[{"_id":"17231","page":"3287-3301","article_processing_charge":"No","corr_author":"1","date_created":"2024-07-14T22:01:10Z","external_id":{"isi":["001230091000001"]},"date_published":"2024-11-01T00:00:00Z","quality_controlled":"1","OA_type":"free access","author":[{"id":"06619f18-9070-11eb-847d-d1ee780bd88b","first_name":"Corentin","last_name":"Fiorebe","full_name":"Fiorebe, Corentin"}],"intvolume":"        44","title":"Examples of projective billiards with open sets of periodic orbits","issue":"11","department":[{"_id":"VaKa"}],"publication_status":"published","publisher":"AIMS","doi":"10.3934/dcds.2024059","type":"journal_article","month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","language":[{"iso":"eng"}],"article_type":"original","publication":"Discrete and Continuous Dynamical Systems- Series A","date_updated":"2026-08-12T06:19:26Z","isi":1,"year":"2024","abstract":[{"text":"In the class of projective billiards, which contains the usual billiards, we exhibit counter-examples to Ivrii's conjecture, which states that in any planar billiard with smooth boundary the set of periodic orbits has zero measure. The counter-examples are polygons admitting a 2-parameters family of n-periodic orbits, with n being either 3 or any even integer greater than 4.","lang":"eng"}],"citation":{"ieee":"C. Fiorebe, “Examples of projective billiards with open sets of periodic orbits,” <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44, no. 11. AIMS, pp. 3287–3301, 2024.","apa":"Fiorebe, C. (2024). Examples of projective billiards with open sets of periodic orbits. <i>Discrete and Continuous Dynamical Systems- Series A</i>. AIMS. <a href=\"https://doi.org/10.3934/dcds.2024059\">https://doi.org/10.3934/dcds.2024059</a>","short":"C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024) 3287–3301.","ista":"Fiorebe C. 2024. Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. 44(11), 3287–3301.","chicago":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>. AIMS, 2024. <a href=\"https://doi.org/10.3934/dcds.2024059\">https://doi.org/10.3934/dcds.2024059</a>.","ama":"Fiorebe C. Examples of projective billiards with open sets of periodic orbits. <i>Discrete and Continuous Dynamical Systems- Series A</i>. 2024;44(11):3287-3301. doi:<a href=\"https://doi.org/10.3934/dcds.2024059\">10.3934/dcds.2024059</a>","mla":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44, no. 11, AIMS, 2024, pp. 3287–301, doi:<a href=\"https://doi.org/10.3934/dcds.2024059\">10.3934/dcds.2024059</a>."},"volume":44,"ddc":["500"],"scopus_import":"1","publication_identifier":{"eissn":["1553-5231"],"issn":["1078-0947"]},"status":"public","oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.3934/dcds.2024059"}]},{"publication_status":"draft","department":[{"_id":"HeEd"}],"license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.48550/arXiv.2212.03128","type":"preprint","title":"Chromatic alpha complexes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"arxiv":["2212.03128"]},"date_published":"2024-02-07T00:00:00Z","author":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano"},{"first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0464-3823","last_name":"Draganov","full_name":"Draganov, Ondrej"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"_id":"15091","corr_author":"1","article_processing_charge":"No","related_material":{"record":[{"id":"18979","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"15094"},{"status":"public","relation":"later_version","id":"20585"}]},"date_created":"2024-03-08T10:13:59Z","article_number":"2212.03128","status":"public","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"OA_place":"repository","oa_version":"Preprint","oa":1,"citation":{"ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” <i>arXiv</i>. .","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Chromatic alpha complexes. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2212.03128\">https://doi.org/10.48550/arXiv.2212.03128</a>","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2212.03128\">10.48550/arXiv.2212.03128</a>","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” <i>ArXiv</i>, 2212.03128, doi:<a href=\"https://doi.org/10.48550/arXiv.2212.03128\">10.48550/arXiv.2212.03128</a>.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2212.03128\">https://doi.org/10.48550/arXiv.2212.03128</a>."},"date_updated":"2026-08-12T06:19:48Z","publication":"arXiv","abstract":[{"lang":"eng","text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided."}],"year":"2024","month":"02","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"07"},{"publication_status":"published","department":[{"_id":"ToHe"}],"type":"conference","doi":"10.1109/ICRA57147.2024.10610284","publisher":"IEEE","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"title":"Overparametrization helps offline-to-online generalization of closed-loop control from pixels","quality_controlled":"1","date_published":"2024-08-08T00:00:00Z","conference":{"location":"Yokohama, Japan","start_date":"2024-05-13","end_date":"2024-05-17","name":"ICRA: International Conference on Robotics and Automation"},"external_id":{"isi":["001294576202044"]},"author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ramin","last_name":"Hasani","full_name":"Hasani, Ramin"},{"full_name":"Amini, Alexander","last_name":"Amini","first_name":"Alexander"},{"first_name":"Tsun Hsuan","last_name":"Wang","full_name":"Wang, Tsun Hsuan"},{"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":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"}],"acknowledgement":"This work was partially supported in parts by the ERC-2020-AdG 101020093. Additionally, it was partially sponsored by the United States Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under Cooperative Agreement Number FA8750-19-2-1000. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the United States Air Force or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. This work was further supported by The Boeing Company and the Office of Naval Research (ONR) Grant N00014-18-1-2830.","_id":"17898","date_created":"2024-09-08T22:01:13Z","article_processing_charge":"No","page":"2774-2782","status":"public","scopus_import":"1","publication_identifier":{"issn":["1050-4729"],"isbn":["9798350384574"]},"oa_version":"None","ec_funded":1,"citation":{"chicago":"Lechner, Mathias, Ramin Hasani, Alexander Amini, Tsun Hsuan Wang, Thomas A Henzinger, and Daniela Rus. “Overparametrization Helps Offline-to-Online Generalization of Closed-Loop Control from Pixels.” In <i>Proceedings of the 2024 IEEE International Conference on Robotics and Automation</i>, 2774–82. IEEE, 2024. <a href=\"https://doi.org/10.1109/ICRA57147.2024.10610284\">https://doi.org/10.1109/ICRA57147.2024.10610284</a>.","ama":"Lechner M, Hasani R, Amini A, Wang TH, Henzinger TA, Rus D. Overparametrization helps offline-to-online generalization of closed-loop control from pixels. In: <i>Proceedings of the 2024 IEEE International Conference on Robotics and Automation</i>. IEEE; 2024:2774-2782. doi:<a href=\"https://doi.org/10.1109/ICRA57147.2024.10610284\">10.1109/ICRA57147.2024.10610284</a>","mla":"Lechner, Mathias, et al. “Overparametrization Helps Offline-to-Online Generalization of Closed-Loop Control from Pixels.” <i>Proceedings of the 2024 IEEE International Conference on Robotics and Automation</i>, IEEE, 2024, pp. 2774–82, doi:<a href=\"https://doi.org/10.1109/ICRA57147.2024.10610284\">10.1109/ICRA57147.2024.10610284</a>.","ieee":"M. Lechner, R. Hasani, A. Amini, T. H. Wang, T. A. Henzinger, and D. Rus, “Overparametrization helps offline-to-online generalization of closed-loop control from pixels,” in <i>Proceedings of the 2024 IEEE International Conference on Robotics and Automation</i>, Yokohama, Japan, 2024, pp. 2774–2782.","apa":"Lechner, M., Hasani, R., Amini, A., Wang, T. H., Henzinger, T. A., &#38; Rus, D. (2024). Overparametrization helps offline-to-online generalization of closed-loop control from pixels. In <i>Proceedings of the 2024 IEEE International Conference on Robotics and Automation</i> (pp. 2774–2782). Yokohama, Japan: IEEE. <a href=\"https://doi.org/10.1109/ICRA57147.2024.10610284\">https://doi.org/10.1109/ICRA57147.2024.10610284</a>","short":"M. Lechner, R. Hasani, A. Amini, T.H. Wang, T.A. Henzinger, D. Rus, in:, Proceedings of the 2024 IEEE International Conference on Robotics and Automation, IEEE, 2024, pp. 2774–2782.","ista":"Lechner M, Hasani R, Amini A, Wang TH, Henzinger TA, Rus D. 2024. Overparametrization helps offline-to-online generalization of closed-loop control from pixels. Proceedings of the 2024 IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, 2774–2782."},"date_updated":"2026-08-12T06:35:50Z","publication":"Proceedings of the 2024 IEEE International Conference on Robotics and Automation","abstract":[{"lang":"eng","text":"There is an ever-growing zoo of modern neural network models that can efficiently learn end-to-end control from visual observations. These advanced deep models, ranging from convolutional to Vision Transformers, from small to gigantic networks, have been extensively tested on offline image classification tasks. In this paper, we study these vision models with respect to the open-loop training to closed-loop generalization abilities, i.e., deployment realizes a causal feedback loop that is not present during training. This causality gap typically emerges in robotics applications such as autonomous driving, where a network is trained to imitate the control commands of a human. In this setting, two situations arise: 1) Closed-loop testing in-distribution, where the test environment shares properties with those of offline training data. 2) Closed-loop testing under distribution shifts and out-of-distribution. Contrary to recently reported results, we show that under proper training guidelines, all vision architectures perform indistinguishably well on in-distribution deployment, resolving the causality gap. In situation 2, We observe that scale is the strongest factor in improving closed-loop generalization regardless of the choice of the model architecture. Our results predict the trend that in the future we will see larger and larger models being used in offline-training-online-deployment imitation learning tasks in robotic applications."}],"year":"2024","isi":1,"month":"08","language":[{"iso":"eng"}],"day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"full_name":"Jin, Lifu","last_name":"Jin","first_name":"Lifu"},{"full_name":"Esposito, Amedeo Roberto","last_name":"Esposito","first_name":"Amedeo Roberto","id":"9583e921-e1ad-11ec-9862-cef099626dc9"},{"full_name":"Gastpar, Michael","last_name":"Gastpar","first_name":"Michael"}],"quality_controlled":"1","date_published":"2024-08-19T00:00:00Z","conference":{"end_date":"2024-07-12","start_date":"2024-07-07","location":"Athens, Greece","name":"ISIT: International Symposium on Information Theory"},"external_id":{"arxiv":["2403.10656"],"isi":["001304426903055"]},"date_created":"2024-09-08T22:01:12Z","corr_author":"1","article_processing_charge":"No","page":"3178-3183","acknowledgement":"The work in this paper was supported in part by the Swiss National Science Foundation under Grant 200364.\r\n","_id":"17893","type":"conference","doi":"10.1109/ISIT57864.2024.10619367","publisher":"IEEE","publication_status":"published","department":[{"_id":"MaMo"}],"title":"Properties of the strong data processing constant for Rényi divergence","abstract":[{"text":"Strong data processing inequalities (SDPI) are an important object of study in Information Theory and have been well studied for f -divergences. Universal upper and lower bounds have been provided along with several applications, connecting them to impossibility (converse) results, concentration of measure, hypercontractivity, and so on. In this paper, we study Renyi divergence and the corresponding SDPI constant whose behavior seems to deviate from that of ordinary <1>-divergences. In particular, one can find examples showing that the universal upper bound relating its SDPI constant to the one of Total Variation does not hold in general. In this work, we prove, however, that the universal lower bound involving the SDPI constant of the Chi-square divergence does indeed hold. Furthermore, we also provide a characterization of the distribution that achieves the supremum when is equal to 2 and consequently compute the SDPI constant for Renyi divergence of the general binary channel.","lang":"eng"}],"year":"2024","isi":1,"date_updated":"2026-08-12T06:38:02Z","publication":"Proceedings of the 2024 IEEE International Symposium on Information Theory","language":[{"iso":"eng"}],"day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2403.10656 "}],"arxiv":1,"oa":1,"oa_version":"Preprint","status":"public","publication_identifier":{"issn":["2157-8095"],"isbn":["9798350382846"]},"scopus_import":"1","citation":{"ieee":"L. Jin, A. R. Esposito, and M. Gastpar, “Properties of the strong data processing constant for Rényi divergence,” in <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>, Athens, Greece, 2024, pp. 3178–3183.","apa":"Jin, L., Esposito, A. R., &#38; Gastpar, M. (2024). Properties of the strong data processing constant for Rényi divergence. In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i> (pp. 3178–3183). Athens, Greece: IEEE. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">https://doi.org/10.1109/ISIT57864.2024.10619367</a>","short":"L. Jin, A.R. Esposito, M. Gastpar, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory, IEEE, 2024, pp. 3178–3183.","ista":"Jin L, Esposito AR, Gastpar M. 2024. Properties of the strong data processing constant for Rényi divergence. Proceedings of the 2024 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 3178–3183.","chicago":"Jin, Lifu, Amedeo Roberto Esposito, and Michael Gastpar. “Properties of the Strong Data Processing Constant for Rényi Divergence.” In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>, 3178–83. IEEE, 2024. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">https://doi.org/10.1109/ISIT57864.2024.10619367</a>.","ama":"Jin L, Esposito AR, Gastpar M. Properties of the strong data processing constant for Rényi divergence. In: <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>. IEEE; 2024:3178-3183. doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">10.1109/ISIT57864.2024.10619367</a>","mla":"Jin, Lifu, et al. “Properties of the Strong Data Processing Constant for Rényi Divergence.” <i>Proceedings of the 2024 IEEE International Symposium on Information Theory</i>, IEEE, 2024, pp. 3178–83, doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619367\">10.1109/ISIT57864.2024.10619367</a>."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1586-1591","day":"19","article_processing_charge":"No","language":[{"iso":"eng"}],"date_created":"2024-09-08T22:01:12Z","_id":"17895","month":"08","acknowledgement":"The work of M. Langberg and A. D. Sarwate was supported in part by the US NSF under awards CCF-1909451 and CCF1909468. B. K. Dey was supported in part by the Bharti Centre\r\nfor Communication in IIT Bombay. ","isi":1,"year":"2024","abstract":[{"text":"We propose a concatenated code construction for a class of discrete-alphabet oblivious arbitrarily varying channels (AVCs) with cost constraints. The code has time and space complexity polynomial in the blocklength n . It uses a Reed-Solomon outer code, logarithmic blocklength random inner codes, and stochastic encoding by permuting the codeword before transmission. When the channel satisfies a condition called strong DS-nonsymmetrizability (a modified version of nonsymmetrizability originally due to Dobrushin and Stambler), we show that the code achieves a rate that for a variety of oblivious AVCs (such as classically studied error/erasure channels) match the known capacities.","lang":"eng"}],"author":[{"last_name":"Dey","first_name":"B. K.","full_name":"Dey, B. K."},{"full_name":"Jaggi, S.","last_name":"Jaggi","first_name":"S."},{"first_name":"M.","last_name":"Langberg","full_name":"Langberg, M."},{"full_name":"Sarwate, A. D.","last_name":"Sarwate","first_name":"A. D."},{"full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","first_name":"Yihan","last_name":"Zhang"}],"conference":{"location":"Athens, Greece","end_date":"2024-07-12","start_date":"2024-07-07","name":"ISIT: International Symposium on Information Theory"},"external_id":{"isi":["001304426901091"]},"date_published":"2024-08-19T00:00:00Z","publication":"Proceedings of the 2024 IEEE International Symposium on Information Theory ","quality_controlled":"1","date_updated":"2026-08-12T06:37:45Z","title":"Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs","citation":{"short":"B.K. Dey, S. Jaggi, M. Langberg, A.D. Sarwate, Y. Zhang, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 1586–1591.","ieee":"B. K. Dey, S. Jaggi, M. Langberg, A. D. Sarwate, and Y. Zhang, “Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs,” in <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, Athens, Greece, 2024, pp. 1586–1591.","apa":"Dey, B. K., Jaggi, S., Langberg, M., Sarwate, A. D., &#38; Zhang, Y. (2024). Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i> (pp. 1586–1591). Athens, Greece: IEEE. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">https://doi.org/10.1109/ISIT57864.2024.10619362</a>","ista":"Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. 2024. Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. Proceedings of the 2024 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 1586–1591.","chicago":"Dey, B. K., S. Jaggi, M. Langberg, A. D. Sarwate, and Yihan Zhang. “Computationally Efficient Codes for Strongly Dobrushin-Stambler Nonsymmetrizable Oblivious AVCs.” In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, 1586–91. IEEE, 2024. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">https://doi.org/10.1109/ISIT57864.2024.10619362</a>.","ama":"Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. In: <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>. IEEE; 2024:1586-1591. doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">10.1109/ISIT57864.2024.10619362</a>","mla":"Dey, B. K., et al. “Computationally Efficient Codes for Strongly Dobrushin-Stambler Nonsymmetrizable Oblivious AVCs.” <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, IEEE, 2024, pp. 1586–91, doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619362\">10.1109/ISIT57864.2024.10619362</a>."},"publisher":"IEEE","oa_version":"None","type":"conference","doi":"10.1109/ISIT57864.2024.10619362","department":[{"_id":"MaMo"}],"publication_identifier":{"issn":["2157-8095"],"isbn":["9798350382846"]},"scopus_import":"1","publication_status":"published","status":"public"},{"acknowledgement":"The work in this paper was supported in part by the Swiss National Science Foundation under Grant 200364.","_id":"17894","corr_author":"1","article_processing_charge":"No","date_created":"2024-09-08T22:01:12Z","page":"2110-2115","quality_controlled":"1","conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2024-07-07","end_date":"2024-07-12","location":"Athens, Greece"},"external_id":{"isi":["001304426902023"]},"date_published":"2024-08-19T00:00:00Z","author":[{"first_name":"Amedeo Roberto","id":"9583e921-e1ad-11ec-9862-cef099626dc9","last_name":"Esposito","full_name":"Esposito, Amedeo Roberto"},{"last_name":"Gastpar","first_name":"Michael","full_name":"Gastpar, Michael"},{"first_name":"Ibrahim","last_name":"Issa","full_name":"Issa, Ibrahim"}],"title":"Variational characterizations of Sibson's α-mutual information","publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"IEEE","type":"conference","doi":"10.1109/ISIT57864.2024.10619378","month":"08","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"19","date_updated":"2026-08-12T06:38:18Z","publication":"Proceedings of the 2024 IEEE International Symposium on Information Theory ","abstract":[{"text":"Sibson's α -mutual information has received renewed attention recently in several contexts: concentration of measure under dependence, statistical learning, hypothesis testing, and estimation theory. In this work, we introduce several variational representations of Sibson's α -mutual information: 1) as a supremum over joint distributions of (a combination of) KL divergences; and 2) as a supremum over functions of opportune expected values. Leveraging them, we produce a variety of novel and known results, including a generalization of transportation-cost inequalities and Fano's inequality.","lang":"eng"}],"isi":1,"year":"2024","citation":{"ista":"Esposito AR, Gastpar M, Issa I. 2024. Variational characterizations of Sibson’s α-mutual information. Proceedings of the 2024 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 2110–2115.","short":"A.R. Esposito, M. Gastpar, I. Issa, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 2110–2115.","ieee":"A. R. Esposito, M. Gastpar, and I. Issa, “Variational characterizations of Sibson’s α-mutual information,” in <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, Athens, Greece, 2024, pp. 2110–2115.","apa":"Esposito, A. R., Gastpar, M., &#38; Issa, I. (2024). Variational characterizations of Sibson’s α-mutual information. In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i> (pp. 2110–2115). Athens, Greece: IEEE. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">https://doi.org/10.1109/ISIT57864.2024.10619378</a>","ama":"Esposito AR, Gastpar M, Issa I. Variational characterizations of Sibson’s α-mutual information. In: <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>. IEEE; 2024:2110-2115. doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">10.1109/ISIT57864.2024.10619378</a>","mla":"Esposito, Amedeo Roberto, et al. “Variational Characterizations of Sibson’s α-Mutual Information.” <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, IEEE, 2024, pp. 2110–15, doi:<a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">10.1109/ISIT57864.2024.10619378</a>.","chicago":"Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Variational Characterizations of Sibson’s α-Mutual Information.” In <i>Proceedings of the 2024 IEEE International Symposium on Information Theory </i>, 2110–15. IEEE, 2024. <a href=\"https://doi.org/10.1109/ISIT57864.2024.10619378\">https://doi.org/10.1109/ISIT57864.2024.10619378</a>."},"status":"public","publication_identifier":{"issn":["2157-8095"],"isbn":["9798350382846"]},"scopus_import":"1","oa_version":"None"},{"publication_identifier":{"eissn":["1860-5974"]},"scopus_import":"1","status":"public","has_accepted_license":"1","oa":1,"oa_version":"Published Version","OA_place":"publisher","arxiv":1,"citation":{"ista":"Chatterjee K, Doyen L. 2024. Stochastic processes with expected stopping time. Logical Methods in Computer Science. 20(4), 11:1-11:34.","apa":"Chatterjee, K., &#38; Doyen, L. (2024). Stochastic processes with expected stopping time. <i>Logical Methods in Computer Science</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/lmcs-20(4:11)2024\">https://doi.org/10.46298/lmcs-20(4:11)2024</a>","ieee":"K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,” <i>Logical Methods in Computer Science</i>, vol. 20, no. 4. EPI Sciences, p. 11:1-11:34, 2024.","short":"K. Chatterjee, L. Doyen, Logical Methods in Computer Science 20 (2024) 11:1-11:34.","ama":"Chatterjee K, Doyen L. Stochastic processes with expected stopping time. <i>Logical Methods in Computer Science</i>. 2024;20(4):11:1-11:34. doi:<a href=\"https://doi.org/10.46298/lmcs-20(4:11)2024\">10.46298/lmcs-20(4:11)2024</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” <i>Logical Methods in Computer Science</i>, vol. 20, no. 4, EPI Sciences, 2024, p. 11:1-11:34, doi:<a href=\"https://doi.org/10.46298/lmcs-20(4:11)2024\">10.46298/lmcs-20(4:11)2024</a>.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” <i>Logical Methods in Computer Science</i>. EPI Sciences, 2024. <a href=\"https://doi.org/10.46298/lmcs-20(4:11)2024\">https://doi.org/10.46298/lmcs-20(4:11)2024</a>."},"ec_funded":1,"volume":20,"DOAJ_listed":"1","ddc":["000"],"publication":"Logical Methods in Computer Science","date_updated":"2026-08-12T06:39:26Z","year":"2024","isi":1,"abstract":[{"text":"Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs.","lang":"eng"}],"month":"11","file_date_updated":"2024-12-09T08:38:48Z","day":"12","alternative_title":["LMCS"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publication_status":"published","type":"journal_article","doi":"10.46298/lmcs-20(4:11)2024","publisher":"EPI Sciences","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"title":"Stochastic processes with expected stopping time","file":[{"file_id":"18633","creator":"dernst","file_size":416814,"access_level":"open_access","date_created":"2024-12-09T08:38:48Z","file_name":"2024_LMCS_Chatterjee.pdf","content_type":"application/pdf","date_updated":"2024-12-09T08:38:48Z","relation":"main_file","checksum":"b3315c74ce18ce0a30ed33d8c9972992","success":1}],"issue":"4","date_published":"2024-11-12T00:00:00Z","external_id":{"arxiv":["2104.07278"],"isi":["001367316400002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"OA_type":"gold","quality_controlled":"1","intvolume":"        20","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"_id":"18630","acknowledgement":"The authors are grateful to the anonymous reviewers of LICS 2021 and of a previous version of this paper for insightful comments that helped improving the presentation. The research presented in this paper was partially supported by the grant ERC CoG 863818 (ForM-SMArt).","page":"11:1-11:34","date_created":"2024-12-08T23:01:56Z","related_material":{"record":[{"id":"10004","relation":"earlier_version","status":"public"}]},"corr_author":"1","article_processing_charge":"Yes"},{"citation":{"ama":"Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. Portable Raman platform for SERS droplets microfludics. In: <i>2024 International Conference on Optical MEMS and Nanophotonics</i>. IEEE; 2024. doi:<a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">10.1109/OMN61224.2024.10685279</a>","mla":"Quintero, Sergio, et al. “Portable Raman Platform for SERS Droplets Microfludics.” <i>2024 International Conference on Optical MEMS and Nanophotonics</i>, IEEE, 2024, doi:<a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">10.1109/OMN61224.2024.10685279</a>.","chicago":"Quintero, Sergio, Maria Relvas, Marta Aranda, Fernando Nodal, Lorena Dieguez, and Sara Abalde-Cela. “Portable Raman Platform for SERS Droplets Microfludics.” In <i>2024 International Conference on Optical MEMS and Nanophotonics</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">https://doi.org/10.1109/OMN61224.2024.10685279</a>.","ista":"Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. 2024. Portable Raman platform for SERS droplets microfludics. 2024 International Conference on Optical MEMS and Nanophotonics. OMN: Conference on Optical MEMS and Nanophotonics.","short":"S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, S. Abalde-Cela, in:, 2024 International Conference on Optical MEMS and Nanophotonics, IEEE, 2024.","apa":"Quintero, S., Relvas, M., Aranda, M., Nodal, F., Dieguez, L., &#38; Abalde-Cela, S. (2024). Portable Raman platform for SERS droplets microfludics. In <i>2024 International Conference on Optical MEMS and Nanophotonics</i>. San Sebastian, Spain: IEEE. <a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">https://doi.org/10.1109/OMN61224.2024.10685279</a>","ieee":"S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, and S. Abalde-Cela, “Portable Raman platform for SERS droplets microfludics,” in <i>2024 International Conference on Optical MEMS and Nanophotonics</i>, San Sebastian, Spain, 2024."},"title":"Portable Raman platform for SERS droplets microfludics","oa_version":"None","type":"conference","doi":"10.1109/OMN61224.2024.10685279","publisher":"IEEE","publication_identifier":{"eissn":["2160-5041"],"isbn":["9798350384925"],"issn":["2160-5033"]},"scopus_import":"1","department":[{"_id":"GradSch"}],"status":"public","publication_status":"published","day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-10-20T22:02:07Z","article_processing_charge":"No","language":[{"iso":"eng"}],"month":"09","_id":"18450","acknowledgement":"The authors acknowledge the financial support of the project HfPT – Health from Portugal, with the reference n.° C644937233-00000047, co-funded by Component C5 – Capitalisation and Business Innovation under the Portuguese Resilience and Recovery Plan, through the NextGenerationEU Fund.","year":"2024","isi":1,"author":[{"first_name":"Sergio","last_name":"Quintero","full_name":"Quintero, Sergio"},{"first_name":"Maria","last_name":"Relvas","full_name":"Relvas, Maria"},{"full_name":"Aranda, Marta","first_name":"Marta","last_name":"Aranda"},{"full_name":"Nodal, Fernando","last_name":"Nodal","first_name":"Fernando","id":"8ad43d5a-1ffe-11ee-8b67-8176f59de781","orcid":"0009-0006-4119-4376"},{"first_name":"Lorena","last_name":"Dieguez","full_name":"Dieguez, Lorena"},{"full_name":"Abalde-Cela, Sara","first_name":"Sara","last_name":"Abalde-Cela"}],"abstract":[{"text":"In this work we present the engineering of a portable platform for sensing SERS signals in droplets microfluidics. This system comprised not only the read-out platform but also a design for the microfluidic devices optimized to enhanced the obtained SERS signals.","lang":"eng"}],"publication":"2024 International Conference on Optical MEMS and Nanophotonics","date_published":"2024-09-27T00:00:00Z","external_id":{"isi":["001327768000060"]},"conference":{"name":"OMN: Conference on Optical MEMS and Nanophotonics","location":"San Sebastian, Spain","end_date":"2024-08-01","start_date":"2024-07-28"},"OA_type":"closed access","date_updated":"2026-08-12T06:40:33Z","quality_controlled":"1"},{"author":[{"full_name":"Wurtz, Jonathan","last_name":"Wurtz","first_name":"Jonathan"},{"last_name":"Sack","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","full_name":"Sack, Stefan"},{"full_name":"Wang, Sheng-Tao","first_name":"Sheng-Tao","last_name":"Wang"}],"intvolume":"         5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2024-08-14T00:00:00Z","quality_controlled":"1","OA_type":"hybrid","page":"1-14","article_processing_charge":"Yes (in subscription journal)","date_created":"2025-01-27T15:00:44Z","_id":"18923","acknowledgement":"The authors would like to thank Alexander Keesling, Maddie Cain, Nate Gemelke, and Phillip Weinberg for helpful discussions and Danylo Lykov who had early contributions to this work.\r\n10.13039/100000185-Defense Advanced Research Projects Agency Noisy Intermediate-Scale Quantum Devices (Grant Number: W911NF2010021), DARPA Small Business Technology Transfer program (Grant Number: 140D0422C0035).","publisher":"IEEE","doi":"10.1109/tqe.2024.3443660","type":"journal_article","department":[{"_id":"MaSe"}],"publication_status":"published","file":[{"checksum":"19b84e35cba05bde72bfe7e0b54c3e6c","relation":"main_file","date_updated":"2025-01-27T15:03:09Z","success":1,"access_level":"open_access","creator":"dernst","file_size":1753095,"file_id":"18924","content_type":"application/pdf","file_name":"2024_IEEEQuantumComputing_Wurtz.pdf","date_created":"2025-01-27T15:03:09Z"}],"title":"Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms","year":"2024","abstract":[{"lang":"eng","text":"Combinatorial optimization is a challenging problem applicable in a wide range of fields from logistics to finance. Recently, quantum computing has been used to attempt to solve these problems using a range of algorithms, including parameterized quantum circuits, adiabatic protocols, and quantum annealing. These solutions typically have several challenges: 1) there is little to no performance gain over classical methods; 2) not all constraints and objectives may be efficiently encoded in the quantum ansatz; and 3) the solution domain of the objective function may not be the same as the bit strings of measurement outcomes. This work presents “nonnative hybrid algorithms”: a framework to overcome these challenges by integrating quantum and classical resources with a hybrid approach. By designing nonnative quantum variational anosatzes that inherit some but not all problem structure, measurement outcomes from the quantum computer can act as a resource to be used by classical routines to indirectly compute optimal solutions, partially overcoming the challenges of contemporary quantum optimization approaches. These methods are demonstrated using a publicly available neutral-atom quantum computer on two simple problems of Max k-Cut and maximum independent set. We find improvements in solution quality when comparing the hybrid algorithm to its “no quantum” version, a demonstration of a “comparative advantage.”"}],"publication":"IEEE Transactions on Quantum Engineering","das_tickbox":"1","date_updated":"2026-08-12T06:42:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"14","file_date_updated":"2025-01-27T15:03:09Z","language":[{"iso":"eng"}],"article_type":"original","month":"08","has_accepted_license":"1","oa":1,"oa_version":"Published Version","OA_place":"publisher","scopus_import":"1","publication_identifier":{"issn":["2689-1808"]},"status":"public","ddc":["530"],"citation":{"ama":"Wurtz J, Sack S, Wang S-T. Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms. <i>IEEE Transactions on Quantum Engineering</i>. 2024;5:1-14. doi:<a href=\"https://doi.org/10.1109/tqe.2024.3443660\">10.1109/tqe.2024.3443660</a>","mla":"Wurtz, Jonathan, et al. “Solving Nonnative Combinatorial Optimization Problems Using Hybrid Quantum–Classical Algorithms.” <i>IEEE Transactions on Quantum Engineering</i>, vol. 5, IEEE, 2024, pp. 1–14, doi:<a href=\"https://doi.org/10.1109/tqe.2024.3443660\">10.1109/tqe.2024.3443660</a>.","chicago":"Wurtz, Jonathan, Stefan Sack, and Sheng-Tao Wang. “Solving Nonnative Combinatorial Optimization Problems Using Hybrid Quantum–Classical Algorithms.” <i>IEEE Transactions on Quantum Engineering</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/tqe.2024.3443660\">https://doi.org/10.1109/tqe.2024.3443660</a>.","ista":"Wurtz J, Sack S, Wang S-T. 2024. Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms. IEEE Transactions on Quantum Engineering. 5, 1–14.","apa":"Wurtz, J., Sack, S., &#38; Wang, S.-T. (2024). Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms. <i>IEEE Transactions on Quantum Engineering</i>. IEEE. <a href=\"https://doi.org/10.1109/tqe.2024.3443660\">https://doi.org/10.1109/tqe.2024.3443660</a>","ieee":"J. Wurtz, S. Sack, and S.-T. Wang, “Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms,” <i>IEEE Transactions on Quantum Engineering</i>, vol. 5. IEEE, pp. 1–14, 2024.","short":"J. Wurtz, S. Sack, S.-T. Wang, IEEE Transactions on Quantum Engineering 5 (2024) 1–14."},"volume":5},{"title":"When do plant hydraulics matter in terrestrial biosphere modelling?","issue":"1","publication_status":"published","publisher":"Wiley","doi":"10.1111/gcb.17022","type":"journal_article","_id":"22563","article_processing_charge":"No","date_created":"2026-07-27T12:30:24Z","keyword":["Ecosystem recovery","Ecosystem responses","Plant hydraulics","Terrestrial biosphere model","Water stress"],"quality_controlled":"1","OA_type":"hybrid","external_id":{"pmid":["37962234 "]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2024-01-01T00:00:00Z","author":[{"full_name":"Paschalis, Athanasios","first_name":"Athanasios","last_name":"Paschalis"},{"full_name":"De Kauwe, Martin G.","first_name":"Martin G.","last_name":"De Kauwe"},{"first_name":"Manon","last_name":"Sabot","full_name":"Sabot, Manon"},{"first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","full_name":"Fatichi, Simone"}],"intvolume":"        30","volume":30,"citation":{"short":"A. Paschalis, M.G. De Kauwe, M. Sabot, S. Fatichi, Global Change Biology 30 (2024).","ieee":"A. Paschalis, M. G. De Kauwe, M. Sabot, and S. Fatichi, “When do plant hydraulics matter in terrestrial biosphere modelling?,” <i>Global Change Biology</i>, vol. 30, no. 1. Wiley, 2024.","apa":"Paschalis, A., De Kauwe, M. G., Sabot, M., &#38; Fatichi, S. (2024). When do plant hydraulics matter in terrestrial biosphere modelling? <i>Global Change Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/gcb.17022\">https://doi.org/10.1111/gcb.17022</a>","ista":"Paschalis A, De Kauwe MG, Sabot M, Fatichi S. 2024. When do plant hydraulics matter in terrestrial biosphere modelling? Global Change Biology. 30(1), e17022.","chicago":"Paschalis, Athanasios, Martin G. De Kauwe, Manon Sabot, and Simone Fatichi. “When Do Plant Hydraulics Matter in Terrestrial Biosphere Modelling?” <i>Global Change Biology</i>. Wiley, 2024. <a href=\"https://doi.org/10.1111/gcb.17022\">https://doi.org/10.1111/gcb.17022</a>.","ama":"Paschalis A, De Kauwe MG, Sabot M, Fatichi S. When do plant hydraulics matter in terrestrial biosphere modelling? <i>Global Change Biology</i>. 2024;30(1). doi:<a href=\"https://doi.org/10.1111/gcb.17022\">10.1111/gcb.17022</a>","mla":"Paschalis, Athanasios, et al. “When Do Plant Hydraulics Matter in Terrestrial Biosphere Modelling?” <i>Global Change Biology</i>, vol. 30, no. 1, e17022, Wiley, 2024, doi:<a href=\"https://doi.org/10.1111/gcb.17022\">10.1111/gcb.17022</a>."},"pmid":1,"article_number":"e17022","status":"public","publication_identifier":{"issn":["1354-1013"],"eissn":["1365-2486"]},"scopus_import":"1","OA_place":"publisher","main_file_link":[{"url":" https://doi.org/10.1111/gcb.17022","open_access":"1"}],"oa_version":"Published Version","oa":1,"month":"01","extern":"1","language":[{"iso":"eng"}],"article_type":"original","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","das_tickbox":"1","date_updated":"2026-08-12T08:44:53Z","publication":"Global Change Biology","abstract":[{"lang":"eng","text":"The ascent of water from the soil to the leaves of vascular plants, described by the study of plant hydraulics, regulates ecosystem responses to environmental forcing and recovery from stress periods. Several approaches to model plant hydraulics have been proposed. In this study, we introduce four different versions of plant hydraulics representations in the terrestrial biosphere model T&C to understand the significance of plant hydraulics to ecosystem functioning. We tested representations of plant hydraulics, investigating plant water capacitance, and long-term xylem damages following drought. The four models we tested were a combination of representations including or neglecting capacitance and including or neglecting xylem damage legacies. Using the models at six case studies spanning semiarid to tropical ecosystems, we quantify how plant xylem flow, plant water storage and long-term xylem damage can modulate overall water and carbon dynamics across multiple time scales. We show that as drought develops, models with plant hydraulics predict a slower onset of plant water stress, and a diurnal variability of water and carbon fluxes closer to observations. Plant water storage was found to be particularly important for the diurnal dynamics of water and carbon fluxes, with models that include plant water capacitance yielding better results. Models including permanent damage to conducting plant tissues show an additional significant drought legacy effect, limiting plant productivity during the recovery phase following major droughts. However, when considering ecosystem responses to the observed climate variability, plant hydraulic modules alone cannot significantly improve the overall model performance, even though they reproduce more realistic water and carbon dynamics. This opens new avenues for model development, explicitly linking plant hydraulics with additional ecosystem processes, such as plant phenology and improved carbon allocation algorithms."}],"year":"2024"},{"doi":"10.1002/qj.4589","type":"journal_article","publisher":"Wiley","publication_status":"published","issue":"758","title":"Evaluation of 30 urban land surface models in the Urban-PLUMBER project: Phase 1 results","intvolume":"       150","author":[{"full_name":"Lipson, Mathew J.","last_name":"Lipson","first_name":"Mathew J."},{"last_name":"Grimmond","first_name":"Sue","full_name":"Grimmond, Sue"},{"last_name":"Best","first_name":"Martin","full_name":"Best, Martin"},{"last_name":"Abramowitz","first_name":"Gab","full_name":"Abramowitz, Gab"},{"full_name":"Coutts, Andrew","last_name":"Coutts","first_name":"Andrew"},{"last_name":"Tapper","first_name":"Nigel","full_name":"Tapper, Nigel"},{"last_name":"Baik","first_name":"Jong‐Jin","full_name":"Baik, Jong‐Jin"},{"first_name":"Meiring","last_name":"Beyers","full_name":"Beyers, Meiring"},{"first_name":"Lewis","last_name":"Blunn","full_name":"Blunn, Lewis"},{"last_name":"Boussetta","first_name":"Souhail","full_name":"Boussetta, Souhail"},{"first_name":"Elie","last_name":"Bou‐Zeid","full_name":"Bou‐Zeid, Elie"},{"first_name":"Martin G.","last_name":"De Kauwe","full_name":"De Kauwe, Martin G."},{"last_name":"de Munck","first_name":"Cécile","full_name":"de Munck, Cécile"},{"full_name":"Demuzere, Matthias","first_name":"Matthias","last_name":"Demuzere"},{"full_name":"Fatichi, Simone","last_name":"Fatichi","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"},{"first_name":"Krzysztof","last_name":"Fortuniak","full_name":"Fortuniak, Krzysztof"},{"full_name":"Han, Beom‐Soon","last_name":"Han","first_name":"Beom‐Soon"},{"full_name":"Hendry, Margaret A.","last_name":"Hendry","first_name":"Margaret A."},{"full_name":"Kikegawa, Yukihiro","last_name":"Kikegawa","first_name":"Yukihiro"},{"first_name":"Hiroaki","last_name":"Kondo","full_name":"Kondo, Hiroaki"},{"full_name":"Lee, Doo‐Il","last_name":"Lee","first_name":"Doo‐Il"},{"full_name":"Lee, Sang‐Hyun","first_name":"Sang‐Hyun","last_name":"Lee"},{"full_name":"Lemonsu, Aude","first_name":"Aude","last_name":"Lemonsu"},{"first_name":"Tiago","last_name":"Machado","full_name":"Machado, Tiago"},{"first_name":"Gabriele","last_name":"Manoli","full_name":"Manoli, Gabriele"},{"last_name":"Martilli","first_name":"Alberto","full_name":"Martilli, Alberto"},{"last_name":"Masson","first_name":"Valéry","full_name":"Masson, Valéry"},{"full_name":"McNorton, Joe","last_name":"McNorton","first_name":"Joe"},{"full_name":"Meili, Naika","last_name":"Meili","first_name":"Naika"},{"full_name":"Meyer, David","first_name":"David","last_name":"Meyer"},{"first_name":"Kerry A.","last_name":"Nice","full_name":"Nice, Kerry A."},{"first_name":"Keith W.","last_name":"Oleson","full_name":"Oleson, Keith W."},{"first_name":"Seung‐Bu","last_name":"Park","full_name":"Park, Seung‐Bu"},{"full_name":"Roth, Michael","first_name":"Michael","last_name":"Roth"},{"full_name":"Schoetter, Robert","first_name":"Robert","last_name":"Schoetter"},{"first_name":"Andrés","last_name":"Simón‐Moral","full_name":"Simón‐Moral, Andrés"},{"full_name":"Steeneveld, Gert‐Jan","first_name":"Gert‐Jan","last_name":"Steeneveld"},{"full_name":"Sun, Ting","first_name":"Ting","last_name":"Sun"},{"first_name":"Yuya","last_name":"Takane","full_name":"Takane, Yuya"},{"last_name":"Thatcher","first_name":"Marcus","full_name":"Thatcher, Marcus"},{"first_name":"Aristofanis","last_name":"Tsiringakis","full_name":"Tsiringakis, Aristofanis"},{"last_name":"Varentsov","first_name":"Mikhail","full_name":"Varentsov, Mikhail"},{"full_name":"Wang, Chenghao","first_name":"Chenghao","last_name":"Wang"},{"first_name":"Zhi‐Hua","last_name":"Wang","full_name":"Wang, Zhi‐Hua"},{"full_name":"Pitman, Andy J.","first_name":"Andy J.","last_name":"Pitman"}],"date_published":"2024-01-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"OA_type":"hybrid","quality_controlled":"1","page":"126-169","keyword":["Benchmark","Energy balance","Intercomparison","Model evaluation","Urban climate","Urban meteorology"],"date_created":"2026-07-27T12:30:25Z","article_processing_charge":"No","_id":"22583","oa":1,"oa_version":"Published Version","OA_place":"publisher","main_file_link":[{"url":"https://doi.org/10.1002/qj.4589","open_access":"1"}],"publication_identifier":{"eissn":["1477-870X"],"issn":["0035-9009"]},"scopus_import":"1","status":"public","citation":{"short":"M.J. Lipson, S. Grimmond, M. Best, G. Abramowitz, A. Coutts, N. Tapper, J. Baik, M. Beyers, L. Blunn, S. Boussetta, E. Bou‐Zeid, M.G. De Kauwe, C. de Munck, M. Demuzere, S. Fatichi, K. Fortuniak, B. Han, M.A. Hendry, Y. Kikegawa, H. Kondo, D. Lee, S. Lee, A. Lemonsu, T. Machado, G. Manoli, A. Martilli, V. Masson, J. McNorton, N. Meili, D. Meyer, K.A. Nice, K.W. Oleson, S. Park, M. Roth, R. Schoetter, A. Simón‐Moral, G. Steeneveld, T. Sun, Y. Takane, M. Thatcher, A. Tsiringakis, M. Varentsov, C. Wang, Z. Wang, A.J. Pitman, Quarterly Journal of the Royal Meteorological Society 150 (2024) 126–169.","ieee":"M. J. Lipson <i>et al.</i>, “Evaluation of 30 urban land surface models in the Urban-PLUMBER project: Phase 1 results,” <i>Quarterly Journal of the Royal Meteorological Society</i>, vol. 150, no. 758. Wiley, pp. 126–169, 2024.","apa":"Lipson, M. J., Grimmond, S., Best, M., Abramowitz, G., Coutts, A., Tapper, N., … Pitman, A. J. (2024). Evaluation of 30 urban land surface models in the Urban-PLUMBER project: Phase 1 results. <i>Quarterly Journal of the Royal Meteorological Society</i>. Wiley. <a href=\"https://doi.org/10.1002/qj.4589\">https://doi.org/10.1002/qj.4589</a>","ista":"Lipson MJ, Grimmond S, Best M, Abramowitz G, Coutts A, Tapper N, Baik J, Beyers M, Blunn L, Boussetta S, Bou‐Zeid E, De Kauwe MG, de Munck C, Demuzere M, Fatichi S, Fortuniak K, Han B, Hendry MA, Kikegawa Y, Kondo H, Lee D, Lee S, Lemonsu A, Machado T, Manoli G, Martilli A, Masson V, McNorton J, Meili N, Meyer D, Nice KA, Oleson KW, Park S, Roth M, Schoetter R, Simón‐Moral A, Steeneveld G, Sun T, Takane Y, Thatcher M, Tsiringakis A, Varentsov M, Wang C, Wang Z, Pitman AJ. 2024. Evaluation of 30 urban land surface models in the Urban-PLUMBER project: Phase 1 results. Quarterly Journal of the Royal Meteorological Society. 150(758), 126–169.","chicago":"Lipson, Mathew J., Sue Grimmond, Martin Best, Gab Abramowitz, Andrew Coutts, Nigel Tapper, Jong‐Jin Baik, et al. “Evaluation of 30 Urban Land Surface Models in the Urban-PLUMBER Project: Phase 1 Results.” <i>Quarterly Journal of the Royal Meteorological Society</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/qj.4589\">https://doi.org/10.1002/qj.4589</a>.","ama":"Lipson MJ, Grimmond S, Best M, et al. Evaluation of 30 urban land surface models in the Urban-PLUMBER project: Phase 1 results. <i>Quarterly Journal of the Royal Meteorological Society</i>. 2024;150(758):126-169. doi:<a href=\"https://doi.org/10.1002/qj.4589\">10.1002/qj.4589</a>","mla":"Lipson, Mathew J., et al. “Evaluation of 30 Urban Land Surface Models in the Urban-PLUMBER Project: Phase 1 Results.” <i>Quarterly Journal of the Royal Meteorological Society</i>, vol. 150, no. 758, Wiley, 2024, pp. 126–69, doi:<a href=\"https://doi.org/10.1002/qj.4589\">10.1002/qj.4589</a>."},"volume":150,"year":"2024","abstract":[{"lang":"eng","text":"Accurately predicting weather and climate in cities is critical for safeguarding human health and strengthening urban resilience. Multimodel evaluations can lead to model improvements; however, there have been no major intercomparisons of urban-focussed land surface models in over a decade. Here, in Phase 1 of the Urban-PLUMBER project, we evaluate the ability of 30 land surface models to simulate surface energy fluxes critical to atmospheric meteorological and air quality simulations. We establish minimum and upper performance expectations for participating models using simple information-limited models as benchmarks. Compared with the last major model intercomparison at the same site, we find broad improvement in the current cohort's predictions of short-wave radiation, sensible and latent heat fluxes, but little or no improvement in long-wave radiation and momentum fluxes. Models with a simple urban representation (e.g., ‘slab’ schemes) generally perform well, particularly when combined with sophisticated hydrological/vegetation models. Some mid-complexity models (e.g., ‘canyon’ schemes) also perform well, indicating efforts to integrate vegetation and hydrology processes have paid dividends. The most complex models that resolve three-dimensional interactions between buildings in general did not perform as well as other categories. However, these models also tended to have the simplest representations of hydrology and vegetation. Models without any urban representation (i.e., vegetation-only land surface models) performed poorly for latent heat fluxes, and reasonably for other energy fluxes at this suburban site. Our analysis identified widespread human errors in initial submissions that substantially affected model performances. Although significant efforts are applied to correct these errors, we conclude that human factors are likely to influence results in this (or any) model intercomparison, particularly where participating scientists have varying experience and first languages. These initial results are for one suburban site, and future phases of Urban-PLUMBER will evaluate models across 20 sites in different urban and regional climate zones."}],"publication":"Quarterly Journal of the Royal Meteorological Society","date_updated":"2026-08-12T08:53:18Z","das_tickbox":"1","day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","language":[{"iso":"eng"}],"extern":"1","month":"01"},{"ddc":["510"],"ec_funded":1,"volume":41,"citation":{"ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. <i>Annales de l’Institut Henri Poincaré C</i>. 2024;41(5):1117-1178. doi:<a href=\"https://doi.org/10.4171/AIHPC/109\">10.4171/AIHPC/109</a>","mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” <i>Annales de l’Institut Henri Poincaré C</i>, vol. 41, no. 5, EMS Press, 2024, pp. 1117–78, doi:<a href=\"https://doi.org/10.4171/AIHPC/109\">10.4171/AIHPC/109</a>.","chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press, 2024. <a href=\"https://doi.org/10.4171/AIHPC/109\">https://doi.org/10.4171/AIHPC/109</a>.","ista":"Fischer JL, Marveggio A. 2024. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincaré C. 41(5), 1117–1178.","short":"J.L. Fischer, A. Marveggio, Annales de l’Institut Henri Poincaré C 41 (2024) 1117–1178.","apa":"Fischer, J. L., &#38; Marveggio, A. (2024). Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press. <a href=\"https://doi.org/10.4171/AIHPC/109\">https://doi.org/10.4171/AIHPC/109</a>","ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow,” <i>Annales de l’Institut Henri Poincaré C</i>, vol. 41, no. 5. EMS Press, pp. 1117–1178, 2024."},"oa":1,"has_accepted_license":"1","oa_version":"Published Version","status":"public","scopus_import":"1","publication_identifier":{"eissn":["1873-1430"],"issn":["0294-1449"]},"article_type":"original","language":[{"iso":"eng"}],"day":"24","file_date_updated":"2024-09-09T07:46:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","abstract":[{"lang":"eng","text":"Phase-field models such as the Allen–Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen–Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow. In the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: as long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen–Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε \r\n1/2\r\n ). Our approach is based on the gradient-flow structure of the Allen–Cahn equation and its limiting motion: building on the recent concept of “gradient-flow calibrations” for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen–Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen–Cahn operator or additional convergence hypotheses for the energy at positive times."}],"year":"2024","isi":1,"date_updated":"2026-08-12T09:15:49Z","publication":"Annales de l'Institut Henri Poincaré C","issue":"5","file":[{"success":1,"relation":"main_file","checksum":"b5ad02d9abd5b4701269cd1ad0a1cc8f","date_updated":"2024-09-09T07:46:42Z","file_name":"2024_AnnInstHPoincare_Fischer.pdf","content_type":"application/pdf","date_created":"2024-09-09T07:46:42Z","creator":"dernst","file_size":1348896,"access_level":"open_access","file_id":"17923"}],"project":[{"call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"title":"Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow","doi":"10.4171/AIHPC/109","type":"journal_article","publisher":"EMS Press","publication_status":"published","department":[{"_id":"JuFi"}],"date_created":"2024-09-01T22:01:09Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"14597"}]},"article_processing_charge":"Yes","corr_author":"1","page":"1117-1178","acknowledgement":"The authors thank Sebastian Hensel for useful and helpful commentson the first draft of this work.\r\nThis project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement no. 948819.","_id":"17481","intvolume":"        41","author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marveggio, Alice","last_name":"Marveggio","id":"25647992-AA84-11E9-9D75-8427E6697425","first_name":"Alice"}],"quality_controlled":"1","date_published":"2024-01-24T00:00:00Z","external_id":{"isi":["001293853900003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"author":[{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","last_name":"Schauer"},{"first_name":"Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"intvolume":"       151","quality_controlled":"1","external_id":{"isi":["001170580200001"],"pmid":["38372390"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2024-02-01T00:00:00Z","corr_author":"1","article_processing_charge":"Yes (via OA deal)","date_created":"2024-03-03T23:00:50Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"14926"}]},"page":"1-18","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","_id":"15048","publisher":"Company of Biologists","type":"journal_article","doi":"10.1242/dev.202316","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"Bio"}],"issue":"4","file":[{"file_id":"15050","access_level":"open_access","file_size":14839986,"creator":"dernst","date_created":"2024-03-04T07:24:43Z","content_type":"application/pdf","file_name":"2024_Development_Schauer.pdf","date_updated":"2024-03-04T07:24:43Z","checksum":"6961ea10012bf0d266681f9628bb8f13","relation":"main_file","success":1}],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","abstract":[{"text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.","lang":"eng"}],"isi":1,"year":"2024","date_updated":"2026-08-12T10:00:14Z","publication":"Development","language":[{"iso":"eng"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-03-04T07:24:43Z","day":"01","month":"02","has_accepted_license":"1","oa_version":"Published Version","oa":1,"status":"public","scopus_import":"1","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"pmid":1,"ddc":["570"],"volume":151,"ec_funded":1,"citation":{"ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. Company of Biologists, pp. 1–18, 2024.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18."}},{"has_accepted_license":"1","oa":1,"oa_version":"Published Version","scopus_import":"1","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"status":"public","article_number":"dev202891","ddc":["599"],"pmid":1,"citation":{"chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>.","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>, vol. 151, no. 15, dev202891, Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>.","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. <i>Development</i>. 2024;151(15). doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>","apa":"Cecalev, D., Vicoso, B., &#38; Galupa, R. (2024). Compensation of gene dosage on the mammalian X. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>","ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” <i>Development</i>, vol. 151, no. 15. Company of Biologists, 2024.","short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891."},"volume":151,"year":"2024","isi":1,"abstract":[{"lang":"eng","text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species."}],"publication":"Development","date_updated":"2026-08-12T10:01:13Z","day":"14","file_date_updated":"2024-08-28T10:32:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","language":[{"iso":"eng"}],"month":"08","doi":"10.1242/dev.202891","type":"journal_article","publisher":"Company of Biologists","department":[{"_id":"BeVi"}],"publication_status":"published","file":[{"access_level":"open_access","creator":"cchlebak","file_size":2085135,"file_id":"17464","content_type":"application/pdf","file_name":"2024_Development_Cecalev.pdf","date_created":"2024-08-28T10:32:16Z","checksum":"5e428bda0440d3f957c694b315a8f2a9","relation":"main_file","date_updated":"2024-08-28T10:32:16Z","success":1}],"issue":"15","title":"Compensation of gene dosage on the mammalian X","intvolume":"       151","author":[{"full_name":"Cecalev, Daniela","last_name":"Cecalev","first_name":"Daniela"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"},{"full_name":"Galupa, Rafael","first_name":"Rafael","last_name":"Galupa"}],"date_published":"2024-08-14T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"pmid":["39140247"],"isi":["001292608800003"]},"quality_controlled":"1","date_created":"2024-08-25T22:01:07Z","article_processing_charge":"Yes (in subscription journal)","_id":"17458","acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release."},{"ddc":["570"],"file":[{"date_updated":"2024-02-02T14:40:31Z","relation":"main_file","checksum":"df7f358ae19a176cf710c0a802ce31b1","success":1,"file_id":"14927","file_size":736,"creator":"rhauschild","access_level":"open_access","date_created":"2024-02-02T14:40:31Z","file_name":"README.md","content_type":"application/octet-stream"},{"date_updated":"2024-02-02T14:40:31Z","relation":"main_file","checksum":"10194cc11619eccd8f4b24472e465b7f","success":1,"file_id":"14928","creator":"rhauschild","file_size":3543,"access_level":"open_access","date_created":"2024-02-02T14:40:31Z","file_name":"Supplementary_file_1.zip","content_type":"application/x-zip-compressed"}],"citation":{"mla":"Hauschild, Robert. <i>Matlab Script for Analysis of Clone Dispersal</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>.","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of Science and Technology Austria, 2024.","short":"R. Hauschild, (2024)."},"title":"Matlab script for analysis of clone dispersal","license":"https://opensource.org/licenses/MIT","publisher":"Institute of Science and Technology Austria","type":"software","has_accepted_license":"1","doi":"10.15479/AT:ISTA:14926","oa":1,"status":"public","department":[{"_id":"Bio"}],"corr_author":"1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15048"}]},"date_created":"2024-02-02T14:42:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"02","file_date_updated":"2024-02-02T14:40:31Z","_id":"14926","month":"02","author":[{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert"}],"year":"2024","date_updated":"2026-08-12T10:00:13Z","tmp":{"legal_code_url":"https://opensource.org/licenses/MIT","name":"The MIT License","short":"MIT"},"date_published":"2024-02-02T00:00:00Z"},{"_id":"22234","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","article_processing_charge":"No","corr_author":"1","related_material":{"record":[{"id":"20249","status":"public","relation":"used_in_publication"}]},"date_created":"2026-07-02T10:38:53Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2024-07-22T00:00:00Z","date_updated":"2026-08-12T12:15:33Z","OA_type":"green","year":"2024","author":[{"full_name":"Browning, Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"},{"full_name":"Sutherland, Andrew","first_name":"Andrew","last_name":"Sutherland"}],"abstract":[{"text":"Lists of nontrivial integral points on some (families of) cubic surfaces. (2024-07-18)","lang":"eng"}],"title":"Data and code for: Integral points on cubic surfaces: heuristics and numerics","citation":{"ista":"Browning TD, Sutherland A. 2024. Data and code for: Integral points on cubic surfaces: heuristics and numerics, Göttingen Research Online Data, <a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>.","ieee":"T. D. Browning and A. Sutherland, “Data and code for: Integral points on cubic surfaces: heuristics and numerics.” Göttingen Research Online Data, 2024.","apa":"Browning, T. D., &#38; Sutherland, A. (2024). Data and code for: Integral points on cubic surfaces: heuristics and numerics. Göttingen Research Online Data. <a href=\"https://doi.org/10.25625/4FLFH8\">https://doi.org/10.25625/4FLFH8</a>","short":"T.D. Browning, A. Sutherland, (2024).","mla":"Browning, Timothy D., and Andrew Sutherland. <i>Data and Code for: Integral Points on Cubic Surfaces: Heuristics and Numerics</i>. Göttingen Research Online Data, 2024, doi:<a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>.","ama":"Browning TD, Sutherland A. Data and code for: Integral points on cubic surfaces: heuristics and numerics. 2024. doi:<a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>","chicago":"Browning, Timothy D, and Andrew Sutherland. “Data and Code for: Integral Points on Cubic Surfaces: Heuristics and Numerics.” Göttingen Research Online Data, 2024. <a href=\"https://doi.org/10.25625/4FLFH8\">https://doi.org/10.25625/4FLFH8</a>."},"ddc":["500"],"contributor":[{"first_name":"Florian Alexander","orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425","last_name":"Wilsch"}],"department":[{"_id":"TiBr"}],"status":"public","publisher":"Göttingen Research Online Data","type":"research_data_reference","oa_version":"Published Version","has_accepted_license":"1","oa":1,"doi":"10.25625/4FLFH8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25625/4FLFH8"}],"OA_place":"repository"},{"title":"LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening","project":[{"name":"LGI1 antibody-induced pathophysiology in synapses","_id":"05970B30-7A3F-11EA-A408-12923DDC885E","grant_number":"I04638"}],"issue":"5","file":[{"date_created":"2025-01-09T13:42:42Z","file_name":"2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf","content_type":"application/pdf","file_id":"18815","file_size":855818,"creator":"dernst","access_level":"open_access","success":1,"date_updated":"2025-01-09T13:42:42Z","relation":"main_file","checksum":"1e6d1230e0387f72752e3268f5330c9e"}],"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Wolters Kluwer","doi":"10.1212/NXI.0000000000200284","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"acknowledgement":"The authors thank Claudia Sommer for expert technical assistance, the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. ","_id":"17457","article_processing_charge":"Yes","date_created":"2024-08-25T22:01:07Z","related_material":{"link":[{"url":"https://doi.org/10.1101/2023.10.04.560631","relation":"earlier_version"}]},"page":"e200284","quality_controlled":"1","OA_type":"gold","external_id":{"pmid":["39141878"],"isi":["001291908600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2024-09-01T00:00:00Z","author":[{"first_name":"Andreas","last_name":"Ritzau-Jost","full_name":"Ritzau-Jost, Andreas"},{"last_name":"Gsell","first_name":"Felix","full_name":"Gsell, Felix"},{"first_name":"Josefine","last_name":"Sell","full_name":"Sell, Josefine"},{"full_name":"Sachs, Stefan","last_name":"Sachs","first_name":"Stefan"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","first_name":"Jacqueline-Claire"},{"full_name":"Kirmann, Toni","last_name":"Kirmann","first_name":"Toni"},{"first_name":"Sebastian","last_name":"Maaß","full_name":"Maaß, Sebastian"},{"full_name":"Irani, Sarosh R.","first_name":"Sarosh R.","last_name":"Irani"},{"full_name":"Werner, Christian","last_name":"Werner","first_name":"Christian"},{"full_name":"Geis, Christian","first_name":"Christian","last_name":"Geis"},{"full_name":"Sauer, Markus","last_name":"Sauer","first_name":"Markus"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"first_name":"Stefan","last_name":"Hallermann","full_name":"Hallermann, Stefan"}],"intvolume":"        11","volume":11,"citation":{"ista":"Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology &#38; Neuroinflammation. 11(5), e200284.","ieee":"A. Ritzau-Jost <i>et al.</i>, “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024.","apa":"Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C., Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>","short":"A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber, T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S. Hallermann, Neurology, Neuroimmunology &#38; Neuroinflammation 11 (2024) e200284.","mla":"Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>.","ama":"Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. 2024;11(5):e200284. doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>","chicago":"Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer, 2024. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>."},"pmid":1,"ddc":["570"],"DOAJ_listed":"1","status":"public","publication_identifier":{"eissn":["2332-7812"]},"scopus_import":"1","OA_place":"publisher","oa_version":"Published Version","has_accepted_license":"1","oa":1,"month":"09","language":[{"iso":"eng"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-01-09T13:42:42Z","day":"01","date_updated":"2026-08-12T14:17:59Z","publication":"Neurology, Neuroimmunology & Neuroinflammation","abstract":[{"text":"Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1) cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate\r\nautoantibody-induced synaptic strengthening.","lang":"eng"}],"isi":1,"year":"2024"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.48550/arXiv.2403.06833","type":"preprint","publication_status":"submitted","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"file":[{"creator":"ezverev","file_size":530972,"access_level":"open_access","file_id":"19064","file_name":"2403.06833v3.pdf","content_type":"application/pdf","date_created":"2025-02-20T10:11:45Z","relation":"main_file","checksum":"35eb43968684b87be59144603ef10af0","date_updated":"2025-02-20T10:11:45Z","success":1}],"title":"Can LLMs separate instructions from data? And what do we even mean by that?","author":[{"full_name":"Zverev, Egor","last_name":"Zverev","id":"05162b19-1340-11ed-8f02-fa94e0e8c3bc","first_name":"Egor"},{"full_name":"Abdelnabi, Sahar","last_name":"Abdelnabi","first_name":"Sahar"},{"last_name":"Tabesh","first_name":"Soroush","orcid":"0009-0003-4119-6281","id":"06000900-6068-11ef-8d61-c2472ef2e752","full_name":"Tabesh, Soroush"},{"last_name":"Fritz","first_name":"Mario","full_name":"Fritz, Mario"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"green","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"arxiv":["2403.06833"]},"date_published":"2024-03-01T00:00:00Z","article_processing_charge":"No","corr_author":"1","date_created":"2025-02-20T10:13:42Z","related_material":{"link":[{"url":" https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed","relation":"software"}]},"acknowledgement":"The authors would like to sincerely thank Juan Rocamonde for valuable feedback to our manuscript. We acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We thank Dan Alistarh for providing us with computational resources. This work was partially funded by the German Federal Ministry of Education and Research (BMBF) under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and Safe AI funded by the European Union under grant agreement No. 101070617. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or European Commission. Neither the European Union nor the European Commission can be held responsible for them.","_id":"19063","arxiv":1,"OA_place":"repository","has_accepted_license":"1","oa":1,"oa_version":"Preprint","article_number":"2403.06833","status":"public","ddc":["000"],"citation":{"chicago":"Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.06833\">https://doi.org/10.48550/arXiv.2403.06833</a>.","mla":"Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” <i>ArXiv</i>, 2403.06833, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>.","ama":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>","apa":"Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., &#38; Lampert, C. (n.d.). Can LLMs separate instructions from data? And what do we even mean by that? <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.06833\">https://doi.org/10.48550/arXiv.2403.06833</a>","ieee":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate instructions from data? And what do we even mean by that?,” <i>arXiv</i>. .","short":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.).","ista":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv, 2403.06833."},"abstract":[{"lang":"eng","text":"Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n"}],"year":"2024","date_updated":"2026-08-13T07:26:54Z","publication":"arXiv","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","file_date_updated":"2025-02-20T10:11:45Z","month":"03"},{"oa_version":"Published Version","has_accepted_license":"1","oa":1,"OA_place":"publisher","scopus_import":"1","publication_identifier":{"issn":["2699-0016"]},"status":"public","ddc":["530"],"pmid":1,"citation":{"ama":"Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. 2024;5(1):33-49. doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>","mla":"Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>, vol. 5, no. 1, Copernicus Publications, 2024, pp. 33–49, doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>.","chicago":"Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>. Copernicus Publications, 2024. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>.","ista":"Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. 5(1), 33–49.","short":"F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda, Magnetic Resonance 5 (2024) 33–49.","apa":"Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C., &#38; Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>","ieee":"F. Napoli <i>et al.</i>, “Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications, pp. 33–49, 2024."},"volume":5,"APC_amount":"1530 EUR","year":"2024","abstract":[{"text":"Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has become a main technique in NMR-based structural biology. In standard deuteration protocols that rely on D2O-based culture media, non-exchangeable amide sites remain deuterated, making these sites unobservable. Here we demonstrate that proteins produced with a H2O-based culture medium doped with deuterated cell lysate allow scientists to overcome this “reprotonation bottleneck” while retaining a high level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence lifetimes of several proteins prepared with this labeling pattern over a range of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling approach are comparable to those of perdeuterated proteins and better than those of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range, many previously unobserved amides become visible. We report how to prepare the deuterated cell lysate for our approach from fractions of perdeuterated cultures which are usually discarded, and we show that such media can be used identically to commercial media. The residual protonation of Hα sites allows for well-resolved Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments.","lang":"eng"}],"publication":"Magnetic Resonance","date_updated":"2025-07-17T08:12:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"19","file_date_updated":"2024-05-22T07:01:15Z","language":[{"iso":"eng"}],"article_type":"original","month":"04","publisher":"Copernicus Publications","acknowledged_ssus":[{"_id":"NMR"}],"type":"journal_article","doi":"10.5194/mr-5-33-2024","department":[{"_id":"PaSc"}],"publication_status":"published","file":[{"date_created":"2024-05-22T07:01:15Z","file_name":"2024_MagneticResonance_Napoli.pdf","content_type":"application/pdf","file_id":"15413","file_size":6657865,"creator":"dernst","access_level":"open_access","success":1,"date_updated":"2024-05-22T07:01:15Z","relation":"main_file","checksum":"80ea50114e428461ca9530d3bd5d89e4"}],"issue":"1","project":[{"name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"title":"Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck","author":[{"full_name":"Napoli, Federico","first_name":"Federico","orcid":"0000-0002-9043-136X","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","last_name":"Napoli"},{"last_name":"Guan","first_name":"Jia-Ying","full_name":"Guan, Jia-Ying"},{"last_name":"Arnaud","first_name":"Charles-Adrien","full_name":"Arnaud, Charles-Adrien"},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"full_name":"Fraga, Hugo","last_name":"Fraga","first_name":"Hugo"},{"full_name":"Breyton, Cécile","last_name":"Breyton","first_name":"Cécile"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda"}],"intvolume":"         5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"pmid":["40384771"]},"date_published":"2024-04-19T00:00:00Z","quality_controlled":"1","OA_type":"gold","page":"33-49","article_processing_charge":"Yes","corr_author":"1","date_created":"2024-05-16T15:02:43Z","_id":"15401","acknowledgement":"We thank Dominique Madern (IBS Grenoble) for providing the plasmid for MalDH and feedback on the article, Alicia Vallet for excellent support at the Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of Max Perutz Labs for the mass spectrometry analysis using the instruments of the Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu (Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University Dortmund) for sharing a paper draft describing a similar study. This work was supported by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis (Lyon) and the reviewers for constructive input.\r\nThis research has been supported by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien Arnaud was funded by GRAL."},{"degree_awarded":"PhD","OA_place":"publisher","oa_version":"Published Version","oa":1,"has_accepted_license":"1","status":"public","publication_identifier":{"issn":["2663-337X"]},"ddc":["514","500","516"],"ec_funded":1,"citation":{"apa":"Cultrera di Montesano, S. (2024). <i>Persistence and Morse theory for discrete geometric structures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>.","mla":"Cultrera di Montesano, Sebastiano. <i>Persistence and Morse Theory for Discrete Geometric Structures</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>.","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>"},"abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"year":"2024","date_updated":"2026-08-13T09:41:57Z","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner"}],"language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"day":"08","file_date_updated":"2024-03-14T14:14:35Z","month":"03","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:15094","type":"dissertation","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"file":[{"success":1,"relation":"main_file","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","date_updated":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","content_type":"application/pdf","date_created":"2024-03-14T08:55:07Z","creator":"scultrer","file_size":4106872,"access_level":"open_access","file_id":"15112"},{"date_updated":"2024-03-14T14:14:35Z","checksum":"bcbd213490f5a7e68855a092bbce93f1","relation":"source_file","date_created":"2024-03-14T08:56:24Z","content_type":"application/zip","file_name":"Thesis (1).zip","file_id":"15113","access_level":"closed","file_size":4746234,"creator":"scultrer"}],"title":"Persistence and Morse theory for discrete geometric structures","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"name":"Mathematics, Computer Science","call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Persistent Homology, Algorithms and Stochastic Geometry"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"author":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano"}],"tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"date_published":"2024-03-08T00:00:00Z","corr_author":"1","article_processing_charge":"No","related_material":{"record":[{"id":"15091","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"15090"},{"id":"15093","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"13182"},{"id":"11658","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11660"}]},"date_created":"2024-03-08T15:28:10Z","page":"108","_id":"15094"}]