":"Shape refinement through explicit heap analysis","citation":{"ieee":"D. Beyer, T. A. Henzinger, G. Théoduloz, and D. Zufferey, “Shape refinement through explicit heap analysis,” presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 263–277.","short":"D. Beyer, T.A. Henzinger, G. Théoduloz, D. Zufferey, in:, D. Rosenblum, G. Taenzer (Eds.), Springer, 2010, pp. 263–277.","apa":"Beyer, D., Henzinger, T. A., Théoduloz, G., & Zufferey, D. (2010). Shape refinement through explicit heap analysis. In D. Rosenblum & G. Taenzer (Eds.) (Vol. 6013, pp. 263–277). Presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus: Springer. https://doi.org/10.1007/978-3-642-12029-9_19","ama":"Beyer D, Henzinger TA, Théoduloz G, Zufferey D. Shape refinement through explicit heap analysis. In: Rosenblum D, Taenzer G, eds. Vol 6013. Springer; 2010:263-277. doi:10.1007/978-3-642-12029-9_19","mla":"Beyer, Dirk, et al. Shape Refinement through Explicit Heap Analysis. Edited by David Rosenblum and Gabriele Taenzer, vol. 6013, Springer, 2010, pp. 263–77, doi:10.1007/978-3-642-12029-9_19.","ista":"Beyer D, Henzinger TA, Théoduloz G, Zufferey D. 2010. Shape refinement through explicit heap analysis. FASE: Fundamental Approaches To Software Engineering, LNCS, vol. 6013, 263–277.","chicago":"Beyer, Dirk, Thomas A Henzinger, Grégory Théoduloz, and Damien Zufferey. “Shape Refinement through Explicit Heap Analysis.” edited by David Rosenblum and Gabriele Taenzer, 6013:263–77. Springer, 2010. https://doi.org/10.1007/978-3-642-12029-9_19."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]},{"_id":"4395","status":"public","conference":{"start_date":"2010-03-20","location":"Pahos, Cyprus","end_date":"2010-03-28","name":"CC: Compiler Construction"},"type":"conference","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Burckhardt, Sebastian, et al. Verifying Local Transformations on Relaxed Memory Models. Edited by Rajiv Gupta, vol. 6011, Springer, 2010, pp. 104–23, doi:10.1007/978-3-642-11970-5_7.","ieee":"S. Burckhardt, M. Musuvathi, and V. Singh, “Verifying local transformations on relaxed memory models,” presented at the CC: Compiler Construction, Pahos, Cyprus, 2010, vol. 6011, pp. 104–123.","short":"S. Burckhardt, M. Musuvathi, V. Singh, in:, R. Gupta (Ed.), Springer, 2010, pp. 104–123.","ama":"Burckhardt S, Musuvathi M, Singh V. Verifying local transformations on relaxed memory models. In: Gupta R, ed. Vol 6011. Springer; 2010:104-123. doi:10.1007/978-3-642-11970-5_7","apa":"Burckhardt, S., Musuvathi, M., & Singh, V. (2010). Verifying local transformations on relaxed memory models. In R. Gupta (Ed.) (Vol. 6011, pp. 104–123). Presented at the CC: Compiler Construction, Pahos, Cyprus: Springer. https://doi.org/10.1007/978-3-642-11970-5_7","chicago":"Burckhardt, Sebastian, Madanlal Musuvathi, and Vasu Singh. “Verifying Local Transformations on Relaxed Memory Models.” edited by Rajiv Gupta, 6011:104–23. Springer, 2010. https://doi.org/10.1007/978-3-642-11970-5_7.","ista":"Burckhardt S, Musuvathi M, Singh V. 2010. Verifying local transformations on relaxed memory models. CC: Compiler Construction, LNCS, vol. 6011, 104–123."},"date_updated":"2021-01-12T07:56:39Z","editor":[{"full_name":"Gupta, Rajiv","last_name":"Gupta","first_name":"Rajiv"}],"title":"Verifying local transformations on relaxed memory models","author":[{"last_name":"Burckhardt","full_name":"Burckhardt, Sebastian","first_name":"Sebastian"},{"first_name":"Madanlal","last_name":"Musuvathi","full_name":"Musuvathi, Madanlal"},{"last_name":"Singh","full_name":"Singh, Vasu","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"1063","oa_version":"None","abstract":[{"text":"The problem of locally transforming or translating programs without altering their semantics is central to the construction of correct compilers. For concurrent shared-memory programs this task is challenging because (1) concurrent threads can observe transformations that would be undetectable in a sequential program, and (2) contemporary multiprocessors commonly use relaxed memory models that complicate the reasoning. In this paper, we present a novel proof methodology for verifying that a local program transformation is sound with respect to a specific hardware memory model, in the sense that it is not observable in any context. The methodology is based on a structural induction and relies on a novel compositional denotational semantics for relaxed memory models that formalizes (1) the behaviors of program fragments as a set of traces, and (2) the effect of memory model relaxations as local trace rewrite operations. To apply this methodology in practice, we implemented a semi- automated tool called Traver and used it to verify/falsify several compiler transformations for a number of different hardware memory models.","lang":"eng"}],"intvolume":" 6011","month":"04","quality_controlled":"1","alternative_title":["LNCS"],"publisher":"Springer","language":[{"iso":"eng"}],"day":"21","year":"2010","publication_status":"published","date_created":"2018-12-11T12:08:38Z","volume":6011,"doi":"10.1007/978-3-642-11970-5_7","date_published":"2010-04-21T00:00:00Z","page":"104 - 123"},{"_id":"3867","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"journal_article","pubrep_id":"504","status":"public","date_updated":"2023-02-23T12:15:42Z","ddc":["000","004"],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:19Z","abstract":[{"text":"Weighted automata are nondeterministic automata with numerical weights on transitions. They can define quantitative languages L that assign to each word w a real number L(w). In the case of infinite words, the value of a run is naturally computed as the maximum, limsup, liminf, limit-average, or discounted-sum of the transition weights. The value of a word w is the supremum of the values of the runs over w. We study expressiveness and closure questions about these quantitative languages. We first show that the set of words with value greater than a threshold can be omega-regular for deterministic limit-average and discounted-sum automata, while this set is always omega-regular when the threshold is isolated (i.e., some neighborhood around the threshold contains no word). In the latter case, we prove that the omega-regular language is robust against small perturbations of the transition weights. We next consider automata with transition weights 0 or 1 and show that they are as expressive as general weighted automata in the limit-average case, but not in the discounted-sum case. Third, for quantitative languages L-1 and L-2, we consider the operations max(L-1, L-2), min(L-1, L-2), and 1 - L-1, which generalize the boolean operations on languages, as well as the sum L-1 + L-2. We establish the closure properties of all classes of quantitative languages with respect to these four operations.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 6","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"0243da726476817f2ea33b48b78be696","file_id":"5312","creator":"system","file_size":216598,"date_updated":"2020-07-14T12:46:19Z","file_name":"IST-2012-55-v1+1_Expressiveness_Closure_Properties_Quantitative_Languages.pdf","date_created":"2018-12-12T10:17:54Z"},{"file_size":302416,"date_updated":"2020-07-14T12:46:19Z","creator":"system","file_name":"IST-2016-55-v2+1_1007.4018.pdf","date_created":"2018-12-12T10:17:55Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5313","checksum":"5e512b8503a9cb263de26331c4ee9cf2"}],"ec_funded":1,"volume":6,"related_material":{"record":[{"id":"4540","status":"public","relation":"earlier_version"}]},"issue":"3","project":[{"name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Expressiveness and Closure Properties for Quantitative Languages.” Logical Methods in Computer Science, vol. 6, no. 3, International Federation of Computational Logic, 2010, pp. 1–23, doi:10.2168/LMCS-6(3:10)2010.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Expressiveness and closure properties for quantitative languages,” Logical Methods in Computer Science, vol. 6, no. 3. International Federation of Computational Logic, pp. 1–23, 2010.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Logical Methods in Computer Science 6 (2010) 1–23.","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2010). Expressiveness and closure properties for quantitative languages. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-6(3:10)2010","ama":"Chatterjee K, Doyen L, Henzinger TA. Expressiveness and closure properties for quantitative languages. Logical Methods in Computer Science. 2010;6(3):1-23. doi:10.2168/LMCS-6(3:10)2010","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Expressiveness and Closure Properties for Quantitative Languages.” Logical Methods in Computer Science. International Federation of Computational Logic, 2010. https://doi.org/10.2168/LMCS-6(3:10)2010.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2010. Expressiveness and closure properties for quantitative languages. Logical Methods in Computer Science. 6(3), 1–23."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"2311","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"title":"Expressiveness and closure properties for quantitative languages","oa":1,"quality_controlled":"1","publisher":"International Federation of Computational Logic","year":"2010","has_accepted_license":"1","publication":"Logical Methods in Computer Science","day":"30","page":"1 - 23","date_created":"2018-12-11T12:05:36Z","doi":"10.2168/LMCS-6(3:10)2010","date_published":"2010-08-30T00:00:00Z"},{"page":"2701 - 2715","date_published":"2010-09-01T00:00:00Z","volume":64,"issue":"9","doi":"10.1111/j.1558-5646.2010.01019.x","date_created":"2018-12-11T11:46:40Z","year":"2010","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Evolution","publisher":"Wiley-Blackwell","scopus_import":1,"quality_controlled":"1","month":"09","intvolume":" 64","abstract":[{"lang":"eng","text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci."}],"oa_version":"None","acknowledgement":"This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.","publist_id":"2780","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Jerome","full_name":"Kelleher, Jerome","last_name":"Kelleher"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"}],"department":[{"_id":"NiBa"}],"title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","date_updated":"2021-01-12T08:00:52Z","citation":{"ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715.","chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.","apa":"Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x","ama":"Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715. doi:10.1111/j.1558-5646.2010.01019.x","short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.","ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” Evolution, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","mla":"Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"474"}]