[{"publist_id":"4730","year":"2014","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Biophysical Society","author":[{"last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"date_created":"2018-12-11T11:56:28Z","date_updated":"2021-01-12T06:56:10Z","volume":106,"month":"03","publication_identifier":{"issn":["00063495"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/"}],"external_id":{"pmid":["24606943"]},"quality_controlled":"1","doi":"10.1016/j.bpj.2014.01.014","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail."}],"issue":"5","_id":"2231","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Noise and information transmission in promoters with multiple internal states","intvolume":" 106","oa_version":"Submitted Version","scopus_import":1,"day":"04","publication":"Biophysical Journal","citation":{"chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal. Biophysical Society, 2014. https://doi.org/10.1016/j.bpj.2014.01.014.","short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.","apa":"Rieckh, G., & Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2014.01.014","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.","ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204.","ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014"},"page":"1194 - 1204","date_published":"2014-03-04T00:00:00Z"},{"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2226","title":"Transient growth of Ekman-Couette flow","status":"public","intvolume":" 89","abstract":[{"text":"Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2014-01-06T00:00:00Z","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","citation":{"ama":"Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(1). doi:10.1103/PhysRevE.89.013001","ista":"Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001.","apa":"Shi, L., Hof, B., & Tilgner, A. (2014). Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.013001","ieee":"L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 1. American Institute of Physics, 2014.","mla":"Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 1, 013001, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.013001.","short":"L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","chicago":"Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette Flow.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.013001."},"day":"06","scopus_import":1,"author":[{"last_name":"Shi","first_name":"Liang","full_name":"Shi, Liang"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"},{"first_name":"Andreas","last_name":"Tilgner","full_name":"Tilgner, Andreas"}],"date_created":"2018-12-11T11:56:26Z","date_updated":"2021-01-12T06:56:08Z","volume":89,"year":"2014","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"American Institute of Physics","publist_id":"4737","article_number":"013001","doi":"10.1103/PhysRevE.89.013001","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.5095"}],"quality_controlled":"1","project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","grant_number":"SFB-TR3-TP10B"}],"month":"01","publication_identifier":{"issn":["15393755"]}},{"month":"03","day":"01","publication_identifier":{"issn":["14396092"]},"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2014-03-01T00:00:00Z","doi":"10.1007/s13127-013-0150-6","quality_controlled":"1","page":"1 - 10","publication":"Organisms Diversity and Evolution","citation":{"mla":"Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” Organisms Diversity and Evolution, vol. 14, no. 1, Springer, 2014, pp. 1–10, doi:10.1007/s13127-013-0150-6.","short":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms Diversity and Evolution 14 (2014) 1–10.","chicago":"Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” Organisms Diversity and Evolution. Springer, 2014. https://doi.org/10.1007/s13127-013-0150-6.","ama":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 2014;14(1):1-10. doi:10.1007/s13127-013-0150-6","ista":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10.","ieee":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto, “Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences,” Organisms Diversity and Evolution, vol. 14, no. 1. Springer, pp. 1–10, 2014.","apa":"Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., & Prieto, J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. Springer. https://doi.org/10.1007/s13127-013-0150-6"},"abstract":[{"lang":"eng","text":"The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent."}],"issue":"1","publist_id":"4734","type":"journal_article","date_created":"2018-12-11T11:56:26Z","date_updated":"2022-08-25T14:42:46Z","oa_version":"None","volume":14,"author":[{"last_name":"Cires Rodriguez","first_name":"Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Cires Rodriguez, Eduardo"},{"last_name":"Baltisberger","first_name":"Matthias","full_name":"Baltisberger, Matthias"},{"full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","first_name":"Candela","last_name":"Cuesta"},{"last_name":"Vargas","first_name":"Pablo","full_name":"Vargas, Pablo"},{"first_name":"José","last_name":"Prieto","full_name":"Prieto, José"}],"publication_status":"published","status":"public","title":"Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences","publisher":"Springer","intvolume":" 14","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"year":"2014","_id":"2227","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"publist_id":"4727","file_date_updated":"2020-07-14T12:45:34Z","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","publication_status":"published","year":"2014","volume":10,"date_updated":"2021-01-12T06:56:11Z","date_created":"2018-12-11T11:56:29Z","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"first_name":"Václav","last_name":"Brožek","full_name":"Brožek, Václav"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"}],"publication_identifier":{"issn":["18605974"]},"month":"02","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"http://repository.ist.ac.at/id/eprint/428","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.2168/LMCS-10(1:13)2014","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with κ limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for ε-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for ε-approximation, for all ε > 0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be ε-approximated in time polynomial in the size of the MDP and 1/ε, and exponential in the number of limit-average functions, for all ε > 0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results."}],"intvolume":" 10","status":"public","ddc":["000"],"title":"Markov decision processes with multiple long-run average objectives","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2234","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":375388,"creator":"system","access_level":"open_access","file_name":"IST-2016-428-v1+1_1104.3489.pdf","checksum":"803edcc2d8c1acfba44a9ec43a5eb9f0","date_created":"2018-12-12T10:07:57Z","date_updated":"2020-07-14T12:45:34Z","relation":"main_file","file_id":"4656"}],"pubrep_id":"428","scopus_import":1,"has_accepted_license":"1","day":"14","citation":{"chicago":"Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Markov Decision Processes with Multiple Long-Run Average Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2014. https://doi.org/10.2168/LMCS-10(1:13)2014.","short":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, Logical Methods in Computer Science 10 (2014).","mla":"Brázdil, Tomáš, et al. “Markov Decision Processes with Multiple Long-Run Average Objectives.” Logical Methods in Computer Science, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:13)2014.","apa":"Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., & Kučera, A. (2014). Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-10(1:13)2014","ieee":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Markov decision processes with multiple long-run average objectives,” Logical Methods in Computer Science, vol. 10, no. 1. International Federation of Computational Logic, 2014.","ista":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2014. Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. 10(1).","ama":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. 2014;10(1). doi:10.2168/LMCS-10(1:13)2014"},"publication":"Logical Methods in Computer Science","date_published":"2014-02-14T00:00:00Z"},{"day":"01","has_accepted_license":"1","date_published":"2014-02-01T00:00:00Z","page":"566 - 590","citation":{"mla":"Jetchev, Dimitar, and Krzysztof Z. Pietrzak. How to Fake Auxiliary Input. Edited by Yehuda Lindell, vol. 8349, Springer, 2014, pp. 566–90, doi:10.1007/978-3-642-54242-8_24.","short":"D. Jetchev, K.Z. Pietrzak, in:, Y. Lindell (Ed.), Springer, 2014, pp. 566–590.","chicago":"Jetchev, Dimitar, and Krzysztof Z Pietrzak. “How to Fake Auxiliary Input.” edited by Yehuda Lindell, 8349:566–90. Springer, 2014. https://doi.org/10.1007/978-3-642-54242-8_24.","ama":"Jetchev D, Pietrzak KZ. How to fake auxiliary input. In: Lindell Y, ed. Vol 8349. Springer; 2014:566-590. doi:10.1007/978-3-642-54242-8_24","ista":"Jetchev D, Pietrzak KZ. 2014. How to fake auxiliary input. TCC: Theory of Cryptography Conference, LNCS, vol. 8349, 566–590.","ieee":"D. Jetchev and K. Z. Pietrzak, “How to fake auxiliary input,” presented at the TCC: Theory of Cryptography Conference, San Diego, USA, 2014, vol. 8349, pp. 566–590.","apa":"Jetchev, D., & Pietrzak, K. Z. (2014). How to fake auxiliary input. In Y. Lindell (Ed.) (Vol. 8349, pp. 566–590). Presented at the TCC: Theory of Cryptography Conference, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54242-8_24"},"abstract":[{"lang":"eng","text":"Consider a joint distribution (X,A) on a set. We show that for any family of distinguishers, there exists a simulator such that 1 no function in can distinguish (X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient than the functions in. For the most interesting settings of the parameters (in particular, the cryptographic case where X has superlogarithmic min-entropy, ε > 0 is negligible and consists of circuits of polynomial size), we can make the simulator h deterministic. As an illustrative application of our theorem, we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09. Our proof is simpler and quantitatively much better than the original proof using the dense model theorem, giving meaningful security guarantees if instantiated with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and Pass gave an interactive variant of our main theorem, and used it to investigate weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version of our theorem using their new uniform min-max theorem."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","file":[{"file_id":"5275","relation":"main_file","date_created":"2018-12-12T10:17:21Z","date_updated":"2020-07-14T12:45:34Z","checksum":"42960325c29dcd8d832edadcc3ce0045","file_name":"IST-2016-681-v1+1_869_1_.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":313528}],"pubrep_id":"681","title":"How to fake auxiliary input","status":"public","ddc":["004"],"intvolume":" 8349","_id":"2236","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"02","publication_identifier":{"isbn":["978-364254241-1"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2014-02-26","start_date":"2014-02-24","location":"San Diego, USA","name":"TCC: Theory of Cryptography Conference"},"doi":"10.1007/978-3-642-54242-8_24","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://repository.ist.ac.at/id/eprint/681"}],"file_date_updated":"2020-07-14T12:45:34Z","ec_funded":1,"publist_id":"4725","date_updated":"2021-01-12T06:56:12Z","date_created":"2018-12-11T11:56:29Z","volume":8349,"author":[{"first_name":"Dimitar","last_name":"Jetchev","full_name":"Jetchev, Dimitar"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"publication_status":"published","editor":[{"full_name":"Lindell, Yehuda","first_name":"Yehuda","last_name":"Lindell"}],"department":[{"_id":"KrPi"}],"publisher":"Springer","year":"2014"},{"page":"691 - 704","quality_controlled":"1","citation":{"mla":"Gadeyne, Astrid, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” Cell, vol. 156, no. 4, Cell Press, 2014, pp. 691–704, doi:10.1016/j.cell.2014.01.039.","short":"A. Gadeyne, C. Sánchez Rodríguez, S. Vanneste, S. Di Rubbo, H. Zauber, K. Vanneste, J. Van Leene, N. De Winne, D. Eeckhout, G. Persiau, E. Van De Slijke, B. Cannoot, L. Vercruysse, J. Mayers, M. Adamowski, U. Kania, M. Ehrlich, A. Schweighofer, T. Ketelaar, S. Maere, S. Bednarek, J. Friml, K. Gevaert, E. Witters, E. Russinova, S. Persson, G. De Jaeger, D. Van Damme, Cell 156 (2014) 691–704.","chicago":"Gadeyne, Astrid, Clara Sánchez Rodríguez, Steffen Vanneste, Simone Di Rubbo, Henrik Zauber, Kevin Vanneste, Jelle Van Leene, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” Cell. Cell Press, 2014. https://doi.org/10.1016/j.cell.2014.01.039.","ama":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, et al. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. 2014;156(4):691-704. doi:10.1016/j.cell.2014.01.039","ista":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Mayers J, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar T, Maere S, Bednarek S, Friml J, Gevaert K, Witters E, Russinova E, Persson S, De Jaeger G, Van Damme D. 2014. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. 156(4), 691–704.","ieee":"A. Gadeyne et al., “The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants,” Cell, vol. 156, no. 4. Cell Press, pp. 691–704, 2014.","apa":"Gadeyne, A., Sánchez Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H., Vanneste, K., … Van Damme, D. (2014). The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.01.039"},"publication":"Cell","language":[{"iso":"eng"}],"date_published":"2014-02-13T00:00:00Z","doi":"10.1016/j.cell.2014.01.039","scopus_import":1,"publication_identifier":{"issn":["00928674"]},"month":"02","day":"13","intvolume":" 156","publisher":"Cell Press","department":[{"_id":"JiFr"}],"status":"public","title":"The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants","publication_status":"published","_id":"2240","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","volume":156,"oa_version":"None","date_updated":"2021-01-12T06:56:13Z","date_created":"2018-12-11T11:56:31Z","author":[{"full_name":"Gadeyne, Astrid","last_name":"Gadeyne","first_name":"Astrid"},{"last_name":"Sánchez Rodríguez","first_name":"Clara","full_name":"Sánchez Rodríguez, Clara"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Di Rubbo","first_name":"Simone","full_name":"Di Rubbo, Simone"},{"first_name":"Henrik","last_name":"Zauber","full_name":"Zauber, Henrik"},{"last_name":"Vanneste","first_name":"Kevin","full_name":"Vanneste, Kevin"},{"full_name":"Van Leene, Jelle","first_name":"Jelle","last_name":"Van Leene"},{"full_name":"De Winne, Nancy","first_name":"Nancy","last_name":"De Winne"},{"last_name":"Eeckhout","first_name":"Dominique","full_name":"Eeckhout, Dominique"},{"last_name":"Persiau","first_name":"Geert","full_name":"Persiau, Geert"},{"first_name":"Eveline","last_name":"Van De Slijke","full_name":"Van De Slijke, Eveline"},{"last_name":"Cannoot","first_name":"Bernard","full_name":"Cannoot, Bernard"},{"last_name":"Vercruysse","first_name":"Leen","full_name":"Vercruysse, Leen"},{"full_name":"Mayers, Jonathan","last_name":"Mayers","first_name":"Jonathan"},{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","last_name":"Kania","full_name":"Kania, Urszula"},{"full_name":"Ehrlich, Matthias","first_name":"Matthias","last_name":"Ehrlich"},{"full_name":"Schweighofer, Alois","last_name":"Schweighofer","first_name":"Alois"},{"full_name":"Ketelaar, Tijs","first_name":"Tijs","last_name":"Ketelaar"},{"full_name":"Maere, Steven","first_name":"Steven","last_name":"Maere"},{"full_name":"Bednarek, Sebastian","last_name":"Bednarek","first_name":"Sebastian"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gevaert, Kris","first_name":"Kris","last_name":"Gevaert"},{"full_name":"Witters, Erwin","last_name":"Witters","first_name":"Erwin"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"full_name":"Persson, Staffan","last_name":"Persson","first_name":"Staffan"},{"full_name":"De Jaeger, Geert","first_name":"Geert","last_name":"De Jaeger"},{"first_name":"Daniël","last_name":"Van Damme","full_name":"Van Damme, Daniël"}],"type":"journal_article","issue":"4","publist_id":"4721","abstract":[{"text":"Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.","lang":"eng"}]},{"publist_id":"4722","ec_funded":1,"year":"2014","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","author":[{"last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"}],"volume":49,"date_created":"2018-12-11T11:56:30Z","date_updated":"2021-01-12T06:56:13Z","publication_identifier":{"isbn":["978-145032544-8"]},"month":"01","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"quality_controlled":"1","doi":"10.1145/2535838.2535875","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2014-01-24","start_date":"2014-01-22","location":"San Diego, USA"},"language":[{"iso":"eng"}],"type":"conference","issue":"1","abstract":[{"text":"The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce battery transition systems. In this model, a battery is viewed as consisting of two parts-the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank. Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the !-regular modelchecking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots.","lang":"eng"}],"_id":"2239","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 49","title":"Battery transition systems","status":"public","oa_version":"None","scopus_import":1,"day":"13","citation":{"short":"U. Boker, T.A. Henzinger, A. Radhakrishna, in:, ACM, 2014, pp. 595–606.","mla":"Boker, Udi, et al. Battery Transition Systems. Vol. 49, no. 1, ACM, 2014, pp. 595–606, doi:10.1145/2535838.2535875.","chicago":"Boker, Udi, Thomas A Henzinger, and Arjun Radhakrishna. “Battery Transition Systems,” 49:595–606. ACM, 2014. https://doi.org/10.1145/2535838.2535875.","ama":"Boker U, Henzinger TA, Radhakrishna A. Battery transition systems. In: Vol 49. ACM; 2014:595-606. doi:10.1145/2535838.2535875","apa":"Boker, U., Henzinger, T. A., & Radhakrishna, A. (2014). Battery transition systems (Vol. 49, pp. 595–606). Presented at the POPL: Principles of Programming Languages, San Diego, USA: ACM. https://doi.org/10.1145/2535838.2535875","ieee":"U. Boker, T. A. Henzinger, and A. Radhakrishna, “Battery transition systems,” presented at the POPL: Principles of Programming Languages, San Diego, USA, 2014, vol. 49, no. 1, pp. 595–606.","ista":"Boker U, Henzinger TA, Radhakrishna A. 2014. Battery transition systems. POPL: Principles of Programming Languages vol. 49, 595–606."},"page":"595 - 606","date_published":"2014-01-13T00:00:00Z"},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/nature12977","publication_identifier":{"issn":["00280836"]},"month":"02","publisher":"Nature Publishing Group","department":[{"_id":"SyCr"}],"publication_status":"published","year":"2014","volume":506,"date_created":"2018-12-11T11:56:29Z","date_updated":"2021-01-12T06:56:11Z","author":[{"full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"first_name":"Juliet","last_name":"Osborne","full_name":"Osborne, Juliet"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"}],"publist_id":"4726","page":"364 - 366","citation":{"ieee":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations between honeybees and bumblebees as a threat to wild pollinators,” Nature, vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014.","apa":"Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., & Brown, M. (2014). Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12977","ista":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488), 364–366.","ama":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 2014;506(7488):364-366. doi:10.1038/nature12977","chicago":"Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature12977.","short":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014) 364–366.","mla":"Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” Nature, vol. 506, no. 7488, Nature Publishing Group, 2014, pp. 364–66, doi:10.1038/nature12977."},"publication":"Nature","date_published":"2014-02-20T00:00:00Z","scopus_import":1,"day":"20","intvolume":" 506","title":"Disease associations between honeybees and bumblebees as a threat to wild pollinators","status":"public","_id":"2235","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"7488","abstract":[{"text":"Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators.","lang":"eng"}]},{"doi":"10.1016/j.neuron.2013.11.011","date_published":"2014-01-22T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” Neuron, vol. 81, no. 2, Elsevier, 2014, pp. 314–20, doi:10.1016/j.neuron.2013.11.011.","short":"K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K. Matsui, Neuron 81 (2014) 314–320.","chicago":"Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2013.11.011.","ama":"Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 2014;81(2):314-320. doi:10.1016/j.neuron.2013.11.011","ista":"Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K. 2014. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 81(2), 314–320.","apa":"Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R., & Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.11.011","ieee":"K. Beppu et al., “Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage,” Neuron, vol. 81, no. 2. Elsevier, pp. 314–320, 2014."},"publication":"Neuron","page":"314 - 320","quality_controlled":"1","publication_identifier":{"issn":["08966273"]},"month":"01","day":"22","scopus_import":1,"author":[{"first_name":"Kaoru","last_name":"Beppu","full_name":"Beppu, Kaoru"},{"full_name":"Sasaki, Takuya","last_name":"Sasaki","first_name":"Takuya"},{"full_name":"Tanaka, Kenji","last_name":"Tanaka","first_name":"Kenji"},{"full_name":"Yamanaka, Akihiro","first_name":"Akihiro","last_name":"Yamanaka"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"}],"volume":81,"oa_version":"None","date_created":"2018-12-11T11:56:31Z","date_updated":"2021-01-12T06:56:14Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2241","year":"2014","department":[{"_id":"RySh"}],"publisher":"Elsevier","intvolume":" 81","publication_status":"published","title":"Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage","status":"public","publist_id":"4715","issue":"2","abstract":[{"lang":"eng","text":"The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage."}],"type":"journal_article"},{"publication_identifier":{"issn":["10643745"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/978-1-62703-592-7_23","quality_controlled":"1","publist_id":"4704","volume":1056,"date_created":"2018-12-11T11:56:32Z","date_updated":"2021-01-12T06:56:15Z","author":[{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu"},{"first_name":"Petr","last_name":"Skůpa","full_name":"Skůpa, Petr"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"}],"editor":[{"last_name":"Hicks","first_name":"Glenn","full_name":"Hicks, Glenn"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"}],"department":[{"_id":"JiFr"}],"publisher":"Springer","publication_status":"published","year":"2014","day":"01","series_title":"Methods in Molecular Biology","scopus_import":1,"date_published":"2014-01-01T00:00:00Z","page":"255 - 264","citation":{"ama":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds. Plant Chemical Genomics. Vol 1056. Methods in Molecular Biology. Springer; 2014:255-264. doi:10.1007/978-1-62703-592-7_23","ista":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Plant Chemical Genomics. Methods in Molecular Biology, vol. 1056, 255–264.","apa":"Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., & Friml, J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In G. Hicks & S. Robert (Eds.), Plant Chemical Genomics (Vol. 1056, pp. 255–264). Springer. https://doi.org/10.1007/978-1-62703-592-7_23","ieee":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml, “Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters,” in Plant Chemical Genomics, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014, pp. 255–264.","mla":"Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” Plant Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, vol. 1056, Springer, 2014, pp. 255–64, doi:10.1007/978-1-62703-592-7_23.","short":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:, G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.","chicago":"Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” In Plant Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64. Methods in Molecular Biology. Springer, 2014. https://doi.org/10.1007/978-1-62703-592-7_23."},"publication":"Plant Chemical Genomics","abstract":[{"lang":"eng","text":"Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. "}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","oa_version":"None","intvolume":" 1056","title":"Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2245"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2013.11.032","date_published":"2014-02-13T00:00:00Z","quality_controlled":"1","page":"73 - 91","publication":"Theoretical Computer Science","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.3777"}],"citation":{"mla":"Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” Theoretical Computer Science, vol. 521, Elsevier, 2014, pp. 73–91, doi:10.1016/j.tcs.2013.11.032.","short":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer Science 521 (2014) 73–91.","chicago":"Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea. “Alternating Traps in Muller and Parity Games.” Theoretical Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2013.11.032.","ama":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller and parity games. Theoretical Computer Science. 2014;521:73-91. doi:10.1016/j.tcs.2013.11.032","ista":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps in Muller and parity games. Theoretical Computer Science. 521, 73–91.","apa":"Grinshpun, A., Phalitnonkiat, P., Rubin, S., & Tarfulea, A. (2014). Alternating traps in Muller and parity games. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2013.11.032","ieee":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps in Muller and parity games,” Theoretical Computer Science, vol. 521. Elsevier, pp. 73–91, 2014."},"oa":1,"day":"13","month":"02","publication_identifier":{"issn":["03043975"]},"scopus_import":1,"date_updated":"2021-01-12T06:56:16Z","date_created":"2018-12-11T11:56:33Z","volume":521,"oa_version":"Submitted Version","author":[{"last_name":"Grinshpun","first_name":"Andrey","full_name":"Grinshpun, Andrey"},{"last_name":"Phalitnonkiat","first_name":"Pakawat","full_name":"Phalitnonkiat, Pakawat"},{"full_name":"Rubin, Sasha","first_name":"Sasha","last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrei","last_name":"Tarfulea","full_name":"Tarfulea, Andrei"}],"status":"public","title":"Alternating traps in Muller and parity games","publication_status":"published","intvolume":" 521","department":[{"_id":"KrCh"}],"publisher":"Elsevier","_id":"2246","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. ","lang":"eng"}],"publist_id":"4703","type":"journal_article"},{"language":[{"iso":"eng"}],"date_published":"2014-02-14T00:00:00Z","doi":"10.1016/j.febslet.2014.01.009","quality_controlled":"1","page":"632 - 640","publication":"FEBS Letters","citation":{"ama":"Dueck A, Eichner A, Sixt MK, Meister G. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. 2014;588(4):632-640. doi:10.1016/j.febslet.2014.01.009","ieee":"A. Dueck, A. Eichner, M. K. Sixt, and G. Meister, “A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation,” FEBS Letters, vol. 588, no. 4. Elsevier, pp. 632–640, 2014.","apa":"Dueck, A., Eichner, A., Sixt, M. K., & Meister, G. (2014). A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. Elsevier. https://doi.org/10.1016/j.febslet.2014.01.009","ista":"Dueck A, Eichner A, Sixt MK, Meister G. 2014. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. 588(4), 632–640.","short":"A. Dueck, A. Eichner, M.K. Sixt, G. Meister, FEBS Letters 588 (2014) 632–640.","mla":"Dueck, Anne, et al. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” FEBS Letters, vol. 588, no. 4, Elsevier, 2014, pp. 632–40, doi:10.1016/j.febslet.2014.01.009.","chicago":"Dueck, Anne, Alexander Eichner, Michael K Sixt, and Gunter Meister. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” FEBS Letters. Elsevier, 2014. https://doi.org/10.1016/j.febslet.2014.01.009."},"day":"14","month":"02","publication_identifier":{"issn":["00145793"]},"scopus_import":1,"date_created":"2018-12-11T11:56:31Z","date_updated":"2021-01-12T06:56:14Z","volume":588,"oa_version":"None","author":[{"full_name":"Dueck, Anne","first_name":"Anne","last_name":"Dueck"},{"last_name":"Eichner","first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Meister, Gunter","last_name":"Meister","first_name":"Gunter"}],"status":"public","title":"A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation","publication_status":"published","publisher":"Elsevier","intvolume":" 588","department":[{"_id":"MiSi"}],"_id":"2242","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","abstract":[{"text":"MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages.","lang":"eng"}],"publist_id":"4714","issue":"4","type":"journal_article"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2014-01-01T00:00:00Z","page":"10 - 20","citation":{"short":"D. Kuchibhatla, W. Sherman, B. Chung, S. Cook, G. Schneider, B. Eisenhaber, D. Karlin, Journal of Virology 88 (2014) 10–20.","mla":"Kuchibhatla, Durga, et al. “Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’ Viral Proteins.” Journal of Virology, vol. 88, no. 1, ASM, 2014, pp. 10–20, doi:10.1128/JVI.02595-13.","chicago":"Kuchibhatla, Durga, Westley Sherman, Betty Chung, Shelley Cook, Georg Schneider, Birgit Eisenhaber, and David Karlin. “Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’ Viral Proteins.” Journal of Virology. ASM, 2014. https://doi.org/10.1128/JVI.02595-13.","ama":"Kuchibhatla D, Sherman W, Chung B, et al. Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently “orphan” viral proteins. Journal of Virology. 2014;88(1):10-20. doi:10.1128/JVI.02595-13","ieee":"D. Kuchibhatla et al., “Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’ viral proteins,” Journal of Virology, vol. 88, no. 1. ASM, pp. 10–20, 2014.","apa":"Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber, B., & Karlin, D. (2014). Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently “orphan” viral proteins. Journal of Virology. ASM. https://doi.org/10.1128/JVI.02595-13","ista":"Kuchibhatla D, Sherman W, Chung B, Cook S, Schneider G, Eisenhaber B, Karlin D. 2014. Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’ viral proteins. Journal of Virology. 88(1), 10–20."},"publication":"Journal of Virology","issue":"1","abstract":[{"text":"The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as "genus specific" by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virionsd.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5029","checksum":"2c121b5e884992dfec5605bdf4e659da","date_updated":"2020-07-14T12:45:34Z","date_created":"2018-12-12T10:13:43Z","access_level":"open_access","file_name":"IST-2016-417-v1+1_J._Virol.-2014-Kuchibhatla-10-20.pdf","content_type":"application/pdf","file_size":825756,"creator":"system"}],"pubrep_id":"417","intvolume":" 88","title":"Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently \"orphan\" viral proteins","status":"public","ddc":["570"],"_id":"2250","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0022538X"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1128/JVI.02595-13","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publist_id":"4698","file_date_updated":"2020-07-14T12:45:34Z","volume":88,"date_updated":"2021-01-12T06:56:17Z","date_created":"2018-12-11T11:56:34Z","author":[{"last_name":"Kuchibhatla","first_name":"Durga","full_name":"Kuchibhatla, Durga"},{"last_name":"Sherman","first_name":"Westley","full_name":"Sherman, Westley"},{"last_name":"Chung","first_name":"Betty","full_name":"Chung, Betty"},{"full_name":"Cook, Shelley","first_name":"Shelley","last_name":"Cook"},{"full_name":"Schneider, Georg","id":"329095A0-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Schneider"},{"first_name":"Birgit","last_name":"Eisenhaber","full_name":"Eisenhaber, Birgit"},{"last_name":"Karlin","first_name":"David","full_name":"Karlin, David"}],"publisher":"ASM","department":[{"_id":"MD"}],"publication_status":"published","year":"2014"},{"scopus_import":1,"day":"08","has_accepted_license":"1","page":"140 - 152","publication":"Neuron","citation":{"ista":"Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 81(1), 140–152.","ieee":"A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations,” Neuron, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.","apa":"Pernia-Andrade, A., & Jonas, P. M. (2014). Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.046","ama":"Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 2014;81(1):140-152. doi:10.1016/j.neuron.2013.09.046","chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2013.09.046.","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” Neuron, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:10.1016/j.neuron.2013.09.046.","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152."},"date_published":"2014-01-08T00:00:00Z","type":"journal_article","abstract":[{"text":"Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus.","lang":"eng"}],"issue":"1","title":"Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations","ddc":["570"],"status":"public","intvolume":" 81","_id":"2254","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf","file_size":4373072,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4773","checksum":"438547cfcd9045a22f065f2019f07849","date_updated":"2020-07-14T12:45:35Z","date_created":"2018-12-12T10:09:48Z"}],"pubrep_id":"422","month":"01","publication_identifier":{"issn":["08966273"]},"quality_controlled":"1","project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548"},{"call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2013.09.046","file_date_updated":"2020-07-14T12:45:35Z","publist_id":"4692","ec_funded":1,"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Elsevier","year":"2014","date_created":"2018-12-11T11:56:35Z","date_updated":"2021-01-12T06:56:19Z","volume":81,"author":[{"last_name":"Pernia-Andrade","first_name":"Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87","full_name":"Pernia-Andrade, Alejandro"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}]},{"month":"02","publication_identifier":{"issn":["09628436"]},"external_id":{"pmid":["24366138"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1098/rstb.2012.0528","language":[{"iso":"eng"}],"article_number":"20120528","file_date_updated":"2020-07-14T12:45:34Z","publist_id":"4697","year":"2014","acknowledgement":"CC BY 3.0","pmid":1,"publication_status":"published","publisher":"Royal Society, The","department":[{"_id":"JoCs"}],"author":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dupret","first_name":"David","full_name":"Dupret, David"}],"date_created":"2018-12-11T11:56:34Z","date_updated":"2021-01-12T06:56:18Z","volume":369,"scopus_import":1,"day":"05","article_processing_charge":"No","has_accepted_license":"1","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","citation":{"chicago":"Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2014. https://doi.org/10.1098/rstb.2012.0528.","short":"J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 369 (2014).","mla":"Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635, 20120528, Royal Society, The, 2014, doi:10.1098/rstb.2012.0528.","ieee":"J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and learning-associated hippocampal maps,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635. Royal Society, The, 2014.","apa":"Csicsvari, J. L., & Dupret, D. (2014). Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2012.0528","ista":"Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 369(1635), 20120528.","ama":"Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2014;369(1635). doi:10.1098/rstb.2012.0528"},"date_published":"2014-02-05T00:00:00Z","type":"journal_article","abstract":[{"text":"Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps.","lang":"eng"}],"issue":"1635","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2251","ddc":["570"],"status":"public","title":"Sharp wave/ripple network oscillations and learning-associated hippocampal maps","intvolume":" 369","pubrep_id":"527","oa_version":"Published Version","file":[{"file_name":"IST-2016-527-v1+1_20120528.full.pdf","access_level":"open_access","creator":"system","file_size":771896,"content_type":"application/pdf","file_id":"5006","relation":"main_file","date_created":"2018-12-12T10:13:24Z","date_updated":"2020-07-14T12:45:34Z","checksum":"51beb33de71c9c19e0c205a20d206f9a"}]},{"month":"01","publication_identifier":{"issn":["09607412"]},"quality_controlled":"1","project":[{"_id":"256BDAB0-B435-11E9-9278-68D0E5697425","name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/tpj.12369"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/tpj.12369","publist_id":"4694","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","year":"2014","date_created":"2018-12-11T11:56:35Z","date_updated":"2021-01-12T06:56:18Z","volume":77,"author":[{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Wang, Bangjun","first_name":"Bangjun","last_name":"Wang"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Pollmann","first_name":"Stephan","full_name":"Pollmann, Stephan"},{"full_name":"Schenck, Daniel","first_name":"Daniel","last_name":"Schenck"},{"full_name":"Lüthen, Hartwig","first_name":"Hartwig","last_name":"Lüthen"},{"last_name":"Schulz","first_name":"Alexander","full_name":"Schulz, Alexander"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"}],"scopus_import":1,"day":"01","article_processing_charge":"No","article_type":"original","page":"108 - 118","publication":"Plant Journal","citation":{"ama":"Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 2014;77(1):108-118. doi:10.1111/tpj.12369","ieee":"A. Bailly et al., “Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth,” Plant Journal, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.","apa":"Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., … Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/tpj.12369","ista":"Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 77(1), 108–118.","short":"A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz, J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.","mla":"Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” Plant Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:10.1111/tpj.12369.","chicago":"Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” Plant Journal. Wiley-Blackwell, 2014. https://doi.org/10.1111/tpj.12369."},"date_published":"2014-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.","lang":"eng"}],"issue":"1","title":"Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth","status":"public","intvolume":" 77","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2253","oa_version":"Published Version"},{"publist_id":"4701","issue":"1","abstract":[{"text":"Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.","lang":"eng"}],"type":"journal_article","volume":322,"oa_version":"None","date_updated":"2021-01-12T06:56:16Z","date_created":"2018-12-11T11:56:33Z","author":[{"first_name":"Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel"},{"last_name":"Metscher","first_name":"Brian","full_name":"Metscher, Brian"},{"last_name":"Müller","first_name":"Gerd","full_name":"Müller, Gerd"}],"publisher":"Wiley-Blackwell","department":[{"_id":"CaHe"}],"intvolume":" 322","status":"public","title":"Thumbs down: A molecular-morphogenetic approach to avian digit homology","publication_status":"published","year":"2014","_id":"2248","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["15525007"]},"month":"01","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2014-01-01T00:00:00Z","doi":"10.1002/jez.b.22545","page":"1 - 12","quality_controlled":"1","citation":{"short":"D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322 (2014) 1–12.","mla":"Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12, doi:10.1002/jez.b.22545.","chicago":"Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/jez.b.22545.","ama":"Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2014;322(1):1-12. doi:10.1002/jez.b.22545","ieee":"D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic approach to avian digit homology,” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 322, no. 1. Wiley-Blackwell, pp. 1–12, 2014.","apa":"Capek, D., Metscher, B., & Müller, G. (2014). Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley-Blackwell. https://doi.org/10.1002/jez.b.22545","ista":"Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 322(1), 1–12."},"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution"},{"publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2014","volume":77,"date_updated":"2021-01-12T06:56:17Z","date_created":"2018-12-11T11:56:34Z","author":[{"first_name":"Yani","last_name":"Chen","full_name":"Chen, Yani"},{"last_name":"Aung","first_name":"Kyaw","full_name":"Aung, Kyaw"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"first_name":"Kathryn","last_name":"Walicki","full_name":"Walicki, Kathryn"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Brandizzí","first_name":"Federica","full_name":"Brandizzí, Federica"}],"publist_id":"4699","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/"}],"language":[{"iso":"eng"}],"doi":"10.1111/tpj.12373","publication_identifier":{"issn":["09607412"]},"month":"01","intvolume":" 77","title":"Inter-regulation of the unfolded protein response and auxin signaling","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2249","oa_version":"Submitted Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes."}],"page":"97 - 107","citation":{"short":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal 77 (2014) 97–107.","mla":"Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” Plant Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107, doi:10.1111/tpj.12373.","chicago":"Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” Plant Journal. Wiley-Blackwell, 2014. https://doi.org/10.1111/tpj.12373.","ama":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 2014;77(1):97-107. doi:10.1111/tpj.12373","ieee":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation of the unfolded protein response and auxin signaling,” Plant Journal, vol. 77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.","apa":"Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., & Brandizzí, F. (2014). Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/tpj.12373","ista":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107."},"publication":"Plant Journal","date_published":"2014-01-01T00:00:00Z","scopus_import":1,"day":"01"},{"article_processing_charge":"No","publication_identifier":{"issn":["00221503"]},"month":"01","day":"01","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2014-01-01T00:00:00Z","doi":"10.1093/jhered/est063","page":"130 - 135","quality_controlled":"1","citation":{"mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.","short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University Press, 2014. https://doi.org/10.1093/jhered/est063.","ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063","ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014.","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063"},"publication":"Journal of Heredity","issue":"1","publist_id":"4695","abstract":[{"text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.","lang":"eng"}],"type":"journal_article","oa_version":"None","volume":105,"date_created":"2018-12-11T11:56:35Z","date_updated":"2022-08-25T14:45:42Z","author":[{"full_name":"Phadke, Sujal","first_name":"Sujal","last_name":"Phadke"},{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"first_name":"Tuan","last_name":"Pham","full_name":"Pham, Tuan"},{"full_name":"Pham, Stephanie","last_name":"Pham","first_name":"Stephanie"},{"full_name":"Zufall, Rebecca","first_name":"Rebecca","last_name":"Zufall"}],"intvolume":" 105","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","publication_status":"published","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2252","year":"2014"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1093/nar/gkt1290","language":[{"iso":"eng"}],"month":"03","year":"2014","acknowledgement":"California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]. Funding for open access charge: California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]\r\nCC BY 3,0","department":[{"_id":"SiHi"}],"publisher":"Oxford University Press","publication_status":"published","author":[{"last_name":"Zhu","first_name":"Fangfang","full_name":"Zhu, Fangfang"},{"last_name":"Gamboa","first_name":"Matthew","full_name":"Gamboa, Matthew"},{"full_name":"Farruggio, Alfonso","last_name":"Farruggio","first_name":"Alfonso"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"first_name":"Bosiljka","last_name":"Tasic","full_name":"Tasic, Bosiljka"},{"full_name":"Schüle, Birgitt","last_name":"Schüle","first_name":"Birgitt"},{"full_name":"Chen Tsai, Yanru","last_name":"Chen Tsai","first_name":"Yanru"},{"last_name":"Calos","first_name":"Michele","full_name":"Calos, Michele"}],"volume":42,"date_created":"2018-12-11T11:56:38Z","date_updated":"2021-01-12T06:56:22Z","article_number":"e34","publist_id":"4684","file_date_updated":"2020-07-14T12:45:35Z","citation":{"ama":"Zhu F, Gamboa M, Farruggio A, et al. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. 2014;42(5). doi:10.1093/nar/gkt1290","ista":"Zhu F, Gamboa M, Farruggio A, Hippenmeyer S, Tasic B, Schüle B, Chen Tsai Y, Calos M. 2014. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. 42(5), e34.","apa":"Zhu, F., Gamboa, M., Farruggio, A., Hippenmeyer, S., Tasic, B., Schüle, B., … Calos, M. (2014). DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkt1290","ieee":"F. Zhu et al., “DICE, an efficient system for iterative genomic editing in human pluripotent stem cells,” Nucleic Acids Research, vol. 42, no. 5. Oxford University Press, 2014.","mla":"Zhu, Fangfang, et al. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” Nucleic Acids Research, vol. 42, no. 5, e34, Oxford University Press, 2014, doi:10.1093/nar/gkt1290.","short":"F. Zhu, M. Gamboa, A. Farruggio, S. Hippenmeyer, B. Tasic, B. Schüle, Y. Chen Tsai, M. Calos, Nucleic Acids Research 42 (2014).","chicago":"Zhu, Fangfang, Matthew Gamboa, Alfonso Farruggio, Simon Hippenmeyer, Bosiljka Tasic, Birgitt Schüle, Yanru Chen Tsai, and Michele Calos. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” Nucleic Acids Research. Oxford University Press, 2014. https://doi.org/10.1093/nar/gkt1290."},"publication":"Nucleic Acids Research","date_published":"2014-03-05T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2261","intvolume":" 42","ddc":["571","610"],"title":"DICE, an efficient system for iterative genomic editing in human pluripotent stem cells","status":"public","pubrep_id":"961","file":[{"file_id":"4738","relation":"main_file","checksum":"e9268f5f96a820f04d7ebbf85927c3cb","date_created":"2018-12-12T10:09:15Z","date_updated":"2020-07-14T12:45:35Z","access_level":"open_access","file_name":"IST-2018-961-v1+1_2014_Hippenmeyer_DICE.pdf","creator":"system","file_size":11044478,"content_type":"application/pdf"}],"oa_version":"Preprint","type":"journal_article","issue":"5","abstract":[{"text":"To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.","lang":"eng"}]},{"month":"01","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-94-007-7687-6_1","date_published":"2014-01-01T00:00:00Z","page":"1 - 24","quality_controlled":"1","citation":{"ama":"Hippenmeyer S. Molecular pathways controlling the sequential steps of cortical projection neuron migration. In: Nguyen L, ed. Cellular and Molecular Control of Neuronal Migration. Vol 800. Springer; 2014:1-24. doi:10.1007/978-94-007-7687-6_1","apa":"Hippenmeyer, S. (2014). Molecular pathways controlling the sequential steps of cortical projection neuron migration. In L. Nguyen (Ed.), Cellular and Molecular Control of Neuronal Migration (Vol. 800, pp. 1–24). Springer. https://doi.org/10.1007/978-94-007-7687-6_1","ieee":"S. Hippenmeyer, “Molecular pathways controlling the sequential steps of cortical projection neuron migration,” in Cellular and Molecular Control of Neuronal Migration, vol. 800, L. Nguyen, Ed. Springer, 2014, pp. 1–24.","ista":"Hippenmeyer S. 2014.Molecular pathways controlling the sequential steps of cortical projection neuron migration. In: Cellular and Molecular Control of Neuronal Migration. Advances in Experimental Medicine and Biology, vol. 800, 1–24.","short":"S. Hippenmeyer, in:, L. Nguyen (Ed.), Cellular and Molecular Control of Neuronal Migration, Springer, 2014, pp. 1–24.","mla":"Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps of Cortical Projection Neuron Migration.” Cellular and Molecular Control of Neuronal Migration, edited by Laurent Nguyen, vol. 800, Springer, 2014, pp. 1–24, doi:10.1007/978-94-007-7687-6_1.","chicago":"Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps of Cortical Projection Neuron Migration.” In Cellular and Molecular Control of Neuronal Migration, edited by Laurent Nguyen, 800:1–24. Springer, 2014. https://doi.org/10.1007/978-94-007-7687-6_1."},"publication":" Cellular and Molecular Control of Neuronal Migration","publist_id":"4679","abstract":[{"lang":"eng","text":"Coordinated migration of newly-born neurons to their target territories is essential for correct neuronal circuit assembly in the developing brain. Although a cohort of signaling pathways has been implicated in the regulation of cortical projection neuron migration, the precise molecular mechanisms and how a balanced interplay of cell-autonomous and non-autonomous functions of candidate signaling molecules controls the discrete steps in the migration process, are just being revealed. In this chapter, I will focally review recent advances that improved our understanding of the cell-autonomous and possible cell-nonautonomous functions of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential steps of cortical projection neuron migration. I will then elaborate on the emerging concept that the Reelin signaling pathway, acts exactly at precise stages in the course of cortical projection neuron migration. Lastly, I will discuss how finely tuned transcriptional programs and downstream effectors govern particular aspects in driving radial migration at discrete stages and how they regulate the precise positioning of cortical projection neurons in the developing cerebral cortex."}],"alternative_title":["Advances in Experimental Medicine and Biology"],"type":"book_chapter","volume":800,"oa_version":"None","date_updated":"2021-01-12T06:56:23Z","date_created":"2018-12-11T11:56:39Z","author":[{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"publisher":"Springer","intvolume":" 800","editor":[{"full_name":"Nguyen, Laurent","last_name":"Nguyen","first_name":"Laurent"}],"department":[{"_id":"SiHi"}],"title":"Molecular pathways controlling the sequential steps of cortical projection neuron migration","publication_status":"published","status":"public","_id":"2265","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2014"},{"year":"2014","publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"IEEE","author":[{"last_name":"Olsson","first_name":"Carl","full_name":"Olsson, Carl"},{"first_name":"Johannes","last_name":"Ulen","full_name":"Ulen, Johannes"},{"full_name":"Boykov, Yuri","first_name":"Yuri","last_name":"Boykov"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"date_updated":"2021-01-12T06:56:28Z","date_created":"2018-12-11T11:56:42Z","file_date_updated":"2020-07-14T12:45:36Z","publist_id":"4669","oa":1,"quality_controlled":"1","conference":{"name":"ICCV: International Conference on Computer Vision","location":"Sydney, Australia","start_date":"2013-12-01","end_date":"2013-12-08"},"doi":"10.1109/ICCV.2013.365","language":[{"iso":"eng"}],"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2275","title":"Partial enumeration and curvature regularization","status":"public","ddc":["000"],"pubrep_id":"566","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:36Z","date_created":"2018-12-12T10:09:30Z","checksum":"4a74b5c92d6dcd2348c2c10ec8dd18bf","relation":"main_file","file_id":"4754","content_type":"application/pdf","file_size":378601,"creator":"system","file_name":"IST-2016-566-v1+1_iccv13_part_enumeration.pdf","access_level":"open_access"}],"type":"conference","abstract":[{"text":"Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches. \r\nThis partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed. \r\nOur main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach.\r\n","lang":"eng"}],"citation":{"ama":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. Partial enumeration and curvature regularization. In: IEEE; 2014:2936-2943. doi:10.1109/ICCV.2013.365","ieee":"C. Olsson, J. Ulen, Y. Boykov, and V. Kolmogorov, “Partial enumeration and curvature regularization,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2014, pp. 2936–2943.","apa":"Olsson, C., Ulen, J., Boykov, Y., & Kolmogorov, V. (2014). Partial enumeration and curvature regularization (pp. 2936–2943). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.365","ista":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. 2014. Partial enumeration and curvature regularization. ICCV: International Conference on Computer Vision, 2936–2943.","short":"C. Olsson, J. Ulen, Y. Boykov, V. Kolmogorov, in:, IEEE, 2014, pp. 2936–2943.","mla":"Olsson, Carl, et al. Partial Enumeration and Curvature Regularization. IEEE, 2014, pp. 2936–43, doi:10.1109/ICCV.2013.365.","chicago":"Olsson, Carl, Johannes Ulen, Yuri Boykov, and Vladimir Kolmogorov. “Partial Enumeration and Curvature Regularization,” 2936–43. IEEE, 2014. https://doi.org/10.1109/ICCV.2013.365."},"page":"2936 - 2943","date_published":"2014-03-03T00:00:00Z","scopus_import":1,"day":"03","has_accepted_license":"1"},{"_id":"2285","user_id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","intvolume":" 23","status":"public","title":"Morpho-physiological criteria divide dentate gyrus interneurons into classes","ddc":["570"],"pubrep_id":"461","file":[{"access_level":"open_access","file_name":"IST-2016-461-v1+1_Hosp_et_al-2014-Hippocampus.pdf","creator":"system","file_size":801589,"content_type":"application/pdf","file_id":"5178","relation":"main_file","checksum":"ff6bc75a79dbc985a2e31b79253e6444","date_created":"2018-12-12T10:15:54Z","date_updated":"2020-07-14T12:45:37Z"}],"oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity."}],"citation":{"chicago":"Hosp, Jonas, Michael Strüber, Yuchio Yanagawa, Kunihiko Obata, Imre Vida, Peter M Jonas, and Marlene Bartos. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons into Classes.” Hippocampus. Wiley-Blackwell, 2014. https://doi.org/10.1002/hipo.22214.","mla":"Hosp, Jonas, et al. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons into Classes.” Hippocampus, vol. 23, no. 2, Wiley-Blackwell, 2014, pp. 189–203, doi:10.1002/hipo.22214.","short":"J. Hosp, M. Strüber, Y. Yanagawa, K. Obata, I. Vida, P.M. Jonas, M. Bartos, Hippocampus 23 (2014) 189–203.","ista":"Hosp J, Strüber M, Yanagawa Y, Obata K, Vida I, Jonas PM, Bartos M. 2014. Morpho-physiological criteria divide dentate gyrus interneurons into classes. Hippocampus. 23(2), 189–203.","apa":"Hosp, J., Strüber, M., Yanagawa, Y., Obata, K., Vida, I., Jonas, P. M., & Bartos, M. (2014). Morpho-physiological criteria divide dentate gyrus interneurons into classes. Hippocampus. Wiley-Blackwell. https://doi.org/10.1002/hipo.22214","ieee":"J. Hosp et al., “Morpho-physiological criteria divide dentate gyrus interneurons into classes,” Hippocampus, vol. 23, no. 2. Wiley-Blackwell, pp. 189–203, 2014.","ama":"Hosp J, Strüber M, Yanagawa Y, et al. Morpho-physiological criteria divide dentate gyrus interneurons into classes. Hippocampus. 2014;23(2):189-203. doi:10.1002/hipo.22214"},"publication":"Hippocampus","page":"189 - 203","date_published":"2014-02-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","year":"2014","acknowledgement":"Funded by Deutsche Forschungsgemeinschaft. Grant Numbers: SFB 505, SFB 780, BA1582/2-1 Excellence Initiative of the German Research Foundation (Spemann Graduate School). Grant Number: GSC-4 Lichtenberg Professorship-Award (VW-Foundation); Schram-Foundation; Excellence Initiative Brain Links-Brain Tools. The authors thank Drs. Jonas-Frederic Sauer and Claudio Elgueta for critically reading the manuscript. They also thank Karin Winterhalter, Margit Northemann and Ulrich Nöller for technical assistance.","department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","publication_status":"published","author":[{"full_name":"Hosp, Jonas","last_name":"Hosp","first_name":"Jonas"},{"full_name":"Strüber, Michael","first_name":"Michael","last_name":"Strüber"},{"first_name":"Yuchio","last_name":"Yanagawa","full_name":"Yanagawa, Yuchio"},{"full_name":"Obata, Kunihiko","first_name":"Kunihiko","last_name":"Obata"},{"last_name":"Vida","first_name":"Imre","full_name":"Vida, Imre"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"}],"volume":23,"date_updated":"2021-01-12T06:56:32Z","date_created":"2018-12-11T11:56:46Z","publist_id":"4646","file_date_updated":"2020-07-14T12:45:37Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1002/hipo.22214","language":[{"iso":"eng"}],"month":"02"},{"abstract":[{"lang":"eng","text":"We prove the universality of the β-ensembles with convex analytic potentials and for any β >\r\n0, i.e. we show that the spacing distributions of log-gases at any inverse temperature β coincide with those of the Gaussian β-ensembles."}],"publist_id":"4197","issue":"6","type":"journal_article","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"full_name":"Bourgade, Paul","first_name":"Paul","last_name":"Bourgade"},{"full_name":"Yau, Horng","first_name":"Horng","last_name":"Yau"}],"date_created":"2018-12-11T11:59:08Z","date_updated":"2021-01-12T06:59:07Z","volume":163,"oa_version":"Preprint","_id":"2699","user_id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","year":"2014","status":"public","publication_status":"published","title":"Universality of general β-ensembles","publisher":"Duke University Press","intvolume":" 163","department":[{"_id":"LaEr"}],"month":"04","day":"01","scopus_import":1,"doi":"10.1215/00127094-2649752","date_published":"2014-04-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Duke Mathematical Journal","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.2272"}],"citation":{"ama":"Erdös L, Bourgade P, Yau H. Universality of general β-ensembles. Duke Mathematical Journal. 2014;163(6):1127-1190. doi:10.1215/00127094-2649752","ista":"Erdös L, Bourgade P, Yau H. 2014. Universality of general β-ensembles. Duke Mathematical Journal. 163(6), 1127–1190.","ieee":"L. Erdös, P. Bourgade, and H. Yau, “Universality of general β-ensembles,” Duke Mathematical Journal, vol. 163, no. 6. Duke University Press, pp. 1127–1190, 2014.","apa":"Erdös, L., Bourgade, P., & Yau, H. (2014). Universality of general β-ensembles. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2649752","mla":"Erdös, László, et al. “Universality of General β-Ensembles.” Duke Mathematical Journal, vol. 163, no. 6, Duke University Press, 2014, pp. 1127–90, doi:10.1215/00127094-2649752.","short":"L. Erdös, P. Bourgade, H. Yau, Duke Mathematical Journal 163 (2014) 1127–1190.","chicago":"Erdös, László, Paul Bourgade, and Horng Yau. “Universality of General β-Ensembles.” Duke Mathematical Journal. Duke University Press, 2014. https://doi.org/10.1215/00127094-2649752."},"quality_controlled":"1","page":"1127 - 1190"},{"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","acknowledgement":"Krishnendu Chatterjee is supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407 (RiSE), ERC Starting Grant (279307: Graph Games) and Microsoft faculty fellowship. Mickael Randour is supported by F.R.S.-FNRS. fellowship. \r\nJean-François Raskin is supported by ERC Starting Grant (279499: inVEST).Thanks to D. Sbabo for useful pointers, V. Bruyère for comments on a preliminary draft, and A. Bohy for fruitful discussions about the Acacia+ tool. We are grateful to the anonymous reviewers for their insightful comments. ","year":"2014","date_created":"2018-12-11T11:59:14Z","date_updated":"2023-02-21T16:06:56Z","volume":51,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Mickael","last_name":"Randour","full_name":"Randour, Mickael"},{"full_name":"Raskin, Jean","first_name":"Jean","last_name":"Raskin"}],"related_material":{"record":[{"id":"10904","relation":"earlier_version","status":"public"}]},"publist_id":"4176","quality_controlled":"1","project":[{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"external_id":{"arxiv":["1201.5073"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1201.5073"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00236-013-0182-6","month":"06","status":"public","title":"Strategy synthesis for multi-dimensional quantitative objectives","intvolume":" 51","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2716","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω ω -regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on vector addition systems with states. Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts.","lang":"eng"}],"issue":"3-4","article_type":"original","page":"129 - 163","publication":"Acta Informatica","citation":{"ieee":"K. Chatterjee, M. Randour, and J. Raskin, “Strategy synthesis for multi-dimensional quantitative objectives,” Acta Informatica, vol. 51, no. 3–4. Springer, pp. 129–163, 2014.","apa":"Chatterjee, K., Randour, M., & Raskin, J. (2014). Strategy synthesis for multi-dimensional quantitative objectives. Acta Informatica. Springer. https://doi.org/10.1007/s00236-013-0182-6","ista":"Chatterjee K, Randour M, Raskin J. 2014. Strategy synthesis for multi-dimensional quantitative objectives. Acta Informatica. 51(3–4), 129–163.","ama":"Chatterjee K, Randour M, Raskin J. Strategy synthesis for multi-dimensional quantitative objectives. Acta Informatica. 2014;51(3-4):129-163. doi:10.1007/s00236-013-0182-6","chicago":"Chatterjee, Krishnendu, Mickael Randour, and Jean Raskin. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” Acta Informatica. Springer, 2014. https://doi.org/10.1007/s00236-013-0182-6.","short":"K. Chatterjee, M. Randour, J. Raskin, Acta Informatica 51 (2014) 129–163.","mla":"Chatterjee, Krishnendu, et al. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” Acta Informatica, vol. 51, no. 3–4, Springer, 2014, pp. 129–63, doi:10.1007/s00236-013-0182-6."},"date_published":"2014-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"file":[{"relation":"main_file","file_id":"5232","checksum":"1d4a046f1af945c407c5c4d411d4c5e4","date_created":"2018-12-12T10:16:43Z","date_updated":"2020-07-14T12:45:52Z","access_level":"open_access","file_name":"IST-2016-544-v1+1_2012-P-11-PHTheoryPractice.pdf","content_type":"application/pdf","file_size":435320,"creator":"system"}],"oa_version":"Submitted Version","pubrep_id":"544","status":"public","title":"Persistent homology: Theory and practice","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2905","abstract":[{"lang":"eng","text":"Persistent homology is a recent grandchild of homology that has found use in\r\nscience and engineering as well as in mathematics. This paper surveys the method as well\r\nas the applications, neglecting completeness in favor of highlighting ideas and directions."}],"type":"conference","date_published":"2014-01-01T00:00:00Z","page":"31 - 50","citation":{"short":"H. Edelsbrunner, D. Morozovy, in:, European Mathematical Society Publishing House, 2014, pp. 31–50.","mla":"Edelsbrunner, Herbert, and Dmitriy Morozovy. Persistent Homology: Theory and Practice. European Mathematical Society Publishing House, 2014, pp. 31–50, doi:10.4171/120-1/3.","chicago":"Edelsbrunner, Herbert, and Dmitriy Morozovy. “Persistent Homology: Theory and Practice,” 31–50. European Mathematical Society Publishing House, 2014. https://doi.org/10.4171/120-1/3.","ama":"Edelsbrunner H, Morozovy D. Persistent homology: Theory and practice. In: European Mathematical Society Publishing House; 2014:31-50. doi:10.4171/120-1/3","ieee":"H. Edelsbrunner and D. Morozovy, “Persistent homology: Theory and practice,” presented at the ECM: European Congress of Mathematics, Kraków, Poland, 2014, pp. 31–50.","apa":"Edelsbrunner, H., & Morozovy, D. (2014). Persistent homology: Theory and practice (pp. 31–50). Presented at the ECM: European Congress of Mathematics, Kraków, Poland: European Mathematical Society Publishing House. https://doi.org/10.4171/120-1/3","ista":"Edelsbrunner H, Morozovy D. 2014. Persistent homology: Theory and practice. ECM: European Congress of Mathematics, 31–50."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","date_created":"2018-12-11T12:00:16Z","date_updated":"2021-01-12T07:00:36Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"first_name":"Dmitriy","last_name":"Morozovy","full_name":"Morozovy, Dmitriy"}],"publication_status":"published","publisher":"European Mathematical Society Publishing House","department":[{"_id":"HeEd"}],"acknowledgement":"This research is partially supported by NSF under grant DBI-0820624, by ESF under the Research Networking Programme, and by the Russian Government Project 11.G34.31.0053.","year":"2014","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3842","language":[{"iso":"eng"}],"conference":{"name":"ECM: European Congress of Mathematics","end_date":"2012-07-07","start_date":"2012-07-02","location":"Kraków, Poland"},"doi":"10.4171/120-1/3","quality_controlled":"1","oa":1,"month":"01"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2014.08.019","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.2450"}],"month":"12","volume":560,"date_created":"2018-12-11T11:53:43Z","date_updated":"2023-02-23T11:04:00Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2916"}]},"author":[{"full_name":"Cerny, Pavol","first_name":"Pavol","last_name":"Cerny"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna"}],"publisher":"Elsevier","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","year":"2014","publist_id":"5392","ec_funded":1,"date_published":"2014-12-04T00:00:00Z","page":"348 - 363","citation":{"mla":"Cerny, Pavol, et al. “Interface Simulation Distances.” Theoretical Computer Science, vol. 560, no. 3, Elsevier, 2014, pp. 348–63, doi:10.1016/j.tcs.2014.08.019.","short":"P. Cerny, M. Chmelik, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 560 (2014) 348–363.","chicago":"Cerny, Pavol, Martin Chmelik, Thomas A Henzinger, and Arjun Radhakrishna. “Interface Simulation Distances.” Theoretical Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2014.08.019.","ama":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. Interface simulation distances. Theoretical Computer Science. 2014;560(3):348-363. doi:10.1016/j.tcs.2014.08.019","ista":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. 2014. Interface simulation distances. Theoretical Computer Science. 560(3), 348–363.","apa":"Cerny, P., Chmelik, M., Henzinger, T. A., & Radhakrishna, A. (2014). Interface simulation distances. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2014.08.019","ieee":"P. Cerny, M. Chmelik, T. A. Henzinger, and A. Radhakrishna, “Interface simulation distances,” Theoretical Computer Science, vol. 560, no. 3. Elsevier, pp. 348–363, 2014."},"publication":"Theoretical Computer Science","day":"04","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 560","title":"Interface simulation distances","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1733","issue":"3","abstract":[{"text":"The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces, and how to synthesize an interface from incompatible requirements. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The computation of the winning set for Büchi objectives in alternating games on graphs is a central problem in computer-aided verification with a large number of applications. The long-standing best known upper bound for solving the problem is Õ(n ⋅ m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n ⋅ m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2)-time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n ⋅ m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m>n4/3 an earlier bound of O(m ⋅ √m)). We then show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. Our algorithms are the first dynamic algorithms for this problem. We then consider another core graph theoretic problem in verification of probabilistic systems, namely computing the maximal end-component decomposition of a graph. We present two improved static algorithms for the maximal end-component decomposition problem. Our first algorithm is an O(m ⋅ √m)-time algorithm, and our second algorithm is an O(n2)-time algorithm which is obtained using the same technique as for alternating Büchi games. Thus, we obtain an O(min &lcu;m ⋅ √m,n2})-time algorithm improving the long-standing O(n ⋅ m) time bound. Finally, we show how to maintain the maximal end-component decomposition of a graph under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per edge deletion, and O(m) worst-case time per edge insertion. Again, our algorithms are the first dynamic algorithms for this problem."}],"issue":"3","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"2141","status":"public","title":"Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition","intvolume":" 61","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Journal of the ACM","citation":{"chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. “Efficient and Dynamic Algorithms for Alternating Büchi Games and Maximal End-Component Decomposition.” Journal of the ACM. ACM, 2014. https://doi.org/10.1145/2597631.","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. “Efficient and Dynamic Algorithms for Alternating Büchi Games and Maximal End-Component Decomposition.” Journal of the ACM, vol. 61, no. 3, a15, ACM, 2014, doi:10.1145/2597631.","short":"K. Chatterjee, M.H. Henzinger, Journal of the ACM 61 (2014).","ista":"Chatterjee K, Henzinger MH. 2014. Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition. Journal of the ACM. 61(3), a15.","apa":"Chatterjee, K., & Henzinger, M. H. (2014). Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition. Journal of the ACM. ACM. https://doi.org/10.1145/2597631","ieee":"K. Chatterjee and M. H. Henzinger, “Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition,” Journal of the ACM, vol. 61, no. 3. ACM, 2014.","ama":"Chatterjee K, Henzinger MH. Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition. Journal of the ACM. 2014;61(3). doi:10.1145/2597631"},"date_published":"2014-05-01T00:00:00Z","article_number":"a15","publist_id":"4883","ec_funded":1,"year":"2014","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"ACM","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"related_material":{"record":[{"id":"3165","status":"public","relation":"earlier_version"}]},"date_updated":"2023-02-23T11:15:12Z","date_created":"2018-12-11T11:55:57Z","volume":61,"month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprints.cs.univie.ac.at/3933/"}],"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/2597631","language":[{"iso":"eng"}]},{"pubrep_id":"432","file":[{"file_size":1568524,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-432-v1+1_journal.pone.0085841.pdf","access_level":"open_access","date_created":"2018-12-12T10:13:28Z","date_updated":"2020-07-14T12:46:06Z","checksum":"1d5816b343abe5eadc3eb419bcece971","relation":"main_file","file_id":"5011"}],"oa_version":"Published Version","_id":"3263","user_id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","ddc":["570"],"title":"Adaptation to changes in higher-order stimulus statistics in the salamander retina","status":"public","issue":"1","abstract":[{"lang":"eng","text":"Adaptation in the retina is thought to optimize the encoding of natural light signals into sequences of spikes sent to the brain. While adaptive changes in retinal processing to the variations of the mean luminance level and second-order stimulus statistics have been documented before, no such measurements have been performed when higher-order moments of the light distribution change. We therefore measured the ganglion cell responses in the tiger salamander retina to controlled changes in the second (contrast), third (skew) and fourth (kurtosis) moments of the light intensity distribution of spatially uniform temporally independent stimuli. The skew and kurtosis of the stimuli were chosen to cover the range observed in natural scenes. We quantified adaptation in ganglion cells by studying linear-nonlinear models that capture well the retinal encoding properties across all stimuli. We found that the encoding properties of retinal ganglion cells change only marginally when higher-order statistics change, compared to the changes observed in response to the variation in contrast. By analyzing optimal coding in LN-type models, we showed that neurons can maintain a high information rate without large dynamic adaptation to changes in skew or kurtosis. This is because, for uncorrelated stimuli, spatio-temporal summation within the receptive field averages away non-gaussian aspects of the light intensity distribution."}],"type":"journal_article","date_published":"2014-01-21T00:00:00Z","citation":{"chicago":"Tkačik, Gašper, Anandamohan Ghosh, Elad Schneidman, and Ronen Segev. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0085841.","short":"G. Tkačik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).","mla":"Tkačik, Gašper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.","apa":"Tkačik, G., Ghosh, A., Schneidman, E., & Segev, R. (2014). Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0085841","ieee":"G. Tkačik, A. Ghosh, E. Schneidman, and R. Segev, “Adaptation to changes in higher-order stimulus statistics in the salamander retina,” PLoS One, vol. 9, no. 1. Public Library of Science, 2014.","ista":"Tkačik G, Ghosh A, Schneidman E, Segev R. 2014. Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. 9(1), e85841.","ama":"Tkačik G, Ghosh A, Schneidman E, Segev R. Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085841"},"publication":"PLoS One","has_accepted_license":"1","day":"21","scopus_import":1,"author":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"last_name":"Ghosh","first_name":"Anandamohan","full_name":"Ghosh, Anandamohan"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"full_name":"Segev, Ronen","first_name":"Ronen","last_name":"Segev"}],"volume":9,"date_updated":"2021-01-12T07:42:14Z","date_created":"2018-12-11T12:02:20Z","acknowledgement":"This work was supported by The Israel Science Foundation and The Human Frontiers Science Program.\r\nWe thank the referees for helping significantly improve this paper. We also thank Vijay Balasubramanian, Kristina Simmons, and Jason Prentice for stimulating discussions. GT wishes to thank the faculty and students of the “Methods in Computational Neuroscience” course at Marine Biological Laboratory, Woods Hole.\r\n","year":"2014","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","publist_id":"3385","file_date_updated":"2020-07-14T12:46:06Z","article_number":"e85841","doi":"10.1371/journal.pone.0085841","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"01"},{"month":"09","conference":{"location":"Rome, Italy","start_date":"2014-09-02","end_date":"2014-09-05","name":"CONCUR: Concurrency Theory"},"doi":"10.1007/978-3-662-44584-6_37","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publist_id":"4992","ec_funded":1,"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"related_material":{"record":[{"id":"3354","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-11T11:55:27Z","date_updated":"2023-02-23T11:23:36Z","volume":8704,"year":"2014","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","editor":[{"last_name":"Baldan","first_name":"Paolo","full_name":"Baldan, Paolo"},{"full_name":"Gorla, Daniele","last_name":"Gorla","first_name":"Daniele"}],"day":"01","date_published":"2014-09-01T00:00:00Z","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","citation":{"short":"K. Chatterjee, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 544–559.","mla":"Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 544–59, doi:10.1007/978-3-662-44584-6_37.","chicago":"Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:544–59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_37.","ama":"Chatterjee K. Qualitative concurrent parity games: Bounded rationality. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:544-559. doi:10.1007/978-3-662-44584-6_37","apa":"Chatterjee, K. (2014). Qualitative concurrent parity games: Bounded rationality. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 544–559). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_37","ieee":"K. Chatterjee, “Qualitative concurrent parity games: Bounded rationality,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 544–559.","ista":"Chatterjee K. 2014. Qualitative concurrent parity games: Bounded rationality. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 544–559."},"page":"544 - 559","abstract":[{"lang":"eng","text":"We study two-player concurrent games on finite-state graphs played for an infinite number of rounds, where in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. The objectives are ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). While the qualitative analysis problem for concurrent parity games with infinite-memory, infinite-precision randomized strategies was studied before, we study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies. In terms of precision, strategies can be deterministic, uniform, finite-precision, or infinite-precision; and in terms of memory, strategies can be memoryless, finite-memory, or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies. We show that the winning sets can be computed in (n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. Our symbolic algorithms are based on a characterization of the winning sets as μ-calculus formulas, however, our μ-calculus formulas are crucially different from the ones for concurrent parity games (without bounded rationality); and our memoryless witness strategy constructions are significantly different from the infinite-memory witness strategy constructions for concurrent parity games."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2054","status":"public","title":"Qualitative concurrent parity games: Bounded rationality","intvolume":" 8704"},{"publication_status":"published","status":"public","title":"Robust multi-property combiners for hash functions","publisher":"Springer","department":[{"_id":"KrPi"}],"intvolume":" 27","user_id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","_id":"2852","year":"2014","date_created":"2018-12-11T11:59:56Z","date_updated":"2023-02-23T11:17:53Z","oa_version":"None","volume":27,"author":[{"last_name":"Fischlin","first_name":"Marc","full_name":"Fischlin, Marc"},{"last_name":"Lehmann","first_name":"Anja","full_name":"Lehmann, Anja"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"related_material":{"record":[{"id":"3225","relation":"earlier_version","status":"public"}]},"type":"journal_article","abstract":[{"lang":"eng","text":"A robust combiner for hash functions takes two candidate implementations and constructs a hash function which is secure as long as at least one of the candidates is secure. So far, hash function combiners only aim at preserving a single property such as collision-resistance or pseudorandomness. However, when hash functions are used in protocols like TLS they are often required to provide several properties simultaneously. We therefore put forward the notion of robust multi-property combiners and elaborate on different definitions for such combiners. We then propose a combiner that provably preserves (target) collision-resistance, pseudorandomness, and being a secure message authentication code. This combiner satisfies the strongest notion we propose, which requires that the combined function satisfies every security property which is satisfied by at least one of the underlying hash function. If the underlying hash functions have output length n, the combiner has output length 2 n. This basically matches a known lower bound for black-box combiners for collision-resistance only, thus the other properties can be achieved without penalizing the length of the hash values. We then propose a combiner which also preserves the property of being indifferentiable from a random oracle, slightly increasing the output length to 2 n+ω(log n). Moreover, we show how to augment our constructions in order to make them also robust for the one-wayness property, but in this case require an a priory upper bound on the input length."}],"issue":"3","publist_id":"3940","quality_controlled":"1","page":"397 - 428","publication":"Journal of Cryptology","citation":{"apa":"Fischlin, M., Lehmann, A., & Pietrzak, K. Z. (2014). Robust multi-property combiners for hash functions. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-013-9148-7","ieee":"M. Fischlin, A. Lehmann, and K. Z. Pietrzak, “Robust multi-property combiners for hash functions,” Journal of Cryptology, vol. 27, no. 3. Springer, pp. 397–428, 2014.","ista":"Fischlin M, Lehmann A, Pietrzak KZ. 2014. Robust multi-property combiners for hash functions. Journal of Cryptology. 27(3), 397–428.","ama":"Fischlin M, Lehmann A, Pietrzak KZ. Robust multi-property combiners for hash functions. Journal of Cryptology. 2014;27(3):397-428. doi:10.1007/s00145-013-9148-7","chicago":"Fischlin, Marc, Anja Lehmann, and Krzysztof Z Pietrzak. “Robust Multi-Property Combiners for Hash Functions.” Journal of Cryptology. Springer, 2014. https://doi.org/10.1007/s00145-013-9148-7.","short":"M. Fischlin, A. Lehmann, K.Z. Pietrzak, Journal of Cryptology 27 (2014) 397–428.","mla":"Fischlin, Marc, et al. “Robust Multi-Property Combiners for Hash Functions.” Journal of Cryptology, vol. 27, no. 3, Springer, 2014, pp. 397–428, doi:10.1007/s00145-013-9148-7."},"language":[{"iso":"eng"}],"date_published":"2014-07-01T00:00:00Z","doi":"10.1007/s00145-013-9148-7","scopus_import":1,"month":"07","day":"01"},{"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0107518","language":[{"iso":"eng"}],"article_number":"0107518","publist_id":"7352","file_date_updated":"2020-07-14T12:46:34Z","year":"2014","acknowledgement":"The study was funded by the University of Vienna (Focus of Excellence grant), the Galápagos Conservation Trust, and the Ethologische Gesellschaft e.V.","publisher":"Public Library of Science","department":[{"_id":"CampIT"}],"publication_status":"published","author":[{"first_name":"Arno","last_name":"Cimadom","full_name":"Cimadom, Arno"},{"first_name":"Angel","last_name":"Ulloa","full_name":"Ulloa, Angel"},{"first_name":"Patrick","last_name":"Meidl","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Meidl, Patrick"},{"last_name":"Zöttl","first_name":"Markus","full_name":"Zöttl, Markus"},{"full_name":"Zöttl, Elisabet","first_name":"Elisabet","last_name":"Zöttl"},{"full_name":"Fessl, Birgit","last_name":"Fessl","first_name":"Birgit"},{"full_name":"Nemeth, Erwin","first_name":"Erwin","last_name":"Nemeth"},{"full_name":"Dvorak, Michael","first_name":"Michael","last_name":"Dvorak"},{"last_name":"Cunninghame","first_name":"Francesca","full_name":"Cunninghame, Francesca"},{"full_name":"Tebbich, Sabine","last_name":"Tebbich","first_name":"Sabine"}],"volume":9,"date_created":"2018-12-11T11:46:38Z","date_updated":"2021-01-12T08:00:48Z","scopus_import":1,"has_accepted_license":"1","day":"23","citation":{"chicago":"Cimadom, Arno, Angel Ulloa, Patrick Meidl, Markus Zöttl, Elisabet Zöttl, Birgit Fessl, Erwin Nemeth, Michael Dvorak, Francesca Cunninghame, and Sabine Tebbich. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding Success in Darwin’s Finches.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107518.","mla":"Cimadom, Arno, et al. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding Success in Darwin’s Finches.” PLoS One, vol. 9, no. 9, 0107518, Public Library of Science, 2014, doi:10.1371/journal.pone.0107518.","short":"A. Cimadom, A. Ulloa, P. Meidl, M. Zöttl, E. Zöttl, B. Fessl, E. Nemeth, M. Dvorak, F. Cunninghame, S. Tebbich, PLoS One 9 (2014).","ista":"Cimadom A, Ulloa A, Meidl P, Zöttl M, Zöttl E, Fessl B, Nemeth E, Dvorak M, Cunninghame F, Tebbich S. 2014. Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. PLoS One. 9(9), 0107518.","ieee":"A. Cimadom et al., “Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","apa":"Cimadom, A., Ulloa, A., Meidl, P., Zöttl, M., Zöttl, E., Fessl, B., … Tebbich, S. (2014). Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107518","ama":"Cimadom A, Ulloa A, Meidl P, et al. Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107518"},"publication":"PLoS One","date_published":"2014-09-23T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance) is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"468","intvolume":" 9","status":"public","title":"Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin's finches","ddc":["576"],"pubrep_id":"954","file":[{"access_level":"open_access","file_name":"IST-2018-954-v1+1_2014_Meidl_Invasive_parasites.PDF","content_type":"application/pdf","file_size":489387,"creator":"system","relation":"main_file","file_id":"5103","checksum":"b24e7518ccd41effed0d7d9e2498f67f","date_updated":"2020-07-14T12:46:34Z","date_created":"2018-12-12T10:14:48Z"}],"oa_version":"Published Version"},{"doi":"10.4204/EPTCS.146.11","conference":{"name":"SR: Strategic Reasoning","end_date":"2014-04-06","start_date":"2014-04-05","location":"Grenoble, France"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","month":"04","author":[{"first_name":"Benjamin","last_name":"Aminof","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","full_name":"Aminof, Benjamin"},{"last_name":"Rubin","first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","full_name":"Rubin, Sasha"}],"volume":146,"date_created":"2018-12-11T11:46:41Z","date_updated":"2021-01-12T08:00:53Z","year":"2014","publisher":"Open Publishing Association","department":[{"_id":"KrCh"}],"publication_status":"published","publist_id":"7345","ec_funded":1,"file_date_updated":"2020-07-14T12:46:35Z","date_published":"2014-04-01T00:00:00Z","citation":{"ista":"Aminof B, Rubin S. 2014. First cycle games. Electronic Proceedings in Theoretical Computer Science, EPTCS. SR: Strategic Reasoning, EPTCS, vol. 146, 83–90.","ieee":"B. Aminof and S. Rubin, “First cycle games,” in Electronic Proceedings in Theoretical Computer Science, EPTCS, Grenoble, France, 2014, vol. 146, pp. 83–90.","apa":"Aminof, B., & Rubin, S. (2014). First cycle games. In Electronic Proceedings in Theoretical Computer Science, EPTCS (Vol. 146, pp. 83–90). Grenoble, France: Open Publishing Association. https://doi.org/10.4204/EPTCS.146.11","ama":"Aminof B, Rubin S. First cycle games. In: Electronic Proceedings in Theoretical Computer Science, EPTCS. Vol 146. Open Publishing Association; 2014:83-90. doi:10.4204/EPTCS.146.11","chicago":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” In Electronic Proceedings in Theoretical Computer Science, EPTCS, 146:83–90. Open Publishing Association, 2014. https://doi.org/10.4204/EPTCS.146.11.","mla":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” Electronic Proceedings in Theoretical Computer Science, EPTCS, vol. 146, Open Publishing Association, 2014, pp. 83–90, doi:10.4204/EPTCS.146.11.","short":"B. Aminof, S. Rubin, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing Association, 2014, pp. 83–90."},"publication":"Electronic Proceedings in Theoretical Computer Science, EPTCS","page":"83 - 90","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"952","file":[{"checksum":"4d7b4ab82980cca2b96ac7703992a8c8","date_created":"2018-12-12T10:17:08Z","date_updated":"2020-07-14T12:46:35Z","relation":"main_file","file_id":"5260","file_size":100115,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-952-v1+1_2014_Rubin_First_cycle.pdf"}],"oa_version":"Published Version","_id":"475","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 146","status":"public","title":"First cycle games","ddc":["004"],"abstract":[{"lang":"eng","text":"First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard. "}],"type":"conference","alternative_title":["EPTCS"]},{"author":[{"full_name":"Biedl, Therese","first_name":"Therese","last_name":"Biedl"},{"first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"}],"related_material":{"record":[{"id":"481","status":"public","relation":"later_version"}]},"date_created":"2022-03-21T07:09:03Z","date_updated":"2023-02-23T12:20:55Z","volume":8889,"acknowledgement":"T. Biedl was supported by NSERC and the Ross and Muriel Cheriton Fellowship. P. Palfrader was supported by Austrian Science Fund (FWF): P25816-N15.","year":"2014","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","month":"11","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783319130750"],"isbn":["9783319130743"],"eissn":["1611-3349"]},"conference":{"end_date":"2014-12-17","location":"Jeonju, Korea","start_date":"2014-12-15","name":"ISAAC: International Symposium on Algorithms and Computation"},"doi":"10.1007/978-3-319-13075-0_10","language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"In this paper, we introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist.\r\nUsing our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","_id":"10892","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Planar matchings for weighted straight skeletons","status":"public","intvolume":" 8889","day":"08","article_processing_charge":"No","scopus_import":"1","date_published":"2014-11-08T00:00:00Z","publication":"25th International Symposium, ISAAC 2014","citation":{"chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” In 25th International Symposium, ISAAC 2014, 8889:117–27. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13075-0_10.","short":"T. Biedl, S. Huber, P. Palfrader, in:, 25th International Symposium, ISAAC 2014, Springer Nature, 2014, pp. 117–127.","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” 25th International Symposium, ISAAC 2014, vol. 8889, Springer Nature, 2014, pp. 117–27, doi:10.1007/978-3-319-13075-0_10.","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” in 25th International Symposium, ISAAC 2014, Jeonju, Korea, 2014, vol. 8889, pp. 117–127.","apa":"Biedl, T., Huber, S., & Palfrader, P. (2014). Planar matchings for weighted straight skeletons. In 25th International Symposium, ISAAC 2014 (Vol. 8889, pp. 117–127). Jeonju, Korea: Springer Nature. https://doi.org/10.1007/978-3-319-13075-0_10","ista":"Biedl T, Huber S, Palfrader P. 2014. Planar matchings for weighted straight skeletons. 25th International Symposium, ISAAC 2014. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 8889, 117–127.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. In: 25th International Symposium, ISAAC 2014. Vol 8889. Springer Nature; 2014:117-127. doi:10.1007/978-3-319-13075-0_10"},"page":"117-127"},{"volume":4,"date_created":"2018-12-11T11:47:02Z","date_updated":"2021-01-12T08:01:30Z","author":[{"first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"last_name":"Ezard","first_name":"Thomas","full_name":"Ezard, Thomas"},{"last_name":"Hoyle","first_name":"Rebecca","full_name":"Hoyle, Rebecca"}],"publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publication_status":"published","year":"2014","publist_id":"7280","file_date_updated":"2020-07-14T12:46:38Z","language":[{"iso":"eng"}],"doi":"10.1002/ece3.1150","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"07","oa_version":"Published Version","file":[{"checksum":"e32abf75a248e7a11811fd7f60858769","date_created":"2018-12-12T10:11:31Z","date_updated":"2020-07-14T12:46:38Z","relation":"main_file","file_id":"4886","file_size":621582,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf"}],"pubrep_id":"934","intvolume":" 4","ddc":["530","571"],"title":"Fitness consequences of maternal and grandmaternal effects","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"537","issue":"15","abstract":[{"lang":"eng","text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring."}],"type":"journal_article","date_published":"2014-07-19T00:00:00Z","page":"3139 - 3145","citation":{"ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","apa":"Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150","ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150","chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1150.","short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:10.1002/ece3.1150."},"publication":"Ecology and Evolution","has_accepted_license":"1","day":"19","scopus_import":1},{"date_published":"2014-01-01T00:00:00Z","page":"1 - 4","citation":{"short":"K. Chatterjee, in:, Springer, 2014, pp. 1–4.","mla":"Chatterjee, Krishnendu. Partial-Observation Stochastic Reachability and Parity Games. Vol. 8634, no. PART 1, Springer, 2014, pp. 1–4, doi:10.1007/978-3-662-44522-8_1.","chicago":"Chatterjee, Krishnendu. “Partial-Observation Stochastic Reachability and Parity Games,” 8634:1–4. Springer, 2014. https://doi.org/10.1007/978-3-662-44522-8_1.","ama":"Chatterjee K. Partial-observation stochastic reachability and parity games. In: Vol 8634. Springer; 2014:1-4. doi:10.1007/978-3-662-44522-8_1","apa":"Chatterjee, K. (2014). Partial-observation stochastic reachability and parity games (Vol. 8634, pp. 1–4). Presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary: Springer. https://doi.org/10.1007/978-3-662-44522-8_1","ieee":"K. Chatterjee, “Partial-observation stochastic reachability and parity games,” presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary, 2014, vol. 8634, no. PART 1, pp. 1–4.","ista":"Chatterjee K. 2014. Partial-observation stochastic reachability and parity games. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 8634, 1–4."},"day":"01","scopus_import":1,"oa_version":"None","pubrep_id":"141","title":"Partial-observation stochastic reachability and parity games","status":"public","intvolume":" 8634","_id":"1903","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider two-player zero-sum partial-observation stochastic games on graphs. Based on the information available to the players these games can be classified as follows: (a) general partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) perfect-observation (both players have complete view of the game). The one-sided partial-observation games subsumes the important special case of one-player partial-observation stochastic games (or partial-observation Markov decision processes (POMDPs)). Based on the randomization available for the strategies, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. We consider all these classes of games with reachability, and parity objectives that can express all ω-regular objectives. The analysis problems are classified into the qualitative analysis that asks for the existence of a strategy that ensures the objective with probability 1; and the quantitative analysis that asks for the existence of a strategy that ensures the objective with probability at least λ (0,1). In this talk we will cover a wide range of results: for perfect-observation games; for POMDPs; for one-sided partial-observation games; and for general partial-observation games."}],"issue":"PART 1","alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"location":"Budapest, Hungary","start_date":"2014-08-25","end_date":"2014-08-29","name":"MFCS: Mathematical Foundations of Computer Science"},"doi":"10.1007/978-3-662-44522-8_1","quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"01","date_updated":"2023-02-23T12:23:43Z","date_created":"2018-12-11T11:54:38Z","volume":8634,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"2211"},{"id":"5381","relation":"earlier_version","status":"public"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2014","ec_funded":1,"publist_id":"5192"},{"day":"01","scopus_import":1,"date_published":"2014-04-01T00:00:00Z","publication":"ACM Transactions on Computational Logic (TOCL)","citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic (TOCL). ACM, 2014. https://doi.org/10.1145/2579821.","short":"K. Chatterjee, L. Doyen, ACM Transactions on Computational Logic (TOCL) 15 (2014).","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 2, 16, ACM, 2014, doi:10.1145/2579821.","ieee":"K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to win when belief fails,” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 2. ACM, 2014.","apa":"Chatterjee, K., & Doyen, L. (2014). Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2579821","ista":"Chatterjee K, Doyen L. 2014. Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic (TOCL). 15(2), 16.","ama":"Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic (TOCL). 2014;15(2). doi:10.1145/2579821"},"abstract":[{"lang":"eng","text":"In two-player finite-state stochastic games of partial observation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distribution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or positively (i.e., with positive probability), no matter the strategy of the second player. We classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two-sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Our main results for pure strategies are as follows: (1) For one-sided games with player 2 having perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strategies are not sufficient, and we present an exponential upper bound on memory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algorithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 having perfect observation we show that nonelementarymemory is both necessary and sufficient for both almost-sure and positive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least nonelementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence result exhibit serious flaws in previous results of the literature: we show a nonelementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed."}],"issue":"2","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2211","status":"public","title":"Partial-observation stochastic games: How to win when belief fails","intvolume":" 15","month":"04","doi":"10.1145/2579821","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.2141"}],"oa":1,"external_id":{"arxiv":["1107.2141"]},"quality_controlled":"1","publist_id":"4759","article_number":"16","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1903"},{"id":"2955","status":"public","relation":"earlier_version"},{"id":"5381","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-11T11:56:21Z","date_updated":"2023-02-23T12:23:43Z","volume":15,"year":"2014","publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}]},{"citation":{"ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 15(4), 27.","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications with accumulative values,” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 4. ACM, 2014.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2014). Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2629686","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 2014;15(4). doi:10.1145/2629686","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic (TOCL). ACM, 2014. https://doi.org/10.1145/2629686.","mla":"Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 4, 27, ACM, 2014, doi:10.1145/2629686.","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 15 (2014)."},"publication":"ACM Transactions on Computational Logic (TOCL)","article_type":"original","date_published":"2014-09-16T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"16","_id":"2038","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","status":"public","ddc":["000","004"],"title":"Temporal specifications with accumulative values","pubrep_id":"192","file":[{"access_level":"open_access","file_name":"IST-2014-192-v1+1_AccumulativeValues.pdf","creator":"system","content_type":"application/pdf","file_size":346184,"file_id":"4851","relation":"main_file","checksum":"354c41d37500b56320afce94cf9a99c2","date_created":"2018-12-12T10:10:59Z","date_updated":"2020-07-14T12:45:26Z"}],"oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Recently, there has been an effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions. At the heart of quantitative objectives lies the accumulation of values along a computation. It is often the accumulated sum, as with energy objectives, or the accumulated average, as with mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point in time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire infinite computation. We study the border of decidability for such quantitative extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with both prefix-accumulation assertions, or extending LTL with both path-accumulation assertions, results in temporal logics whose model-checking problem is decidable. Moreover, the prefix-accumulation assertions may be generalized with "controlled accumulation," allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that this branching-time logic is, in a sense, the maximal logic with one or both of the prefix-accumulation assertions that permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL, makes the problem undecidable."}],"oa":1,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1145/2629686","language":[{"iso":"eng"}],"month":"09","year":"2014","acknowledgement":"The research was supported in part by ERC Starting grant 278410 (QUALITY).","publisher":"ACM","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3356"},{"id":"5385","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker","first_name":"Udi"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"volume":15,"date_updated":"2023-02-23T12:23:54Z","date_created":"2018-12-11T11:55:21Z","article_number":"27","ec_funded":1,"publist_id":"5013","file_date_updated":"2020-07-14T12:45:26Z"},{"ec_funded":1,"publist_id":"4822","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5404"}]},"date_created":"2018-12-11T11:56:04Z","date_updated":"2023-02-23T12:24:48Z","volume":8573,"year":"2014","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","month":"01","conference":{"start_date":"2014-07-08","location":"Copenhagen, Denmark","end_date":"2014-07-11","name":"ICST: International Conference on Software Testing, Verification and Validation"},"doi":"10.1007/978-3-662-43951-7_11","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5734"}],"external_id":{"arxiv":["1404.5734"]},"oa":1,"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"abstract":[{"lang":"eng","text":"We study two-player (zero-sum) concurrent mean-payoff games played on a finite-state graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lies in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP ∩ coNP is the long-standing best known bound). We present a variant of the strategy-iteration algorithm by Hoffman and Karp; show that both our algorithm and the classical value-iteration algorithm can approximate the value in exponential time; and identify a subclass where the value-iteration algorithm is a FPTAS. We also show that the exact value can be expressed in the existential theory of the reals, and establish square-root sum hardness for a related class of games."}],"issue":"Part 2","type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"2162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The complexity of ergodic mean payoff games","intvolume":" 8573","day":"01","date_published":"2014-01-01T00:00:00Z","citation":{"ama":"Chatterjee K, Ibsen-Jensen R. The complexity of ergodic mean payoff games. In: Vol 8573. Springer; 2014:122-133. doi:10.1007/978-3-662-43951-7_11","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2014). The complexity of ergodic mean payoff games (Vol. 8573, pp. 122–133). Presented at the ICST: International Conference on Software Testing, Verification and Validation, Copenhagen, Denmark: Springer. https://doi.org/10.1007/978-3-662-43951-7_11","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The complexity of ergodic mean payoff games,” presented at the ICST: International Conference on Software Testing, Verification and Validation, Copenhagen, Denmark, 2014, vol. 8573, no. Part 2, pp. 122–133.","ista":"Chatterjee K, Ibsen-Jensen R. 2014. The complexity of ergodic mean payoff games. ICST: International Conference on Software Testing, Verification and Validation, LNCS, vol. 8573, 122–133.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Springer, 2014, pp. 122–133.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic Mean Payoff Games. Vol. 8573, no. Part 2, Springer, 2014, pp. 122–33, doi:10.1007/978-3-662-43951-7_11.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Ergodic Mean Payoff Games,” 8573:122–33. Springer, 2014. https://doi.org/10.1007/978-3-662-43951-7_11."},"page":"122 - 133"},{"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Nain, Sumit","last_name":"Nain","first_name":"Sumit"},{"full_name":"Vardi, Moshe","first_name":"Moshe","last_name":"Vardi"}],"related_material":{"record":[{"id":"5408","status":"public","relation":"earlier_version"}]},"date_created":"2018-12-11T11:56:21Z","date_updated":"2023-02-23T12:24:58Z","volume":8412,"year":"2014","acknowledgement":"This research was supported by European project Cassting (FP7-601148), NSF grants CNS 1049862 and CCF-1139011, by NSF Expe ditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"ec_funded":1,"publist_id":"4757","conference":{"name":"FoSSaCS: Foundations of Software Science and Computation Structures","end_date":"2014-04-13","location":"Grenoble, France","start_date":"2014-04-05"},"doi":"10.1007/978-3-642-54830-7_16","language":[{"iso":"eng"}],"external_id":{"arxiv":["1401.3289"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.3289"}],"oa":1,"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"month":"04","oa_version":"Preprint","_id":"2213","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The complexity of partial-observation stochastic parity games with finite-memory strategies","intvolume":" 8412","abstract":[{"lang":"eng","text":"We consider two-player partial-observation stochastic games on finitestate graphs where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are ε-regular conditions specified as parity objectives. The qualitative-analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). These qualitative-analysis problems are known to be undecidable. However in many applications the relevant question is the existence of finite-memory strategies, and the qualitative-analysis problems under finite-memory strategies was recently shown to be decidable in 2EXPTIME.We improve the complexity and show that the qualitative-analysis problems for partial-observation stochastic parity games under finite-memory strategies are EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2014-04-01T00:00:00Z","citation":{"ista":"Chatterjee K, Doyen L, Nain S, Vardi M. 2014. The complexity of partial-observation stochastic parity games with finite-memory strategies. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 242–257.","ieee":"K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, “The complexity of partial-observation stochastic parity games with finite-memory strategies,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 242–257.","apa":"Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2014). The complexity of partial-observation stochastic parity games with finite-memory strategies (Vol. 8412, pp. 242–257). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_16","ama":"Chatterjee K, Doyen L, Nain S, Vardi M. The complexity of partial-observation stochastic parity games with finite-memory strategies. In: Vol 8412. Springer; 2014:242-257. doi:10.1007/978-3-642-54830-7_16","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. “The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies,” 8412:242–57. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_16.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. Vol. 8412, Springer, 2014, pp. 242–57, doi:10.1007/978-3-642-54830-7_16.","short":"K. Chatterjee, L. Doyen, S. Nain, M. Vardi, in:, Springer, 2014, pp. 242–257."},"page":"242 - 257","day":"01","scopus_import":1},{"_id":"2212","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Perfect-information stochastic mean-payoff parity games","status":"public","intvolume":" 8412","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2 1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic). We present an algorithm running in time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which the objective can be ensured with probability 1, where n is the number of states of the game, d the number of priorities of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states in 2 1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective). "}],"citation":{"ama":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-information stochastic mean-payoff parity games. In: Vol 8412. Springer; 2014:210-225. doi:10.1007/978-3-642-54830-7_14","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, “Perfect-information stochastic mean-payoff parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 210–225.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2014). Perfect-information stochastic mean-payoff parity games (Vol. 8412, pp. 210–225). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_14","ista":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2014. Perfect-information stochastic mean-payoff parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 210–225.","short":"K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, in:, Springer, 2014, pp. 210–225.","mla":"Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff Parity Games. Vol. 8412, Springer, 2014, pp. 210–25, doi:10.1007/978-3-642-54830-7_14.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. “Perfect-Information Stochastic Mean-Payoff Parity Games,” 8412:210–25. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_14."},"page":"210 - 225","date_published":"2014-04-01T00:00:00Z","scopus_import":1,"day":"01","acknowledgement":"This research was supported by European project Cassting (FP7-601148).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/128.","year":"2014","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"full_name":"Gimbert, Hugo","first_name":"Hugo","last_name":"Gimbert"},{"first_name":"Youssouf","last_name":"Oualhadj","full_name":"Oualhadj, Youssouf"}],"related_material":{"record":[{"id":"5405","relation":"earlier_version","status":"public"}]},"date_updated":"2023-02-23T12:24:50Z","date_created":"2018-12-11T11:56:21Z","volume":8412,"ec_funded":1,"publist_id":"4758","quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"conference":{"location":"Grenoble, France","start_date":"2014-04-05","end_date":"2014-04-13","name":"FoSSaCS: Foundations of Software Science and Computation Structures"},"doi":"10.1007/978-3-642-54830-7_14","language":[{"iso":"eng"}],"month":"04"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://dl.acm.org/citation.cfm?doid=2562059.2562141"}],"citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Ritankar Majumdar. “Edit Distance for Timed Automata,” 303–12. Springer, 2014. https://doi.org/10.1145/2562059.2562141.","short":"K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, in:, Springer, 2014, pp. 303–312.","mla":"Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. Springer, 2014, pp. 303–12, doi:10.1145/2562059.2562141.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, “Edit distance for timed automata,” presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany, 2014, pp. 303–312.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2014). Edit distance for timed automata (pp. 303–312). Presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562141","ista":"Chatterjee K, Ibsen-Jensen R, Majumdar R. 2014. Edit distance for timed automata. HSCC: Hybrid Systems - Computation and Control, 303–312.","ama":"Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit distance for timed automata. In: Springer; 2014:303-312. doi:10.1145/2562059.2562141"},"quality_controlled":"1","page":"303 - 312","conference":{"end_date":"2017-04-17","start_date":"2017-04-15","location":"Berlin, Germany","name":"HSCC: Hybrid Systems - Computation and Control"},"doi":"10.1145/2562059.2562141","date_published":"2014-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"01","_id":"2216","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","title":"Edit distance for timed automata","status":"public","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"}],"related_material":{"record":[{"id":"5409","status":"public","relation":"earlier_version"}]},"date_created":"2018-12-11T11:56:22Z","date_updated":"2023-02-23T12:25:01Z","oa_version":"Submitted Version","type":"conference","abstract":[{"text":"The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in time stamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than δ away from the parameter, for δ > 0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and analogous decidability results hold for rectangular automata.","lang":"eng"}],"publist_id":"4752"},{"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"28","month":"01","page":"20","citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. Compositional Specifications for IOCO Testing. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-148-v2-1.","mla":"Daca, Przemyslaw, et al. Compositional Specifications for IOCO Testing. IST Austria, 2014, doi:10.15479/AT:IST-2014-148-v2-1.","short":"P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, Compositional Specifications for IOCO Testing, IST Austria, 2014.","ista":"Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing, IST Austria, 20p.","apa":"Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional specifications for IOCO testing. IST Austria. https://doi.org/10.15479/AT:IST-2014-148-v2-1","ieee":"P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, Compositional specifications for IOCO testing. IST Austria, 2014.","ama":"Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional Specifications for IOCO Testing. IST Austria; 2014. doi:10.15479/AT:IST-2014-148-v2-1"},"oa":1,"language":[{"iso":"eng"}],"date_published":"2014-01-28T00:00:00Z","doi":"10.15479/AT:IST-2014-148-v2-1","alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"text":"Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing.\r\nIn this paper, we study compositional properties of the IOCO-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the IOCO conformance relation, the resulting methodology can be applied to a broader class of systems.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:46Z","department":[{"_id":"ToHe"}],"publisher":"IST Austria","ddc":["000"],"publication_status":"published","title":"Compositional specifications for IOCO testing","status":"public","_id":"5411","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","file_size":534732,"content_type":"application/pdf","file_name":"IST-2014-148-v2+1_main_tr.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:46Z","date_created":"2018-12-12T11:54:21Z","checksum":"0e03aba625cc334141a3148432aa5760","file_id":"5543","relation":"main_file"}],"date_updated":"2023-02-23T10:31:07Z","date_created":"2018-12-12T11:39:11Z","related_material":{"record":[{"id":"2167","status":"public","relation":"later_version"}]},"pubrep_id":"152","author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Willibald","last_name":"Krenn","full_name":"Krenn, Willibald"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}]},{"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:47Z","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.\r\nWe introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.\r\nWe present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. 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CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v2-2.","short":"K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic Systems, IST Austria, 2014.","chicago":"Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v2-2.","ama":"Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v2-2","ista":"Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic systems, IST Austria, 33p.","apa":"Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v2-2","ieee":"K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis of probabilistic systems. 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We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.\r\nWe introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.\r\nWe present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. \r\nWe have implemented our algorithms and show that the compositional analysis leads to significant improvements. ","lang":"eng"}],"oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v3-1.","mla":"Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v3-1.","short":"K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic Systems, IST Austria, 2014.","ista":"Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic systems, IST Austria, 33p.","ieee":"K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis of probabilistic systems. IST Austria, 2014.","apa":"Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v3-1","ama":"Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v3-1"},"page":"33","date_published":"2014-02-07T00:00:00Z","doi":"10.15479/AT:IST-2014-153-v3-1","language":[{"iso":"eng"}],"month":"02","day":"07","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]}},{"related_material":{"record":[{"status":"public","relation":"later_version","id":"2063"},{"id":"5413","status":"public","relation":"later_version"},{"relation":"later_version","status":"public","id":"5414"}]},"pubrep_id":"153","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"}],"file":[{"file_name":"IST-2014-153-v1+1_main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":423322,"file_id":"5500","relation":"main_file","date_updated":"2020-07-14T12:46:47Z","date_created":"2018-12-12T11:53:39Z","checksum":"4d6cda4bebed970926403ad6ad8c745f"}],"oa_version":"Published Version","date_updated":"2023-02-23T12:25:18Z","date_created":"2018-12-12T11:39:11Z","_id":"5412","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IST Austria","status":"public","title":"CEGAR for qualitative analysis of probabilistic systems","ddc":["000"],"publication_status":"published","abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.\r\nWe introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.\r\nWe present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:47Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"date_published":"2014-01-29T00:00:00Z","doi":"10.15479/AT:IST-2014-153-v1-1","language":[{"iso":"eng"}],"citation":{"short":"K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic Systems, IST Austria, 2014.","mla":"Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v1-1.","chicago":"Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v1-1.","ama":"Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v1-1","apa":"Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v1-1","ieee":"K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis of probabilistic systems. IST Austria, 2014.","ista":"Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic systems, IST Austria, 31p."},"oa":1,"page":"31","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"01","day":"29"},{"alternative_title":["LNCS"],"type":"conference","issue":"Part 2","abstract":[{"text":"We consider multi-player graph games with partial-observation and parity objective. While the decision problem for three-player games with a coalition of the first and second players against the third player is undecidable in general, we present a decidability result for partial-observation games where the first and third player are in a coalition against the second player, thus where the second player is adversarial but weaker due to partial-observation. We establish tight complexity bounds in the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness for parity objectives. The symmetric case of player 1 more informed than player 2 is much more complicated, and we show that already in the case where player 1 has perfect observation, memory of size non-elementary is necessary in general for reachability objectives, and the problem is decidable for safety and reachability objectives. From our results we derive new complexity results for partial-observation stochastic games.","lang":"eng"}],"intvolume":" 8573","status":"public","title":"Games with a weak adversary","_id":"2163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","day":"01","page":"110 - 121","citation":{"apa":"Chatterjee, K., & Doyen, L. (2014). Games with a weak adversary. In Lecture Notes in Computer Science (Vol. 8573, pp. 110–121). Copenhagen, Denmark: Springer. https://doi.org/10.1007/978-3-662-43951-7_10","ieee":"K. Chatterjee and L. Doyen, “Games with a weak adversary,” in Lecture Notes in Computer Science, Copenhagen, Denmark, 2014, vol. 8573, no. Part 2, pp. 110–121.","ista":"Chatterjee K, Doyen L. 2014. Games with a weak adversary. Lecture Notes in Computer Science. ICALP: Automata, Languages and Programming, LNCS, vol. 8573, 110–121.","ama":"Chatterjee K, Doyen L. Games with a weak adversary. In: Lecture Notes in Computer Science. Vol 8573. Springer; 2014:110-121. doi:10.1007/978-3-662-43951-7_10","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Games with a Weak Adversary.” In Lecture Notes in Computer Science, 8573:110–21. Springer, 2014. https://doi.org/10.1007/978-3-662-43951-7_10.","short":"K. Chatterjee, L. Doyen, in:, Lecture Notes in Computer Science, Springer, 2014, pp. 110–121.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Games with a Weak Adversary.” Lecture Notes in Computer Science, vol. 8573, no. Part 2, Springer, 2014, pp. 110–21, doi:10.1007/978-3-662-43951-7_10."},"publication":"Lecture Notes in Computer Science","date_published":"2014-01-01T00:00:00Z","publist_id":"4821","ec_funded":1,"department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","year":"2014","acknowledgement":"This research was partly supported by European project Cassting (FP7-601148).\r\nTechnical Report under https://research-explorer.app.ist.ac.at/record/5418\r\n","volume":8573,"date_created":"2018-12-11T11:56:04Z","date_updated":"2023-02-23T12:25:29Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5418"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"}],"month":"01","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1404.5453"]},"main_file_link":[{"url":"https://arxiv.org/abs/1404.5453","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-43951-7_10","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Copenhagen, Denmark","start_date":"2014-07-08","end_date":"2014-07-11"}},{"page":"34","oa":1,"citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs, IST Austria, 2014.","mla":"Chatterjee, Krishnendu, et al. Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-187-v1-1.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-187-v1-1.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-187-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Improved algorithms for reachability and shortest path on low tree-width graphs. IST Austria, 2014.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Improved algorithms for reachability and shortest path on low tree-width graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-187-v1-1","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Improved algorithms for reachability and shortest path on low tree-width graphs, IST Austria, 34p."},"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2014-187-v1-1","date_published":"2014-04-14T00:00:00Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"14","month":"04","department":[{"_id":"KrCh"}],"publisher":"IST Austria","status":"public","ddc":["000"],"title":"Improved algorithms for reachability and shortest path on low tree-width graphs","publication_status":"published","_id":"5419","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","content_type":"application/pdf","file_size":670031,"file_name":"IST-2014-187-v1+1_main_full_tech.pdf","access_level":"open_access","date_created":"2018-12-12T11:54:25Z","date_updated":"2020-07-14T12:46:50Z","checksum":"c608e66030a4bf51d2d99b451f539b99","file_id":"5548","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2021-01-12T08:02:03Z","date_created":"2018-12-12T11:39:13Z","pubrep_id":"187","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"text":"We consider the reachability and shortest path problems on low tree-width graphs, with n nodes, m edges, and tree-width t, on a standard RAM with wordsize W. We use O to hide polynomial factors of the inverse of the Ackermann function. Our main contributions are three fold:\r\n1. For reachability, we present an algorithm that requires O(n·t2·log(n/t)) preprocessing time, O(n·(t·log(n/t))/W) space, and O(t/W) time for pair queries and O((n·t)/W) time for single-source queries. Note that for constant t our algorithm uses O(n·logn) time for preprocessing; and O(n/W) time for single-source queries, which is faster than depth first search/breath first search (after the preprocessing).\r\n2. We present an algorithm for shortest path that requires O(n·t2) preprocessing time, O(n·t) space, and O(t2) time for pair queries and O(n·t) time single-source queries.\r\n3. We give a space versus query time trade-off algorithm for shortest path that, given any constant >0, requires O(n·t2) preprocessing time, O(n·t2) space, and O(n1−·t2) time for pair queries.\r\nOur algorithms improve all existing results, and use very simple data structures.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:50Z"},{"month":"04","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1145/2562059.2562130","conference":{"end_date":"2014-04-17","location":"Berlin, Germany","start_date":"2014-04-15","name":"HSCC: Hybrid Systems - Computation and Control"},"language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"4751","year":"2014","acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/171","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"id":"5416","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-02-23T12:25:23Z","date_created":"2018-12-11T11:56:23Z","scopus_import":1,"article_processing_charge":"No","day":"01","citation":{"chicago":"Henzinger, Thomas A, and Jan Otop. “Model Measuring for Hybrid Systems.” In Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, 213–22. Springer, 2014. https://doi.org/10.1145/2562059.2562130.","short":"T.A. Henzinger, J. Otop, in:, Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–222.","mla":"Henzinger, Thomas A., and Jan Otop. “Model Measuring for Hybrid Systems.” Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–22, doi:10.1145/2562059.2562130.","apa":"Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems. In Proceedings of the 17th international conference on Hybrid systems: computation and control (pp. 213–222). Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562130","ieee":"T. A. Henzinger and J. Otop, “Model measuring for hybrid systems,” in Proceedings of the 17th international conference on Hybrid systems: computation and control, Berlin, Germany, 2014, pp. 213–222.","ista":"Henzinger TA, Otop J. 2014. Model measuring for hybrid systems. Proceedings of the 17th international conference on Hybrid systems: computation and control. HSCC: Hybrid Systems - Computation and Control, 213–222.","ama":"Henzinger TA, Otop J. Model measuring for hybrid systems. In: Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control. Springer; 2014:213-222. doi:10.1145/2562059.2562130"},"publication":"Proceedings of the 17th international conference on Hybrid systems: computation and control","page":"213 - 222","date_published":"2014-04-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.\r\n\r\nThe contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2217","status":"public","title":"Model measuring for hybrid systems","oa_version":"None"},{"language":[{"iso":"eng"}],"date_published":"2014-02-19T00:00:00Z","doi":"10.15479/AT:IST-2014-172-v1-1","page":"14","oa":1,"citation":{"ieee":"T. A. Henzinger and J. Otop, From model checking to model measuring. IST Austria, 2014.","apa":"Henzinger, T. A., & Otop, J. (2014). From model checking to model measuring. IST Austria. https://doi.org/10.15479/AT:IST-2014-172-v1-1","ista":"Henzinger TA, Otop J. 2014. From model checking to model measuring, IST Austria, 14p.","ama":"Henzinger TA, Otop J. From Model Checking to Model Measuring. IST Austria; 2014. doi:10.15479/AT:IST-2014-172-v1-1","chicago":"Henzinger, Thomas A, and Jan Otop. From Model Checking to Model Measuring. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-172-v1-1.","short":"T.A. Henzinger, J. Otop, From Model Checking to Model Measuring, IST Austria, 2014.","mla":"Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring. IST Austria, 2014, doi:10.15479/AT:IST-2014-172-v1-1."},"day":"19","month":"02","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","date_updated":"2023-02-23T10:38:10Z","date_created":"2018-12-12T11:39:13Z","file":[{"date_created":"2018-12-12T11:53:20Z","date_updated":"2020-07-14T12:46:49Z","checksum":"fcc3eab903cfcd3778b338d2d0d44d18","file_id":"5481","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":383052,"file_name":"IST-2014-172-v1+1_report.pdf","access_level":"open_access"}],"oa_version":"Published Version","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"2327"}]},"pubrep_id":"175","publication_status":"published","title":"From model checking to model measuring","status":"public","ddc":["000"],"department":[{"_id":"ToHe"}],"publisher":"IST Austria","_id":"5417","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M'within distance ρ from M satisfy (or violate)φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata.\r\nThe model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification.\r\nWe show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved.\r\nWe use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. \r\nWe give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:49Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report"},{"abstract":[{"lang":"eng","text":"As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.The contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem."}],"file_date_updated":"2020-07-14T12:46:49Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","oa_version":"Published Version","file":[{"file_name":"IST-2014-171-v1+1_report.pdf","access_level":"open_access","creator":"system","file_size":712077,"content_type":"application/pdf","file_id":"5492","relation":"main_file","date_updated":"2020-07-14T12:46:49Z","date_created":"2018-12-12T11:53:32Z","checksum":"445456d22371e4e49aad2b9a0c13bf80"}],"date_created":"2018-12-12T11:39:12Z","date_updated":"2023-02-23T10:33:21Z","pubrep_id":"171","related_material":{"record":[{"status":"public","relation":"later_version","id":"2217"}]},"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"}],"department":[{"_id":"ToHe"}],"publisher":"IST Austria","publication_status":"published","title":"Model measuring for hybrid systems","status":"public","ddc":["005"],"_id":"5416","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"02","day":"19","language":[{"iso":"eng"}],"date_published":"2014-02-19T00:00:00Z","doi":"10.15479/AT:IST-2014-171-v1-1","page":"22","oa":1,"citation":{"short":"T.A. Henzinger, J. Otop, Model Measuring for Hybrid Systems, IST Austria, 2014.","mla":"Henzinger, Thomas A., and Jan Otop. Model Measuring for Hybrid Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-171-v1-1.","chicago":"Henzinger, Thomas A, and Jan Otop. Model Measuring for Hybrid Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-171-v1-1.","ama":"Henzinger TA, Otop J. Model Measuring for Hybrid Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-171-v1-1","apa":"Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-171-v1-1","ieee":"T. A. Henzinger and J. Otop, Model measuring for hybrid systems. IST Austria, 2014.","ista":"Henzinger TA, Otop J. 2014. Model measuring for hybrid systems, IST Austria, 22p."}},{"month":"03","day":"22","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","page":"18","citation":{"apa":"Chatterjee, K., & Doyen, L. (2014). Games with a weak adversary. 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IST Austria, 2014, doi:10.15479/AT:IST-2014-176-v1-1."},"oa":1,"language":[{"iso":"eng"}],"date_published":"2014-03-22T00:00:00Z","doi":"10.15479/AT:IST-2014-176-v1-1","alternative_title":["IST Austria Technical Report"],"type":"technical_report","file_date_updated":"2020-07-14T12:46:49Z","abstract":[{"text":"We consider multi-player graph games with partial-observation and parity objective. While the decision problem for three-player games with a coalition of the first and second players against the third player is undecidable, we present a decidability result for partial-observation games where the first and third player are in a coalition against the second player, thus where the second player is adversarial but weaker due to partial-observation. We establish tight complexity bounds in the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness for parity objectives. The symmetric case of player 1 more informed than player 2 is much more complicated, and we show that already in the case where player 1 has perfect observation, memory of size non-elementary is necessary in general for reachability objectives, and the problem is decidable for safety and reachability objectives. Our results have tight connections with partial-observation stochastic games for which we derive new complexity results.","lang":"eng"}],"status":"public","title":"Games with a weak adversary","publication_status":"published","ddc":["000","005"],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"_id":"5418","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","date_updated":"2023-02-23T10:30:58Z","date_created":"2018-12-12T11:39:13Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5468","date_updated":"2020-07-14T12:46:49Z","date_created":"2018-12-12T11:53:07Z","checksum":"1d6958aa60050e1c3e932c6e5f34c39f","file_name":"IST-2014-176-v1+1_icalp_14.pdf","access_level":"open_access","content_type":"application/pdf","file_size":328253,"creator":"system"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"2163"}]},"pubrep_id":"176"},{"abstract":[{"text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:50Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5520","checksum":"49e0fd3e62650346daf7dc04604f7a0a","date_updated":"2020-07-14T12:46:50Z","date_created":"2018-12-12T11:53:58Z","access_level":"open_access","file_name":"IST-2014-191-v1+1_main_full.pdf","file_size":584368,"content_type":"application/pdf","creator":"system"}],"date_updated":"2021-01-12T08:02:05Z","date_created":"2018-12-12T11:39:14Z","pubrep_id":"191","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"}],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"title":"The value 1 problem for concurrent mean-payoff games","status":"public","ddc":["000","005"],"publication_status":"published","year":"2014","_id":"5420","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","month":"04","day":"14","language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2014-191-v1-1","date_published":"2014-04-14T00:00:00Z","page":"49","citation":{"ieee":"K. Chatterjee and R. Ibsen-Jensen, The value 1 problem for concurrent mean-payoff games. IST Austria, 2014.","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2014). The value 1 problem for concurrent mean-payoff games. IST Austria. https://doi.org/10.15479/AT:IST-2014-191-v1-1","ista":"Chatterjee K, Ibsen-Jensen R. 2014. The value 1 problem for concurrent mean-payoff games, IST Austria, 49p.","ama":"Chatterjee K, Ibsen-Jensen R. The Value 1 Problem for Concurrent Mean-Payoff Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-191-v1-1","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem for Concurrent Mean-Payoff Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-191-v1-1.","short":"K. Chatterjee, R. Ibsen-Jensen, The Value 1 Problem for Concurrent Mean-Payoff Games, IST Austria, 2014.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem for Concurrent Mean-Payoff Games. IST Austria, 2014, doi:10.15479/AT:IST-2014-191-v1-1."},"oa":1},{"file_date_updated":"2020-07-14T12:46:50Z","abstract":[{"text":"Notes from the Third Plenary for the Research Data Alliance in Dublin, Ireland on March 26 to 28, 2014 with focus on starting an institutional research data repository.","lang":"eng"}],"type":"report","author":[{"full_name":"Porsche, Jana","first_name":"Jana","last_name":"Porsche","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"254","date_updated":"2020-07-14T23:04:56Z","date_created":"2018-12-12T11:39:14Z","oa_version":"None","file":[{"content_type":"application/pdf","file_size":648585,"creator":"system","file_name":"IST-2014-254-v1+1_Dublin_Day_3.pdf","access_level":"open_access","date_created":"2018-12-12T11:53:40Z","date_updated":"2020-07-14T12:46:50Z","checksum":"3954896648ce8afa8f7c4425e71cff08","relation":"main_file","file_id":"5501"},{"checksum":"9a0d42b0b832dfe7e4b22fb6816bcbba","date_updated":"2020-07-14T12:46:50Z","date_created":"2018-12-12T11:53:41Z","relation":"main_file","file_id":"5502","file_size":221339,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2014-254-v1+2_Dublin_Day_1.pdf"},{"file_id":"5503","relation":"main_file","checksum":"498b8d629fb1bd17bff1dc43700a93e6","date_updated":"2020-07-14T12:46:50Z","date_created":"2018-12-12T11:53:42Z","access_level":"open_access","file_name":"IST-2014-254-v1+3_Dublin_Day_2.pdf","creator":"system","content_type":"application/pdf","file_size":187778}],"year":"2014","_id":"5422","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland","ddc":["020"],"department":[{"_id":"E-Lib"}],"publisher":"none","has_accepted_license":"1","date_published":"2014-01-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"apa":"Porsche, J. (2014). Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none.","ieee":"J. Porsche, Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none, 2014.","ista":"Porsche J. 2014. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland, none,p.","ama":"Porsche J. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none; 2014.","chicago":"Porsche, Jana. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none, 2014.","short":"J. Porsche, Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland, none, 2014.","mla":"Porsche, Jana. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none, 2014."},"oa":1},{"month":"09","day":"09","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:IST-2014-305-v1-1","date_published":"2014-09-09T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria; 2014. doi:10.15479/AT:IST-2014-305-v1-1","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria, 2014.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v1-1","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications, IST Austria, 12p.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria, 2014.","mla":"Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v1-1.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v1-1."},"page":"12","file_date_updated":"2020-07-14T12:46:51Z","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty.","lang":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"full_name":"Kanodia, Ayush","last_name":"Kanodia","first_name":"Ayush"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1732"},{"id":"5426","status":"public","relation":"later_version"}]},"pubrep_id":"305","date_updated":"2023-02-23T12:25:52Z","date_created":"2018-12-12T11:39:15Z","file":[{"relation":"main_file","file_id":"5512","date_created":"2018-12-12T11:53:51Z","date_updated":"2020-07-14T12:46:51Z","checksum":"35009d5fad01198341e6c1a3353481b7","file_name":"IST-2014-305-v1+1_main.pdf","access_level":"open_access","file_size":655774,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5424","year":"2014","publication_status":"published","ddc":["005"],"title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","status":"public","publisher":"IST Austria","department":[{"_id":"KrCh"}]},{"month":"09","day":"29","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"date_published":"2014-09-29T00:00:00Z","doi":"10.15479/AT:IST-2014-305-v2-1","language":[{"iso":"eng"}],"citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v2-1.","mla":"Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v2-1.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria, 2014.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications, IST Austria, 10p.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v2-1","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria, 2014.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria; 2014. doi:10.15479/AT:IST-2014-305-v2-1"},"oa":1,"page":"10","file_date_updated":"2020-07-14T12:46:51Z","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty."}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"full_name":"Kanodia, Ayush","last_name":"Kanodia","first_name":"Ayush"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1732"},{"status":"public","relation":"earlier_version","id":"5424"}]},"pubrep_id":"311","date_created":"2018-12-12T11:39:16Z","date_updated":"2023-02-23T12:25:47Z","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:51Z","date_created":"2018-12-12T11:54:15Z","checksum":"730c0a8e97cf2712a884b2cc423f3919","relation":"main_file","file_id":"5537","file_size":656019,"content_type":"application/pdf","creator":"system","file_name":"IST-2014-305-v2+1_main2.pdf","access_level":"open_access"}],"year":"2014","_id":"5426","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","ddc":["005"],"publication_status":"published","status":"public","department":[{"_id":"KrCh"}],"publisher":"IST Austria"},{"file_date_updated":"2020-07-14T12:46:50Z","abstract":[{"lang":"eng","text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm- deadline real-time tasks based on multi-objective graphs: Given a taskset and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. a clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including D(over), that have been proposed in the past, for various tasksets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are tasksets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application. 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A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks, IST Austria, 14p.","ieee":"K. Chatterjee, A. Kössler, A. Pavlogiannis, and U. Schmid, A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. IST Austria, 2014.","apa":"Chatterjee, K., Kössler, A., Pavlogiannis, A., & Schmid, U. (2014). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. IST Austria. https://doi.org/10.15479/AT:IST-2014-300-v1-1","ama":"Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria; 2014. doi:10.15479/AT:IST-2014-300-v1-1","chicago":"Chatterjee, Krishnendu, Alexander Kössler, Andreas Pavlogiannis, and Ulrich Schmid. A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-300-v1-1.","mla":"Chatterjee, Krishnendu, et al. A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria, 2014, doi:10.15479/AT:IST-2014-300-v1-1.","short":"K. Chatterjee, A. Kössler, A. Pavlogiannis, U. Schmid, A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks, IST Austria, 2014."},"oa":1,"page":"14"},{"title":"Optimal tree-decomposition balancing and reachability on low treewidth graphs","status":"public","publication_status":"published","ddc":["000"],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"year":"2014","_id":"5427","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:16Z","date_updated":"2021-01-12T08:02:09Z","file":[{"creator":"system","file_size":405561,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2014-314-v1+1_long.pdf","checksum":"9d3b90bf4fff74664f182f2d95ef727a","date_updated":"2020-07-14T12:46:52Z","date_created":"2018-12-12T11:53:10Z","file_id":"5471","relation":"main_file"}],"oa_version":"Published Version","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"pubrep_id":"314","alternative_title":["IST Austria Technical Report"],"type":"technical_report","file_date_updated":"2020-07-14T12:46:52Z","abstract":[{"lang":"eng","text":"We consider graphs with n nodes together with their tree-decomposition that has b = O ( n ) bags and width t , on the standard RAM computational model with wordsize W = Θ (log n ) . Our contributions are two-fold: Our first contribution is an algorithm that given a graph and its tree-decomposition as input, computes a binary and balanced tree-decomposition of width at most 4 · t + 3 of the graph in O ( b ) time and space, improving a long-standing (from 1992) bound of O ( n · log n ) time for constant treewidth graphs. Our second contribution is on reachability queries for low treewidth graphs. We build on our tree-balancing algorithm and present a data-structure for graph reachability that requires O ( n · t 2 ) preprocessing time, O ( n · t ) space, and O ( d t/ log n e ) time for pair queries, and O ( n · t · log t/ log n ) time for single-source queries. For constant t our data-structure uses O ( n ) time for preprocessing, O (1) time for pair queries, and O ( n/ log n ) time for single-source queries. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries."}],"page":"24","oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-314-v1-1.","mla":"Chatterjee, Krishnendu, et al. Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-314-v1-1.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs, IST Austria, 2014.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Optimal tree-decomposition balancing and reachability on low treewidth graphs, IST Austria, 24p.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Optimal tree-decomposition balancing and reachability on low treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-314-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Optimal tree-decomposition balancing and reachability on low treewidth graphs. IST Austria, 2014.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-314-v1-1"},"language":[{"iso":"eng"}],"date_published":"2014-11-05T00:00:00Z","doi":"10.15479/AT:IST-2014-314-v1-1","day":"05","month":"11","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1"},{"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","month":"09","day":"09","scopus_import":1,"date_published":"2014-09-09T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Optimal Cost Almost-Sure Reachability in POMDPs. IST Austria, 2014.","mla":"Anonymous, 1, et al. Optimal Cost Almost-Sure Reachability in POMDPs. IST Austria, 2014.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Optimal Cost Almost-Sure Reachability in POMDPs, IST Austria, 2014.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2014. Optimal cost almost-sure reachability in POMDPs, IST Austria, 22p.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2014). Optimal cost almost-sure reachability in POMDPs. IST Austria.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Optimal cost almost-sure reachability in POMDPs. IST Austria, 2014.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Optimal Cost Almost-Sure Reachability in POMDPs. IST Austria; 2014."},"oa":1,"page":"22","abstract":[{"lang":"eng","text":" We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objective we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest."}],"file_date_updated":"2020-07-14T12:46:51Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"id":"1529","relation":"later_version","status":"public"}]},"pubrep_id":"307","author":[{"full_name":"Anonymous, 1","last_name":"Anonymous","first_name":"1"},{"full_name":"Anonymous, 2","first_name":"2","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"full_name":"Anonymous, 4","last_name":"Anonymous","first_name":"4"}],"file":[{"date_created":"2018-12-12T11:53:17Z","date_updated":"2020-07-14T12:46:51Z","checksum":"b9668a70d53c550b3cd64f0c77451c3d","file_id":"5478","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2725429,"file_name":"IST-2014-307-v1+1_main.pdf","access_level":"open_access"},{"date_created":"2019-04-16T14:16:12Z","date_updated":"2020-07-14T12:46:51Z","checksum":"808ada1dddecc48ca041526fcc6a9efd","relation":"main_file","file_id":"6322","file_size":117,"content_type":"text/plain","creator":"dernst","file_name":"IST-2014-307-v1+2_authors.txt","access_level":"closed"}],"oa_version":"Published Version","date_updated":"2023-02-23T10:02:57Z","date_created":"2018-12-12T11:39:15Z","_id":"5425","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","publisher":"IST Austria","status":"public","ddc":["000"],"title":"Optimal cost almost-sure reachability in POMDPs","publication_status":"published"},{"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:48Z","abstract":[{"text":"Recently there has been a significant effort to add quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, several basic system properties such as average response time cannot be expressed with weighted automata. In this work, we introduce nested weighted automata as a new formalism for expressing important quantitative properties such as average response time. We establish an almost complete decidability picture for the basic decision problems for nested weighted automata, and illustrate its applicability in several domains. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5415","year":"2014","ddc":["004"],"status":"public","title":"Nested weighted automata","publication_status":"published","publisher":"IST Austria","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1656"},{"status":"public","relation":"later_version","id":"467"},{"id":"5436","status":"public","relation":"later_version"}]},"pubrep_id":"170","date_created":"2018-12-12T11:39:12Z","date_updated":"2023-02-23T12:26:19Z","file":[{"content_type":"application/pdf","file_size":573457,"creator":"system","file_name":"IST-2014-170-v1+1_main.pdf","access_level":"open_access","date_created":"2018-12-12T11:53:36Z","date_updated":"2020-07-14T12:46:48Z","checksum":"31f90dcf2cf899c3f8c6427cfcc2b3c7","relation":"main_file","file_id":"5497"}],"oa_version":"Published Version","month":"02","day":"19","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted Automata. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-170-v1-1.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2014.","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria, 2014, doi:10.15479/AT:IST-2014-170-v1-1.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2014). Nested weighted automata. IST Austria. https://doi.org/10.15479/AT:IST-2014-170-v1-1","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata. IST Austria, 2014.","ista":"Chatterjee K, Henzinger TA, Otop J. 2014. Nested weighted automata, IST Austria, 27p.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria; 2014. doi:10.15479/AT:IST-2014-170-v1-1"},"page":"27","doi":"10.15479/AT:IST-2014-170-v1-1","date_published":"2014-02-19T00:00:00Z","language":[{"iso":"eng"}]},{"publisher":"IST Austria","department":[{"_id":"KrCh"}],"publication_status":"published","title":"The complexity of evolution on graphs","status":"public","ddc":["000","005"],"year":"2014","_id":"5421","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2014-190-v2+2_main_full.pdf","access_level":"open_access","file_size":443529,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5538","date_created":"2018-12-12T11:54:16Z","date_updated":"2020-07-14T12:46:50Z","checksum":"42f3d8b563286eb0d903832bd9a848d3"},{"checksum":"0c9a2fd822309719634495a35957e34d","date_created":"2019-09-06T07:30:20Z","date_updated":"2020-07-14T12:46:50Z","file_id":"6852","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":440911,"access_level":"open_access","file_name":"IST-2014-190-v1+1_main_full.pdf"}],"date_updated":"2023-02-23T12:26:33Z","date_created":"2018-12-12T11:39:14Z","related_material":{"record":[{"id":"5432","status":"public","relation":"later_version"},{"id":"5440","status":"public","relation":"later_version"}]},"pubrep_id":"190","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","file_date_updated":"2020-07-14T12:46:50Z","abstract":[{"lang":"eng","text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are: (1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure). (2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time."}],"page":"27","oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolution on Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-190-v2-2.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolution on Graphs, IST Austria, 2014.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Evolution on Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-190-v2-2.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolution on graphs. IST Austria, 2014.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2014). The complexity of evolution on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-190-v2-2","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2014. The complexity of evolution on graphs, IST Austria, 27p.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolution on Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-190-v2-2"},"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2014-190-v2-2","date_published":"2014-04-18T00:00:00Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"04","day":"18"},{"month":"01","publication_identifier":{"eisbn":["9783642540134"],"issn":["0302-9743"],"isbn":["9783642540127"],"eissn":["1611-3349"]},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1311.3238"]},"language":[{"iso":"eng"}],"conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","location":"San Diego, CA, United States","start_date":"2014-01-19","end_date":"2014-01-21"},"doi":"10.1007/978-3-642-54013-4_5","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"acknowledgement":" Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","year":"2014","date_updated":"2023-02-23T12:52:24Z","date_created":"2022-03-18T13:03:15Z","volume":8318,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Filiot, Emmanuel","first_name":"Emmanuel","last_name":"Filiot"},{"last_name":"Raskin","first_name":"Jean-François","full_name":"Raskin, Jean-François"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"681"}]},"scopus_import":"1","day":"30","article_processing_charge":"No","page":"78-97","publication":"VMCAI 2014: Verification, Model Checking, and Abstract Interpretation","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François Raskin. “Doomsday Equilibria for Omega-Regular Games.” In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, 8318:78–97. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_5.","short":"K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 78–97, doi:10.1007/978-3-642-54013-4_5.","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria for omega-regular games,” in VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 78–97.","apa":"Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J.-F. (2014). Doomsday equilibria for omega-regular games. In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 78–97). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_5","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 78–97.","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular games. In: VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:78-97. doi:10.1007/978-3-642-54013-4_5"},"date_published":"2014-01-30T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.\r\nIn this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.\r\nWe present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games.","lang":"eng"}],"title":"Doomsday equilibria for omega-regular games","status":"public","intvolume":" 8318","_id":"10885","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"status":"public","publication_status":"published","title":"A Short Course in Computational Geometry and Topology","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6853","year":"2014","date_created":"2019-09-06T09:22:33Z","date_updated":"2022-03-04T07:47:54Z","oa_version":"None","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"edition":"1","related_material":{"link":[{"description":"available as eBook via catalog IST BookList","relation":"other","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106"},{"relation":"other","description":"available via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842"}]},"alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"place":"Cham","type":"book","abstract":[{"lang":"eng","text":"This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields."}],"quality_controlled":"1","page":"IX, 110","citation":{"ama":"Edelsbrunner H. A Short Course in Computational Geometry and Topology. 1st ed. Cham: Springer Nature; 2014. doi:10.1007/978-3-319-05957-0","ieee":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed. Cham: Springer Nature, 2014.","apa":"Edelsbrunner, H. (2014). A Short Course in Computational Geometry and Topology (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-05957-0","ista":"Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p.","short":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014.","mla":"Edelsbrunner, Herbert. A Short Course in Computational Geometry and Topology. 1st ed., Springer Nature, 2014, doi:10.1007/978-3-319-05957-0.","chicago":"Edelsbrunner, Herbert. A Short Course in Computational Geometry and Topology. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-05957-0."},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-05957-0","date_published":"2014-01-01T00:00:00Z","series_title":"SpringerBriefs in Applied Sciences and Technology","scopus_import":"1","day":"01","month":"01","article_processing_charge":"No","publication_identifier":{"issn":["2191-530X"],"eisbn":["9-783-3190-5957-0"],"isbn":["9-783-3190-5956-3"],"eissn":["2191-5318"]}},{"month":"06","day":"30","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2014-06-30T00:00:00Z","page":"5","oa":1,"citation":{"ista":"Huszár K, Rolinek M. Playful Math - An introduction to mathematical games, IST Austria, 5p.","apa":"Huszár, K., & Rolinek, M. (n.d.). Playful Math - An introduction to mathematical games. IST Austria.","ieee":"K. Huszár and M. Rolinek, Playful Math - An introduction to mathematical games. IST Austria.","ama":"Huszár K, Rolinek M. Playful Math - An Introduction to Mathematical Games. IST Austria","chicago":"Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction to Mathematical Games. IST Austria, n.d.","mla":"Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction to Mathematical Games. IST Austria.","short":"K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games, IST Austria, n.d."},"file_date_updated":"2020-07-14T12:47:48Z","type":"working_paper","date_created":"2019-11-18T15:57:05Z","date_updated":"2020-07-14T23:11:45Z","oa_version":"Published Version","file":[{"file_size":511233,"content_type":"application/pdf","creator":"dernst","file_name":"2014_Playful_Math_Huszar.pdf","access_level":"open_access","date_created":"2019-11-18T15:57:51Z","date_updated":"2020-07-14T12:47:48Z","checksum":"2b94e5e1f4c3fe8ab89b12806276fb09","relation":"main_file","file_id":"7039"}],"author":[{"last_name":"Huszár","first_name":"Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","full_name":"Huszár, Kristóf"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"}],"title":"Playful Math - An introduction to mathematical games","ddc":["510"],"publication_status":"draft","status":"public","publisher":"IST Austria","department":[{"_id":"VlKo"},{"_id":"UlWa"}],"_id":"7038","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file_date_updated":"2020-07-14T12:45:28Z","publist_id":"4954","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"full_name":"Morgan, Andrew","first_name":"Andrew","last_name":"Morgan"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9747"}]},"date_created":"2018-12-11T11:55:36Z","date_updated":"2023-02-23T14:06:51Z","volume":68,"acknowledgement":"The authors are grateful to the Leverhulme Trust (F/00 215/AW) for funding this work.","year":"2014","publication_status":"published","publisher":"Wiley","department":[{"_id":"CaGu"}],"month":"04","doi":"10.1111/evo.12440","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment."}],"issue":"8","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":467254,"access_level":"open_access","file_name":"2014_Evolution_Lagator.pdf","checksum":"8d459b07e4a11bb5fde92d969184fe48","date_created":"2020-05-14T16:40:31Z","date_updated":"2020-07-14T12:45:28Z","file_id":"7845","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2083","ddc":["570"],"title":"Role of sex and migration in adaptation to sink environments","status":"public","intvolume":" 68","day":"25","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_published":"2014-04-25T00:00:00Z","publication":"Evolution","citation":{"short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305.","mla":"Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:10.1111/evo.12440.","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12440.","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation to sink environments. Evolution. 2014;68(8):2296-2305. doi:10.1111/evo.12440","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley, pp. 2296–2305, 2014.","apa":"Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Role of sex and migration in adaptation to sink environments. Evolution. Wiley. https://doi.org/10.1111/evo.12440","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305."},"article_type":"original","page":"2296 - 2305"},{"date_updated":"2023-02-23T10:27:31Z","date_created":"2021-07-28T15:32:55Z","oa_version":"Published Version","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"last_name":"Morgan","first_name":"Andrew","full_name":"Morgan, Andrew"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2083"}]},"title":"Data from: Role of sex and migration in adaptation to sink environments","status":"public","publisher":"Dryad","department":[{"_id":"CaGu"}],"_id":"9747","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014","abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"type":"research_data_reference","date_published":"2014-04-17T00:00:00Z","doi":"10.5061/dryad.s42n1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"citation":{"ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","apa":"Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.","mla":"Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014)."},"oa":1,"day":"17","month":"04","article_processing_charge":"No"},{"pubrep_id":"437","oa_version":"Published Version","file":[{"file_name":"IST-2016-437-v1+1_journal.pone.0103989.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1013386,"file_id":"5042","relation":"main_file","date_updated":"2020-07-14T12:45:28Z","date_created":"2018-12-12T10:13:55Z","checksum":"2fc62c6739eada4bddf026afbae669db"}],"_id":"2086","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees","status":"public","ddc":["570"],"intvolume":" 9","abstract":[{"text":"Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed.","lang":"eng"}],"issue":"8","type":"journal_article","date_published":"2014-08-06T00:00:00Z","publication":"PLoS One","citation":{"short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, PLoS One 9 (2014).","mla":"Wolf, Stephan, et al. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One, vol. 9, no. 8, e103989, Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.","ama":"Wolf S, Mcmahon D, Lim K, et al. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 2014;9(8). doi:10.1371/journal.pone.0103989","ieee":"S. Wolf et al., “So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees,” PLoS One, vol. 9, no. 8. Public Library of Science, 2014.","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989","ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 9(8), e103989."},"day":"06","has_accepted_license":"1","scopus_import":1,"author":[{"first_name":"Stephan","last_name":"Wolf","full_name":"Wolf, Stephan"},{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"full_name":"Lim, Ka","last_name":"Lim","first_name":"Ka"},{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull"},{"first_name":"Suzanne","last_name":"Clark","full_name":"Clark, Suzanne"},{"first_name":"Robert","last_name":"Paxton","full_name":"Paxton, Robert"},{"full_name":"Osborne, Juliet","first_name":"Juliet","last_name":"Osborne"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9888"}]},"date_updated":"2023-02-23T14:11:56Z","date_created":"2018-12-11T11:55:37Z","volume":9,"year":"2014","acknowledgement":"This study was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative (grant numbers BB/I00097/1 and BB/I000100/1). Rothamsted Research is a national institute of bioscience strategically funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC).","publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:28Z","publist_id":"4949","article_number":"e103989","doi":"10.1371/journal.pone.0103989","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"08"},{"doi":"10.1371/journal.pone.0103989.s003","citation":{"ama":"Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:10.1371/journal.pone.0103989.s003","ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting information, Public Library of Science, 10.1371/journal.pone.0103989.s003.","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989.s003","ieee":"S. Wolf et al., “Supporting information.” Public Library of Science, 2014.","mla":"Wolf, Stephan, et al. Supporting Information. Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.s003.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014).","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.s003."},"day":"06","month":"08","article_processing_charge":"No","date_created":"2021-08-11T14:17:53Z","date_updated":"2023-02-23T10:27:38Z","oa_version":"Published Version","author":[{"full_name":"Wolf, Stephan","last_name":"Wolf","first_name":"Stephan"},{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"full_name":"Lim, Ka","first_name":"Ka","last_name":"Lim"},{"full_name":"Pull, Christopher","last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Clark, Suzanne","last_name":"Clark","first_name":"Suzanne"},{"first_name":"Robert","last_name":"Paxton","full_name":"Paxton, Robert"},{"last_name":"Osborne","first_name":"Juliet","full_name":"Osborne, Juliet"}],"related_material":{"record":[{"id":"2086","status":"public","relation":"used_in_publication"}]},"status":"public","title":"Supporting information","publisher":"Public Library of Science","department":[{"_id":"SyCr"}],"year":"2014","_id":"9888","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results."}],"type":"research_data_reference"},{"date_published":"2014-11-14T00:00:00Z","publication":"PLoS One","citation":{"chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács, PLoS One 9 (2014).","mla":"Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One, vol. 9, no. 11, e111430, Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., & Kovács, K. (2014). Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430","ieee":"A. Lovrics et al., “Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 9(11), e111430.","ama":"Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0111430"},"day":"14","has_accepted_license":"1","scopus_import":1,"pubrep_id":"435","oa_version":"Published Version","file":[{"checksum":"a2289b843f7463eb1233f9ce45e6a943","date_updated":"2020-07-14T12:45:24Z","date_created":"2018-12-12T10:10:58Z","relation":"main_file","file_id":"4850","file_size":829363,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-435-v1+1_journal.pone.0111430.pdf"}],"_id":"2004","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord","status":"public","ddc":["570"],"intvolume":" 9","abstract":[{"text":"We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks.","lang":"eng"}],"issue":"11","type":"journal_article","doi":"10.1371/journal.pone.0111430","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"month":"11","author":[{"full_name":"Lovrics, Anna","first_name":"Anna","last_name":"Lovrics"},{"last_name":"Gao","first_name":"Yu","full_name":"Gao, Yu"},{"last_name":"Juhász","first_name":"Bianka","full_name":"Juhász, Bianka"},{"last_name":"Bock","first_name":"István","full_name":"Bock, István"},{"last_name":"Byrne","first_name":"Helen","full_name":"Byrne, Helen"},{"full_name":"Dinnyés, András","first_name":"András","last_name":"Dinnyés"},{"full_name":"Kovács, Krisztián","first_name":"Krisztián","last_name":"Kovács","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9722"}]},"date_updated":"2023-02-23T14:06:14Z","date_created":"2018-12-11T11:55:09Z","volume":9,"year":"2014","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:24Z","ec_funded":1,"publist_id":"5072","article_number":"e111430"},{"doi":"10.1371/journal.pone.0111430.s006","date_published":"2014-11-14T00:00:00Z","citation":{"ieee":"A. Lovrics et al., “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., & Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, 10.1371/journal.pone.0111430.s006.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","mla":"Lovrics, Anna, et al. Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006."},"article_processing_charge":"No","day":"14","month":"11","oa_version":"Published Version","date_created":"2021-07-26T14:35:00Z","date_updated":"2023-02-23T10:24:07Z","related_material":{"record":[{"id":"2004","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Anna","last_name":"Lovrics","full_name":"Lovrics, Anna"},{"last_name":"Gao","first_name":"Yu","full_name":"Gao, Yu"},{"last_name":"Juhász","first_name":"Bianka","full_name":"Juhász, Bianka"},{"last_name":"Bock","first_name":"István","full_name":"Bock, István"},{"full_name":"Byrne, Helen M.","first_name":"Helen M.","last_name":"Byrne"},{"full_name":"Dinnyés, András","first_name":"András","last_name":"Dinnyés"},{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián","last_name":"Kovács","full_name":"Kovács, Krisztián"}],"publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"status":"public","title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","_id":"9722","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014","type":"research_data_reference"},{"file_date_updated":"2020-07-14T12:45:26Z","publist_id":"5012","ec_funded":1,"article_number":"7p","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"related_material":{"record":[{"id":"9739","relation":"research_data","status":"public"}]},"date_updated":"2023-02-23T14:06:36Z","date_created":"2018-12-11T11:55:22Z","volume":10,"year":"2014","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"month":"09","doi":"10.1371/journal.pcbi.1003818","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time.","lang":"eng"}],"issue":"9","type":"journal_article","pubrep_id":"440","oa_version":"Published Version","file":[{"file_name":"IST-2016-440-v1+1_journal.pcbi.1003818.pdf","access_level":"open_access","file_size":1399093,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4890","date_created":"2018-12-12T10:11:35Z","date_updated":"2020-07-14T12:45:26Z","checksum":"712d4c5787ddf97809cfc962507f0738"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2039","ddc":["510"],"status":"public","title":"The time scale of evolutionary innovation","intvolume":" 10","day":"11","has_accepted_license":"1","scopus_import":1,"date_published":"2014-09-11T00:00:00Z","publication":"PLoS Computational Biology","citation":{"ista":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p.","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public Library of Science, 2014.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time scale of evolutionary innovation. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.","mla":"Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014)."}},{"day":"23","article_processing_charge":"No","scopus_import":"1","date_published":"2014-07-23T00:00:00Z","article_type":"original","page":"1701 - 1710","publication":"Behavioral Ecology and Sociobiology","citation":{"ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. 2014;68(10):1701-1710. doi:10.1007/s00265-014-1778-8","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Increased grooming after repeated brood care provides sanitary benefits in a clonal ant,” Behavioral Ecology and Sociobiology, vol. 68, no. 10. Springer, pp. 1701–1710, 2014.","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2014). Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. Springer. https://doi.org/10.1007/s00265-014-1778-8","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2014. Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. 68(10), 1701–1710.","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, Behavioral Ecology and Sociobiology 68 (2014) 1701–1710.","mla":"Westhus, Claudia, et al. “Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology, vol. 68, no. 10, Springer, 2014, pp. 1701–10, doi:10.1007/s00265-014-1778-8.","chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology. Springer, 2014. https://doi.org/10.1007/s00265-014-1778-8."},"abstract":[{"text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"None","status":"public","title":"Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","intvolume":" 68","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2161","month":"07","publication_identifier":{"issn":["0340-5443"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00265-014-1778-8","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"ec_funded":1,"publist_id":"4823","date_created":"2018-12-11T11:56:03Z","date_updated":"2023-02-23T14:06:46Z","volume":68,"author":[{"first_name":"Claudia","last_name":"Westhus","id":"ca9c6ca9-e8aa-11ec-a586-b9471ede0494","full_name":"Westhus, Claudia"},{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V"},{"full_name":"Tourdot, Edouard","last_name":"Tourdot","first_name":"Edouard"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"full_name":"Doums, Claudie","first_name":"Claudie","last_name":"Doums"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9742"}]},"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Springer","acknowledgement":"We thank Katrin Kellner for colony establishment and characterization, Mike Bidochka for the fungal strain, Meghan Vyleta for fungal strain characterization, Martina Klatt and Simon Tragust for help in the laboratory, Dimitri Missoh for developing the software BioLogic, and Mark Brown and Raphaël Jeanson for discussion and help with data analysis. The study was funded by the European Research Council (ERC Starting Grant to SC; Marie Curie IEF to LVU) and the German Research Foundation DFG (to SC and to JH), and CW received funding by the doctoral school Diversité du Vivant (Cotutelle project to CD and SC).\r\n","year":"2014"},{"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2014.1679","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/","open_access":"1"}],"month":"09","volume":281,"date_created":"2018-12-11T11:55:21Z","date_updated":"2023-02-23T14:06:44Z","related_material":{"record":[{"id":"9741","status":"public","relation":"research_data"}]},"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"},{"full_name":"Neve, Paul","first_name":"Paul","last_name":"Neve"}],"department":[{"_id":"CaGu"}],"publisher":"Royal Society, The","publication_status":"published","acknowledgement":"The project was supported by Leverhulme Trust.","year":"2014","publist_id":"5019","article_number":"20141679","date_published":"2014-09-17T00:00:00Z","citation":{"chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2014. https://doi.org/10.1098/rspb.2014.1679.","short":"M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","mla":"Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20141679, Royal Society, The, 2014, doi:10.1098/rspb.2014.1679.","apa":"Lagator, M., Colegrave, N., & Neve, P. (2014). Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2014.1679","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. Royal Society, The, 2014.","ista":"Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.","ama":"Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.1679"},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"17","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 281","title":"Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","status":"public","_id":"2036","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"1794","abstract":[{"text":" In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. ","lang":"eng"}],"type":"journal_article"},{"citation":{"short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).","mla":"Konrad, Matthias, et al. Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host. Dryad, 2014, doi:10.5061/dryad.vm0vc.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. https://doi.org/10.5061/dryad.vm0vc.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:10.5061/dryad.vm0vc","apa":"Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. https://doi.org/10.5061/dryad.vm0vc","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, 10.5061/dryad.vm0vc."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"doi":"10.5061/dryad.vm0vc","date_published":"2014-11-13T00:00:00Z","article_processing_charge":"No","month":"11","day":"13","_id":"9740","year":"2014","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"SyCr"}],"title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","status":"public","related_material":{"record":[{"id":"1993","relation":"used_in_publication","status":"public"}]},"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad","full_name":"Konrad, Matthias"},{"full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","first_name":"Simon","full_name":"Tragust, Simon"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"oa_version":"Published Version","date_updated":"2023-02-23T10:23:32Z","date_created":"2021-07-28T08:38:40Z","type":"research_data_reference","abstract":[{"text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.","lang":"eng"}]},{"doi":"10.5061/dryad.85dn7","date_published":"2014-08-21T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.85dn7"}],"citation":{"short":"M. Lagator, N. Colegrave, P. Neve, (2014).","mla":"Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014, doi:10.5061/dryad.85dn7.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:10.5061/dryad.85dn7","apa":"Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. https://doi.org/10.5061/dryad.85dn7","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, 10.5061/dryad.85dn7."},"oa":1,"article_processing_charge":"No","month":"08","day":"21","oa_version":"Published Version","date_created":"2021-07-28T08:48:06Z","date_updated":"2023-02-23T10:25:31Z","related_material":{"record":[{"id":"2036","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}],"publisher":"Dryad","department":[{"_id":"CaGu"}],"status":"public","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","_id":"9741","year":"2014","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.","lang":"eng"}],"type":"research_data_reference"},{"citation":{"ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818.s001","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.","mla":"Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014)."},"date_published":"2014-09-11T00:00:00Z","doi":"10.1371/journal.pcbi.1003818.s001","article_processing_charge":"No","day":"11","month":"09","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","status":"public","title":"Detailed proofs for “The time scale of evolutionary innovation”","year":"2014","_id":"9739","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-02-23T10:25:37Z","date_created":"2021-07-28T08:13:57Z","related_material":{"record":[{"id":"2039","status":"public","relation":"used_in_publication"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"full_name":"Novak, Martin","last_name":"Novak","first_name":"Martin"}],"type":"research_data_reference"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2014-01-01T00:00:00Z","page":"198 - 211","citation":{"ama":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578","ista":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 23(1), 198–211.","ieee":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse, “Likelihood-based inference of population history from low-coverage de novo genome assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211, 2014.","apa":"Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse, K. (2014). Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578","mla":"Hearn, Jack, et al. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no. 1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.","short":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular Ecology 23 (2014) 198–211.","chicago":"Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mec.12578."},"publication":"Molecular Ecology","issue":"1","abstract":[{"text":" Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":807444,"creator":"system","file_name":"IST-2016-559-v1+1_Hearn_et_al.pdf","access_level":"open_access","date_created":"2018-12-12T10:07:52Z","date_updated":"2020-07-14T12:45:31Z","checksum":"4de1ab255976a8ae77eb0e55ad62ecc9","relation":"main_file","file_id":"4651"},{"file_id":"4652","relation":"main_file","checksum":"01a8073e071c088500425f910b0f1f71","date_created":"2018-12-12T10:07:53Z","date_updated":"2020-07-14T12:45:31Z","access_level":"open_access","file_name":"IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf","creator":"system","file_size":1518088,"content_type":"application/pdf"}],"oa_version":"Submitted Version","pubrep_id":"559","intvolume":" 23","title":"Likelihood-based inference of population history from low-coverage de novo genome assemblies","status":"public","ddc":["570"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2170","month":"01","language":[{"iso":"eng"}],"doi":"10.1111/mec.12578","quality_controlled":"1","oa":1,"publist_id":"4814","file_date_updated":"2020-07-14T12:45:31Z","volume":23,"date_created":"2018-12-11T11:56:07Z","date_updated":"2023-02-23T14:07:09Z","related_material":{"record":[{"id":"9754","relation":"research_data","status":"public"}]},"author":[{"full_name":"Hearn, Jack","last_name":"Hearn","first_name":"Jack"},{"last_name":"Stone","first_name":"Graham","full_name":"Stone, Graham"},{"first_name":"Lynsey","last_name":"Bunnefeld","full_name":"Bunnefeld, Lynsey"},{"last_name":"Nicholls","first_name":"James","full_name":"Nicholls, James"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"}],"publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2014","acknowledgement":"This work was funded by NERC grants to G Stone, J Nicholls, K Lohse and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856)."},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.nc0gc"}],"citation":{"ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, 10.5061/dryad.nc0gc.","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. https://doi.org/10.5061/dryad.nc0gc","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:10.5061/dryad.nc0gc","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. https://doi.org/10.5061/dryad.nc0gc.","mla":"Tragust, Simon, et al. Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies. Dryad, 2014, doi:10.5061/dryad.nc0gc.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014)."},"oa":1,"date_published":"2014-10-08T00:00:00Z","doi":"10.5061/dryad.nc0gc","month":"10","day":"08","article_processing_charge":"No","title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","status":"public","publisher":"Dryad","department":[{"_id":"SyCr"}],"year":"2014","_id":"9753","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:36:17Z","date_created":"2021-07-30T08:24:11Z","oa_version":"Published Version","author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"first_name":"Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"full_name":"Chapuisat, Michel","last_name":"Chapuisat","first_name":"Michel"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2284"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies."}]},{"title":"Data from: Transformation of stimulus correlations by the retina","status":"public","publisher":"Dryad","department":[{"_id":"GaTk"}],"year":"2014","_id":"9752","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:35:57Z","date_created":"2021-07-30T08:13:52Z","oa_version":"Published Version","author":[{"last_name":"Simmons","first_name":"Kristina","full_name":"Simmons, Kristina"},{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Homann, Jan","last_name":"Homann","first_name":"Jan"},{"full_name":"Yee, Heather","last_name":"Yee","first_name":"Heather"},{"full_name":"Palmer, Stephanie","last_name":"Palmer","first_name":"Stephanie"},{"full_name":"Nelson, Philip","first_name":"Philip","last_name":"Nelson"},{"full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian","first_name":"Vijay"}],"related_material":{"record":[{"id":"2277","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"citation":{"ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:10.5061/dryad.246qg","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. https://doi.org/10.5061/dryad.246qg","ieee":"K. Simmons et al., “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, 10.5061/dryad.246qg.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","mla":"Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/10.5061/dryad.246qg."},"doi":"10.5061/dryad.246qg","date_published":"2014-11-07T00:00:00Z","day":"07","month":"11","article_processing_charge":"No"},{"oa_version":"None","intvolume":" 68","title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9931","issue":"6","abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"type":"journal_article","date_published":"2014-06-03T00:00:00Z","page":"1775-1791","article_type":"original","citation":{"short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.","mla":"Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Evolution, vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:10.1111/evo.12373.","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12373.","ama":"Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 2014;68(6):1775-1791. doi:10.1111/evo.12373","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,” Evolution, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014.","apa":"Dhar, R., Bergmiller, T., & Wagner, A. (2014). Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. Wiley. https://doi.org/10.1111/evo.12373","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 68(6), 1775–1791."},"publication":"Evolution","article_processing_charge":"No","day":"03","scopus_import":"1","volume":68,"date_created":"2021-08-17T09:03:09Z","date_updated":"2023-02-23T14:13:27Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9932"}]},"author":[{"last_name":"Dhar","first_name":"Riddhiman","full_name":"Dhar, Riddhiman"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Wagner, Andreas","last_name":"Wagner","first_name":"Andreas"}],"publisher":"Wiley","department":[{"_id":"CaGu"}],"publication_status":"published","pmid":1,"year":"2014","acknowledgement":"We thank the Functional Genomics Center Zurich for its service in generating sequencing data, M. Ackermann and E. Hayden for helpful discussions, A. de Visser for comments on earlier versions of this manuscript, and M. Moser for help with quantitative PCR. This work was supported by Swiss National Science Foundation (grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in Systems Biology at the University of Zurich. RD acknowledges support from the Forschungskredit program of the University of Zurich. The authors declare no conflict of interest.","language":[{"iso":"eng"}],"doi":"10.1111/evo.12373","quality_controlled":"1","external_id":{"pmid":["24495000"]},"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"06"},{"abstract":[{"text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.","lang":"eng"}],"type":"research_data_reference","date_created":"2021-08-17T09:11:40Z","date_updated":"2023-02-23T14:13:24Z","oa_version":"Published Version","author":[{"full_name":"Dhar, Riddhiman","first_name":"Riddhiman","last_name":"Dhar"},{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Wagner","first_name":"Andreas","full_name":"Wagner, Andreas"}],"related_material":{"record":[{"id":"9931","status":"public","relation":"used_in_publication"}]},"status":"public","title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","department":[{"_id":"CaGu"}],"publisher":"Dryad","_id":"9932","year":"2014","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","month":"01","article_processing_charge":"No","date_published":"2014-01-27T00:00:00Z","doi":"10.5061/dryad.jc402","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.jc402","open_access":"1"}],"citation":{"chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Dryad, 2014. https://doi.org/10.5061/dryad.jc402.","short":"R. Dhar, T. Bergmiller, A. Wagner, (2014).","mla":"Dhar, Riddhiman, et al. Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes. Dryad, 2014, doi:10.5061/dryad.jc402.","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.” Dryad, 2014.","apa":"Dhar, R., Bergmiller, T., & Wagner, A. (2014). Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Dryad. https://doi.org/10.5061/dryad.jc402","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes, Dryad, 10.5061/dryad.jc402.","ama":"Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. 2014. doi:10.5061/dryad.jc402"}},{"date_created":"2018-12-11T11:47:01Z","date_updated":"2023-09-05T14:09:29Z","volume":70,"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10905"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2014","ec_funded":1,"publist_id":"7282","language":[{"iso":"eng"}],"doi":"10.1007/s00453-013-9843-7","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08234"}],"oa":1,"external_id":{"arxiv":["1604.08234"]},"month":"11","oa_version":"Preprint","status":"public","title":"Polynomial-time algorithms for energy games with special weight structures","intvolume":" 70","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"535","abstract":[{"text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2014-11-01T00:00:00Z","article_type":"original","page":"457 - 492","publication":"Algorithmica","citation":{"ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 2014;70(3):457-492. doi:10.1007/s00453-013-9843-7","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” Algorithmica, vol. 70, no. 3. Springer, pp. 457–492, 2014.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. Algorithmica. Springer. https://doi.org/10.1007/s00453-013-9843-7","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:10.1007/s00453-013-9843-7.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set."}],"type":"conference","alternative_title":["Mathematics and Visualization"],"author":[{"first_name":"Valentin","last_name":"Zobel","full_name":"Zobel, Valentin"},{"first_name":"Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"}],"oa_version":"None","date_created":"2022-03-18T13:05:39Z","date_updated":"2023-09-05T14:13:16Z","year":"2014","_id":"10886","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.","publisher":"Springer","department":[{"_id":"HeEd"}],"title":"Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature","publication_status":"published","status":"public","article_processing_charge":"No","publication_identifier":{"eissn":["2197-666X"],"isbn":["9783319040981"],"issn":["1612-3786"],"eisbn":["9783319040998"]},"day":"19","month":"03","scopus_import":"1","doi":"10.1007/978-3-319-04099-8_16","date_published":"2014-03-19T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In: Topological Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature,” in Topological Methods in Data Analysis and Visualization III , 2014, pp. 249–262.","apa":"Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In Topological Methods in Data Analysis and Visualization III (pp. 249–262). Springer. https://doi.org/10.1007/978-3-319-04099-8_16","ista":"Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. Topological Methods in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262.","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–262.","mla":"Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In Topological Methods in Data Analysis and Visualization III , 249–62. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_16."},"publication":"Topological Methods in Data Analysis and Visualization III ","page":"249-262","quality_controlled":"1"},{"page":"219-235","publication":"Tissue Morphogenesis","citation":{"short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis, edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York, NY: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.","ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. Methods in Molecular Biology. New York, NY: Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15","ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson, Ed. New York, NY: Springer, 2014, pp. 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis (Vol. 1189, pp. 219–235). New York, NY: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235."},"date_published":"2014-08-22T00:00:00Z","series_title":"Methods in Molecular Biology","day":"22","article_processing_charge":"No","status":"public","title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","intvolume":" 1189","_id":"6178","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","type":"book_chapter","abstract":[{"lang":"eng","text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo."}],"quality_controlled":"1","external_id":{"pmid":["25245697"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-1164-6_15","month":"08","publication_identifier":{"issn":["1064-3745"],"isbn":["9781493911639","9781493911646"],"eissn":["1940-6029"]},"publication_status":"published","department":[{"_id":"CaHe"}],"editor":[{"last_name":"Nelson","first_name":"Celeste","full_name":"Nelson, Celeste"}],"publisher":"Springer","year":"2014","pmid":1,"date_created":"2019-03-26T08:55:59Z","date_updated":"2023-09-05T14:12:00Z","volume":1189,"author":[{"full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","first_name":"Michael"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin","full_name":"Behrndt, Martin"},{"full_name":"Campinho, Pedro","first_name":"Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416"},{"orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"place":"New York, NY"},{"citation":{"ama":"Seiringer R. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 2014;116:21-41. doi:10.1365/s13291-014-0083-9","ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","ieee":"R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,” Jahresbericht der Deutschen Mathematiker-Vereinigung, vol. 116. Springer Nature, pp. 21–41, 2014.","apa":"Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions. Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature. https://doi.org/10.1365/s13291-014-0083-9","mla":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” Jahresbericht Der Deutschen Mathematiker-Vereinigung, vol. 116, Springer Nature, 2014, pp. 21–41, doi:10.1365/s13291-014-0083-9.","short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41.","chicago":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature, 2014. https://doi.org/10.1365/s13291-014-0083-9."},"publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","page":"21-41","article_type":"original","quality_controlled":"1","doi":"10.1365/s13291-014-0083-9","date_published":"2014-03-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","keyword":["General Medicine"],"publication_identifier":{"issn":["0012-0456"],"eissn":["1869-7135"]},"article_processing_charge":"No","day":"01","month":"03","_id":"10814","year":"2014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","intvolume":" 116","department":[{"_id":"RoSe"}],"status":"public","publication_status":"published","title":"The excitation spectrum for Bose fluids with weak interactions","author":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"volume":116,"oa_version":"None","date_updated":"2023-09-05T14:19:47Z","date_created":"2022-03-04T07:54:39Z","type":"journal_article","abstract":[{"text":"We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field.","lang":"eng"}]},{"date_updated":"2023-09-05T15:33:45Z","date_created":"2022-03-04T08:33:57Z","author":[{"first_name":"David","last_name":"Günther","full_name":"Günther, David"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","first_name":"Jan","full_name":"Reininghaus, Jan"},{"full_name":"Seidel, Hans-Peter","last_name":"Seidel","first_name":"Hans-Peter"},{"full_name":"Weinkauf, Tino","last_name":"Weinkauf","first_name":"Tino"}],"publication_status":"published","editor":[{"full_name":"Bremer, Peer-Timo","first_name":"Peer-Timo","last_name":"Bremer"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"full_name":"Pascucci, Valerio","first_name":"Valerio","last_name":"Pascucci"},{"full_name":"Peikert, Ronald","last_name":"Peikert","first_name":"Ronald"}],"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","acknowledgement":"This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.","year":"2014","ec_funded":1,"place":"Cham","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-04099-8_9","quality_controlled":"1","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7"}],"month":"03","publication_identifier":{"eissn":["2197-666X"],"isbn":["9783319040981"],"eisbn":["9783319040998"],"issn":["1612-3786"]},"oa_version":"None","title":"Notes on the simplification of the Morse-Smale complex","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10817","abstract":[{"lang":"eng","text":"The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption."}],"type":"book_chapter","date_published":"2014-03-19T00:00:00Z","page":"135-150","publication":"Topological Methods in Data Analysis and Visualization III.","citation":{"chicago":"Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf. “Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9.","mla":"Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.” Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.","short":"D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.","ista":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization III. , 135–150.","ieee":"D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the simplification of the Morse-Smale complex,” in Topological Methods in Data Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.","apa":"Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9","ama":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9"},"day":"19","article_processing_charge":"No","series_title":"Mathematics and Visualization","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants."}],"publist_id":"5814","alternative_title":["ISTA Thesis"],"type":"dissertation","date_updated":"2023-09-07T11:38:56Z","date_created":"2018-12-11T11:51:46Z","oa_version":"None","author":[{"last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias"}],"title":"Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus","publication_status":"published","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SyCr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1395","year":"2014","month":"02","day":"01","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Cremer, Sylvia M","last_name":"Cremer","first_name":"Sylvia M","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"date_published":"2014-02-01T00:00:00Z","page":"131","citation":{"short":"M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology Austria, 2014.","mla":"Konrad, Matthias. Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus. Institute of Science and Technology Austria, 2014.","chicago":"Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and Technology Austria, 2014.","ama":"Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 2014.","apa":"Konrad, M. (2014). Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","ieee":"M. Konrad, “Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology Austria, 2014.","ista":"Konrad M. 2014. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria."}},{"alternative_title":["ISTA Thesis"],"type":"dissertation","publist_id":"5805","abstract":[{"lang":"eng","text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants."}],"department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","publication_status":"published","status":"public","_id":"1402","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2014","oa_version":"None","date_created":"2018-12-11T11:51:49Z","date_updated":"2023-09-07T11:39:38Z","author":[{"full_name":"Marhavá, Petra","last_name":"Marhavá","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"01","month":"12","page":"90","citation":{"ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","apa":"Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.","mla":"Marhavá, Petra. Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2014.","chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014."},"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2014-12-01T00:00:00Z"},{"ec_funded":1,"publist_id":"4691","file_date_updated":"2020-07-14T12:45:35Z","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2014","volume":50,"date_created":"2018-12-11T11:56:36Z","date_updated":"2023-09-07T11:41:25Z","related_material":{"record":[{"id":"2843","relation":"earlier_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"1399"}]},"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Pausinger, Florian","first_name":"Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768"}],"publication_identifier":{"issn":["09249907"]},"month":"09","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s10851-013-0468-x","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm."}],"intvolume":" 50","ddc":["000"],"status":"public","title":"Stable length estimates of tube-like shapes","_id":"2255","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:45:35Z","date_created":"2018-12-12T10:16:18Z","checksum":"2f93f3e63a38a85cd4404d7953913b14","file_id":"5204","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":3941391,"file_name":"IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"549","scopus_import":1,"has_accepted_license":"1","day":"01","page":"164 - 177","citation":{"chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” Journal of Mathematical Imaging and Vision. Springer, 2014. https://doi.org/10.1007/s10851-013-0468-x.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” Journal of Mathematical Imaging and Vision, vol. 50, no. 1, Springer, 2014, pp. 164–77, doi:10.1007/s10851-013-0468-x.","short":"H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision 50 (2014) 164–177.","ista":"Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 50(1), 164–177.","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” Journal of Mathematical Imaging and Vision, vol. 50, no. 1. Springer, pp. 164–177, 2014.","apa":"Edelsbrunner, H., & Pausinger, F. (2014). Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. Springer. https://doi.org/10.1007/s10851-013-0468-x","ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 2014;50(1):164-177. doi:10.1007/s10851-013-0468-x"},"publication":"Journal of Mathematical Imaging and Vision","date_published":"2014-09-01T00:00:00Z"},{"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2014-06-11","start_date":"2014-06-08","location":"Kyoto, Japan"},"doi":"10.1145/2582112.2582134","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"06","author":[{"first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"related_material":{"record":[{"id":"1123","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-09-07T11:56:27Z","date_created":"2018-12-11T11:56:03Z","acknowledgement":"Swiss National Science Foundation (Project SNSF-PP00P2-138948)","year":"2014","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"ACM","file_date_updated":"2020-07-14T12:45:30Z","publist_id":"4847","date_published":"2014-06-08T00:00:00Z","publication":"Proceedings of the Annual Symposium on Computational Geometry","citation":{"mla":"Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue of the Whitney Trick.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 171–80, doi:10.1145/2582112.2582134.","short":"I. Mabillard, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 171–180.","chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue of the Whitney Trick.” In Proceedings of the Annual Symposium on Computational Geometry, 171–80. ACM, 2014. https://doi.org/10.1145/2582112.2582134.","ama":"Mabillard I, Wagner U. Eliminating Tverberg points, I. An analogue of the Whitney trick. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:171-180. doi:10.1145/2582112.2582134","ista":"Mabillard I, Wagner U. 2014. Eliminating Tverberg points, I. An analogue of the Whitney trick. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 171–180.","apa":"Mabillard, I., & Wagner, U. (2014). Eliminating Tverberg points, I. An analogue of the Whitney trick. In Proceedings of the Annual Symposium on Computational Geometry (pp. 171–180). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582134","ieee":"I. Mabillard and U. Wagner, “Eliminating Tverberg points, I. An analogue of the Whitney trick,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 171–180."},"page":"171 - 180","day":"08","has_accepted_license":"1","scopus_import":1,"pubrep_id":"534","file":[{"relation":"main_file","file_id":"4735","date_updated":"2020-07-14T12:45:30Z","date_created":"2018-12-12T10:09:12Z","checksum":"2aae223fee8ffeaf57bbabd8d92b6a2c","file_name":"IST-2016-534-v1+1_Eliminating_Tverberg_points_I._An_analogue_of_the_Whitney_trick.pdf","access_level":"open_access","content_type":"application/pdf","file_size":914396,"creator":"system"}],"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2159","ddc":["510"],"title":"Eliminating Tverberg points, I. An analogue of the Whitney trick","status":"public","abstract":[{"lang":"eng","text":"Motivated by topological Tverberg-type problems, we consider multiple (double, triple, and higher multiplicity) selfintersection points of maps from finite simplicial complexes (compact polyhedra) into ℝd and study conditions under which such multiple points can be eliminated. The most classical case is that of embeddings (i.e., maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem, the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary condition for embeddability (namely, vanishing of the van Kampen ob-struction). For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes then one can successively remove these double points by local modifications of the map f. One of the main tools is the famous Whitney trick that permits eliminating pairs of double points of opposite intersection sign. We are interested in generalizing this approach to intersection points of higher multiplicity. We call a point y 2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e., does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time algorithm for deciding this (based on the vanishing of a cohomological obstruction, as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney trick: Given r pairwise disjoint simplices of K such that the intersection of their images contains two r-fold Tverberg points y+ and y- of opposite intersection sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper, we plan to develop this further and present a generalization of the classical Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability of κ-complexes into ℝd for a wider range of dimensions) to intersection points of higher multiplicity."}],"type":"conference"},{"day":"27","has_accepted_license":"1","scopus_import":1,"date_published":"2014-11-27T00:00:00Z","publication":"Ecology and Evolution","citation":{"ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597. doi:10.1002/ece3.1289","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” Ecology and Evolution, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1289","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.","chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289."},"page":"4589 - 4597","abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"issue":"24","type":"journal_article","pubrep_id":"462","file":[{"checksum":"9ab43db1b0fede7bfe560ed77e177b76","date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-12T10:12:28Z","file_id":"4946","relation":"main_file","creator":"system","file_size":118813,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf"}],"oa_version":"Published Version","_id":"2023","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","ddc":["570"],"intvolume":" 4","month":"11","doi":"10.1002/ece3.1289","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"file_date_updated":"2020-07-14T12:45:25Z","ec_funded":1,"publist_id":"5049","author":[{"last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"}],"related_material":{"record":[{"id":"1125","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-09-07T11:55:53Z","date_created":"2018-12-11T11:55:16Z","volume":4,"year":"2014","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}]},{"publication_identifier":{"isbn":["978-331908866-2"]},"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38"}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-319-08867-9_38","conference":{"name":"CAV: Computer Aided Verification","location":"Vienna, Austria","start_date":"2014-07-18","end_date":"2014-07-22"},"language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"4749","file_date_updated":"2020-07-14T12:45:33Z","year":"2014","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1130"}]},"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"},{"last_name":"Ryzhyk","first_name":"Leonid","full_name":"Ryzhyk, Leonid"},{"full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tarrach","first_name":"Thorsten"}],"volume":8559,"date_updated":"2023-09-07T11:57:01Z","date_created":"2018-12-11T11:56:23Z","has_accepted_license":"1","day":"22","citation":{"ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:10.1007/978-3-319-08867-9_38","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559, 568–584.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach, T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_38","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free synthesis for concurrency,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 568–584.","mla":"Cerny, Pavol, et al. Regression-Free Synthesis for Concurrency. Vol. 8559, Springer, 2014, pp. 568–84, doi:10.1007/978-3-319-08867-9_38.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2014, pp. 568–584.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_38."},"page":"568 - 584","date_published":"2014-07-22T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs.","lang":"eng"}],"_id":"2218","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8559","status":"public","ddc":["000"],"title":"Regression-free synthesis for concurrency","pubrep_id":"297","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":416732,"creator":"system","access_level":"open_access","file_name":"IST-2014-297-v1+1_cav14-final.pdf","checksum":"a631d3105509f239724644e77a1212e2","date_updated":"2020-07-14T12:45:33Z","date_created":"2018-12-12T10:13:14Z","relation":"main_file","file_id":"4995"},{"file_name":"IST-2014-297-v2+1_cav14-final2.pdf","access_level":"open_access","creator":"system","file_size":616293,"content_type":"application/pdf","file_id":"4996","relation":"main_file","date_created":"2018-12-12T10:13:15Z","date_updated":"2020-07-14T12:45:33Z","checksum":"f8b0f748cc9fa697ca992cc56c87bc4e"}]},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"}],"oa":1,"external_id":{"arxiv":["1904.07083"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.07083"}],"language":[{"iso":"eng"}],"conference":{"name":"ICST: International Conference on Software Testing, Verification and Validation","end_date":"2014-04-04","start_date":"2014-03-31","location":"Cleveland, USA"},"doi":"10.1109/ICST.2014.50","month":"03","publication_identifier":{"isbn":["978-1-4799-2255-0"],"issn":["2159-4848"]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","year":"2014","date_updated":"2023-09-07T11:58:33Z","date_created":"2018-12-11T11:56:06Z","author":[{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Krenn","first_name":"Willibald","full_name":"Krenn, Willibald"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5411"},{"relation":"dissertation_contains","status":"public","id":"1155"}]},"article_number":"6823899","publist_id":"4817","ec_funded":1,"publication":"IEEE 7th International Conference on Software Testing, Verification and Validation","citation":{"ieee":"P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, “Compositional specifications for IOCO testing,” in IEEE 7th International Conference on Software Testing, Verification and Validation, Cleveland, USA, 2014.","apa":"Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional specifications for IOCO testing. In IEEE 7th International Conference on Software Testing, Verification and Validation. Cleveland, USA: IEEE. https://doi.org/10.1109/ICST.2014.50","ista":"Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing. IEEE 7th International Conference on Software Testing, Verification and Validation. ICST: International Conference on Software Testing, Verification and Validation, 6823899.","ama":"Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional specifications for IOCO testing. In: IEEE 7th International Conference on Software Testing, Verification and Validation. IEEE; 2014. doi:10.1109/ICST.2014.50","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. “Compositional Specifications for IOCO Testing.” In IEEE 7th International Conference on Software Testing, Verification and Validation. IEEE, 2014. https://doi.org/10.1109/ICST.2014.50.","short":"P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, in:, IEEE 7th International Conference on Software Testing, Verification and Validation, IEEE, 2014.","mla":"Daca, Przemyslaw, et al. “Compositional Specifications for IOCO Testing.” IEEE 7th International Conference on Software Testing, Verification and Validation, 6823899, IEEE, 2014, doi:10.1109/ICST.2014.50."},"date_published":"2014-03-01T00:00:00Z","scopus_import":1,"day":"01","article_processing_charge":"No","title":"Compositional specifications for IOCO testing","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2167","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing. In this paper, we study compositional properties of the ioco-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the ioco conformance relation, the resulting methodology can be applied to a broader class of systems."}]},{"day":"01","month":"07","conference":{"end_date":"2014-07-22","location":"Vienna, Austria","start_date":"2014-07-18","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-319-08867-9_31","date_published":"2014-07-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_31.","short":"K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.","mla":"Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. Vol. 8559, Springer, 2014, pp. 473–90, doi:10.1007/978-3-319-08867-9_31.","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2014). CEGAR for qualitative analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_31","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 473–490.","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic systems. In: Vol 8559. Springer; 2014:473-490. doi:10.1007/978-3-319-08867-9_31"},"quality_controlled":"1","page":"473 - 490","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements."}],"publist_id":"4978","ec_funded":1,"type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw"}],"related_material":{"record":[{"id":"5412","status":"public","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"5413"},{"id":"5414","relation":"earlier_version","status":"public"},{"id":"1155","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:55:30Z","date_updated":"2023-09-07T11:58:33Z","oa_version":"None","volume":8559,"_id":"2063","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"CEGAR for qualitative analysis of probabilistic systems","status":"public","publication_status":"published","intvolume":" 8559","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"ec_funded":1,"publist_id":"5076","volume":6,"date_updated":"2023-09-07T12:00:25Z","date_created":"2018-12-11T11:55:08Z","related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","first_name":"Karin","full_name":"Mitosch, Karin"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"}],"department":[{"_id":"ToBo"}],"publisher":"Wiley","publication_status":"published","year":"2014","month":"06","language":[{"iso":"eng"}],"doi":"10.1111/1758-2229.12190","project":[{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"},{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"}],"quality_controlled":"1","issue":"6","abstract":[{"lang":"eng","text":"Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria."}],"type":"journal_article","oa_version":"None","intvolume":" 6","title":"Bacterial responses to antibiotics and their combinations","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2001","day":"22","scopus_import":1,"date_published":"2014-06-22T00:00:00Z","page":"545 - 557","citation":{"ama":"Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 2014;6(6):545-557. doi:10.1111/1758-2229.12190","ista":"Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 6(6), 545–557.","apa":"Mitosch, K., & Bollenbach, M. T. (2014). Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.12190","ieee":"K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their combinations,” Environmental Microbiology Reports, vol. 6, no. 6. Wiley, pp. 545–557, 2014.","mla":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” Environmental Microbiology Reports, vol. 6, no. 6, Wiley, 2014, pp. 545–57, doi:10.1111/1758-2229.12190.","short":"K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014) 545–557.","chicago":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” Environmental Microbiology Reports. Wiley, 2014. https://doi.org/10.1111/1758-2229.12190."},"publication":"Environmental Microbiology Reports"},{"date_updated":"2023-09-07T12:02:27Z","date_created":"2018-12-11T11:55:36Z","volume":8616,"author":[{"last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar"}],"related_material":{"record":[{"id":"838","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publisher":"Springer","editor":[{"full_name":"Garay, Juan","first_name":"Juan","last_name":"Garay"},{"full_name":"Gennaro, Rosario","first_name":"Rosario","last_name":"Gennaro"}],"department":[{"_id":"KrPi"}],"year":"2014","file_date_updated":"2020-07-14T12:45:28Z","publist_id":"4955","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2014-08-21","start_date":"2014-08-17","location":"Santa Barbara, USA","name":"CRYPTO: International Cryptology Conference"},"doi":"10.1007/978-3-662-44371-2_7","quality_controlled":"1","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"oa":1,"month":"01","file":[{"date_created":"2018-12-12T10:13:17Z","date_updated":"2020-07-14T12:45:28Z","checksum":"dab6ab36a5f6af94f2b597e6404ed11d","relation":"main_file","file_id":"4999","content_type":"application/pdf","file_size":492310,"creator":"system","file_name":"IST-2016-682-v1+1_578.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"682","status":"public","title":"The exact PRF-security of NMAC and HMAC","ddc":["000","004"],"intvolume":" 8616","_id":"2082","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC was introduced by Bellare, Canetti and Krawczyk [Crypto'96], who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1) f is a PRF and (2) the function we get when cascading f is weakly collision-resistant. Unfortunately, HMAC is typically instantiated with cryptographic hash functions like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable guarantees for NMAC, Bellare [Crypto'06] showed its security based solely on the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first contribution is a simpler and uniform proof for this fact: If f is an ε-secure PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries), then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security of a modification of NMAC called NI [An and Bellare, Crypto'99] that differs mainly by using a compression function with an additional keying input. This avoids the constant rekeying on multi-block messages in NMAC and allows for a security proof starting by the standard switch from a PRF to a random function, followed by an information-theoretic analysis. We carry out such an analysis, obtaining a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c. The proof borrows combinatorial techniques originally developed for proving the security of CBC-MAC [Bellare et al., Crypto'05]."}],"issue":"1","alternative_title":["LNCS"],"type":"conference","date_published":"2014-01-01T00:00:00Z","page":"113 - 130","citation":{"apa":"Gazi, P., Pietrzak, K. Z., & Rybar, M. (2014). The exact PRF-security of NMAC and HMAC. In J. Garay & R. Gennaro (Eds.) (Vol. 8616, pp. 113–130). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA: Springer. https://doi.org/10.1007/978-3-662-44371-2_7","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact PRF-security of NMAC and HMAC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA, 2014, vol. 8616, no. 1, pp. 113–130.","ista":"Gazi P, Pietrzak KZ, Rybar M. 2014. The exact PRF-security of NMAC and HMAC. CRYPTO: International Cryptology Conference, LNCS, vol. 8616, 113–130.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact PRF-security of NMAC and HMAC. In: Garay J, Gennaro R, eds. Vol 8616. Springer; 2014:113-130. doi:10.1007/978-3-662-44371-2_7","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact PRF-Security of NMAC and HMAC.” edited by Juan Garay and Rosario Gennaro, 8616:113–30. Springer, 2014. https://doi.org/10.1007/978-3-662-44371-2_7.","short":"P. Gazi, K.Z. Pietrzak, M. Rybar, in:, J. Garay, R. Gennaro (Eds.), Springer, 2014, pp. 113–130.","mla":"Gazi, Peter, et al. The Exact PRF-Security of NMAC and HMAC. Edited by Juan Garay and Rosario Gennaro, vol. 8616, no. 1, Springer, 2014, pp. 113–30, doi:10.1007/978-3-662-44371-2_7."},"day":"01","has_accepted_license":"1"},{"page":"774 - 783","publication":"Developmental Cell","citation":{"ieee":"J. Compagnon et al., “The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ,” Developmental Cell, vol. 31, no. 6. Cell Press, pp. 774–783, 2014.","apa":"Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K., Behrndt, M., & Heisenberg, C.-P. J. (2014). The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2014.11.003","ista":"Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783.","ama":"Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 2014;31(6):774-783. doi:10.1016/j.devcel.2014.11.003","chicago":"Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier, Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell. Cell Press, 2014. https://doi.org/10.1016/j.devcel.2014.11.003.","short":"J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha, M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.","mla":"Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell, vol. 31, no. 6, Cell Press, 2014, pp. 774–83, doi:10.1016/j.devcel.2014.11.003."},"date_published":"2014-12-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","status":"public","title":"The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ","intvolume":" 31","_id":"1912","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function.","lang":"eng"}],"issue":"6","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/25535919"}],"external_id":{"pmid":["25535919"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2014.11.003","month":"12","publication_status":"published","publisher":"Cell Press","department":[{"_id":"CaHe"}],"acknowledgement":"We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus, and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing reagents. This work was supported by the Institute of Science and Technology Austria and an Alexander von Humboldt Foundation fellowship to J.C.","year":"2014","pmid":1,"date_updated":"2023-09-07T12:05:08Z","date_created":"2018-12-11T11:54:41Z","volume":31,"author":[{"last_name":"Compagnon","first_name":"Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","full_name":"Compagnon, Julien"},{"full_name":"Barone, Vanessa","last_name":"Barone","first_name":"Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rajshekar","first_name":"Srivarsha","full_name":"Rajshekar, Srivarsha"},{"full_name":"Kottmeier, Rita","last_name":"Kottmeier","first_name":"Rita"},{"full_name":"Pranjic-Ferscha, Kornelija","first_name":"Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"related_material":{"record":[{"id":"961","status":"public","relation":"dissertation_contains"}]},"publist_id":"5182"},{"month":"07","doi":"10.15252/embj.201387695","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194103/","open_access":"1"}],"oa":1,"quality_controlled":"1","publist_id":"4953","related_material":{"record":[{"id":"418","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Grusch, Michael","first_name":"Michael","last_name":"Grusch"},{"full_name":"Schelch, Karin","last_name":"Schelch","first_name":"Karin"},{"full_name":"Riedler, Robert","last_name":"Riedler","first_name":"Robert"},{"full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Differ","first_name":"Christopher","full_name":"Differ, Christopher"},{"full_name":"Berger, Walter","first_name":"Walter","last_name":"Berger"},{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"volume":33,"date_created":"2018-12-11T11:55:37Z","date_updated":"2023-09-07T12:49:09Z","year":"2014","acknowledgement":"European Union Seventh Framework Programme; Human Frontier Science Program; Oesterreichische Nationalbank Anniversary Fund 14211; Austrian Research Promotion Agency; FemTech","publisher":"Wiley-Blackwell","department":[{"_id":"HaJa"}],"publication_status":"published","day":"01","scopus_import":1,"date_published":"2014-07-01T00:00:00Z","citation":{"chicago":"Grusch, Michael, Karin Schelch, Robert Riedler, Eva Gschaider-Reichhart, Christopher Differ, Walter Berger, Álvaro Inglés Prieto, and Harald L Janovjak. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal. Wiley-Blackwell, 2014. https://doi.org/10.15252/embj.201387695.","short":"M. Grusch, K. Schelch, R. Riedler, E. Gschaider-Reichhart, C. Differ, W. Berger, Á. Inglés Prieto, H.L. Janovjak, EMBO Journal 33 (2014) 1713–1726.","mla":"Grusch, Michael, et al. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal, vol. 33, no. 15, Wiley-Blackwell, 2014, pp. 1713–26, doi:10.15252/embj.201387695.","apa":"Grusch, M., Schelch, K., Riedler, R., Gschaider-Reichhart, E., Differ, C., Berger, W., … Janovjak, H. L. (2014). Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. Wiley-Blackwell. https://doi.org/10.15252/embj.201387695","ieee":"M. Grusch et al., “Spatio-temporally precise activation of engineered receptor tyrosine kinases by light,” EMBO Journal, vol. 33, no. 15. Wiley-Blackwell, pp. 1713–1726, 2014.","ista":"Grusch M, Schelch K, Riedler R, Gschaider-Reichhart E, Differ C, Berger W, Inglés Prieto Á, Janovjak HL. 2014. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 33(15), 1713–1726.","ama":"Grusch M, Schelch K, Riedler R, et al. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 2014;33(15):1713-1726. doi:10.15252/embj.201387695"},"publication":"EMBO Journal","page":"1713 - 1726","issue":"15","abstract":[{"lang":"eng","text":"Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2084","intvolume":" 33","status":"public","title":"Spatio-temporally precise activation of engineered receptor tyrosine kinases by light"},{"_id":"2157","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"ERC Advanced Grant No. 267165; Grant GRADR Eurogiga GIG/11/E023 (SNSF-PP00P2-138948); Swiss National Science Foundation (SNSF-200020-138230).","title":"Embeddability in the 3 sphere is decidable","status":"public","publication_status":"published","publisher":"ACM","department":[{"_id":"UlWa"}],"author":[{"last_name":"Matoušek","first_name":"Jiří","full_name":"Matoušek, Jiří"},{"first_name":"Eric","last_name":"Sedgwick","full_name":"Sedgwick, Eric"},{"full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","first_name":"Martin","last_name":"Tancer"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"425"}]},"date_updated":"2023-09-11T13:38:49Z","date_created":"2018-12-11T11:56:02Z","oa_version":"Submitted Version","type":"conference","abstract":[{"text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, i.e., an essential curve in the boundary of X bounding a disk in S3 nX with length bounded by a computable function of the number of tetrahedra of X.","lang":"eng"}],"publist_id":"4849","publication":"Proceedings of the Annual Symposium on Computational Geometry","main_file_link":[{"url":"http://arxiv.org/abs/1402.0815","open_access":"1"}],"oa":1,"citation":{"chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3 Sphere Is Decidable.” In Proceedings of the Annual Symposium on Computational Geometry, 78–84. ACM, 2014. https://doi.org/10.1145/2582112.2582137.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3 Sphere Is Decidable.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84, doi:10.1145/2582112.2582137.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2014). Embeddability in the 3 sphere is decidable. In Proceedings of the Annual Symposium on Computational Geometry (pp. 78–84). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582137","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3 sphere is decidable,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 78–84.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2014. Embeddability in the 3 sphere is decidable. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 78–84.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3 sphere is decidable. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:78-84. doi:10.1145/2582112.2582137"},"quality_controlled":"1","page":"78 - 84","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2014-06-11","location":"Kyoto, Japan","start_date":"2014-06-08"},"doi":"10.1145/2582112.2582137","date_published":"2014-06-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"06"},{"place":"Berlin, Heidelberg","volume":8592,"date_updated":"2023-09-20T09:42:40Z","date_created":"2022-03-21T07:12:16Z","related_material":{"record":[{"id":"1433","relation":"later_version","status":"public"}]},"author":[{"full_name":"Bauer, Ulrich","last_name":"Bauer","first_name":"Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"},{"full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus"},{"full_name":"Wagner, Hubert","first_name":"Hubert","last_name":"Wagner"}],"publisher":"Springer Berlin Heidelberg","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2014","publication_identifier":{"eisbn":["9783662441992"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783662441985"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-44199-2_24","conference":{"location":"Seoul, South Korea","start_date":"2014-08-05","end_date":"2014-08-09","name":"ICMS: International Congress on Mathematical Software"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations."}],"type":"conference","oa_version":"None","intvolume":" 8592","title":"PHAT – Persistent Homology Algorithms Toolbox","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10894","article_processing_charge":"No","day":"01","series_title":"LNCS","scopus_import":"1","date_published":"2014-09-01T00:00:00Z","page":"137-143","citation":{"chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT – Persistent Homology Algorithms Toolbox.” In ICMS 2014: International Congress on Mathematical Software, 8592:137–43. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. https://doi.org/10.1007/978-3-662-44199-2_24.","mla":"Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” ICMS 2014: International Congress on Mathematical Software, vol. 8592, Springer Berlin Heidelberg, 2014, pp. 137–43, doi:10.1007/978-3-662-44199-2_24.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, pp. 137–143.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software. ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology Algorithms Toolbox,” in ICMS 2014: International Congress on Mathematical Software, Seoul, South Korea, 2014, vol. 8592, pp. 137–143.","apa":"Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2014). PHAT – Persistent Homology Algorithms Toolbox. In ICMS 2014: International Congress on Mathematical Software (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-662-44199-2_24","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms Toolbox. In: ICMS 2014: International Congress on Mathematical Software. Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143. doi:10.1007/978-3-662-44199-2_24"},"publication":"ICMS 2014: International Congress on Mathematical Software"}]