[{"quality_controlled":"1","citation":{"mla":"Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” <i>Forum of Mathematics, Sigma</i>, vol. 11, e66, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/fms.2023.65\">10.1017/fms.2023.65</a>.","ista":"Mauri M, Shinder E. 2023. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 11, e66.","chicago":"Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/fms.2023.65\">https://doi.org/10.1017/fms.2023.65</a>.","ama":"Mauri M, Shinder E. Homological Bondal-Orlov localization conjecture for rational singularities. <i>Forum of Mathematics, Sigma</i>. 2023;11. doi:<a href=\"https://doi.org/10.1017/fms.2023.65\">10.1017/fms.2023.65</a>","ieee":"M. Mauri and E. Shinder, “Homological Bondal-Orlov localization conjecture for rational singularities,” <i>Forum of Mathematics, Sigma</i>, vol. 11. Cambridge University Press, 2023.","apa":"Mauri, M., &#38; Shinder, E. (2023). Homological Bondal-Orlov localization conjecture for rational singularities. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2023.65\">https://doi.org/10.1017/fms.2023.65</a>","short":"M. Mauri, E. Shinder, Forum of Mathematics, Sigma 11 (2023)."},"abstract":[{"lang":"eng","text":"Given a resolution of rational singularities  π:X~→X  over a field of characteristic zero, we use a Hodge-theoretic argument to prove that the image of the functor  Rπ∗:Db(X~)→Db(X)\r\n  between bounded derived categories of coherent sheaves generates  Db(X)\r\n  as a triangulated category. This gives a weak version of the Bondal–Orlov localization conjecture [BO02], answering a question from [PS21]. The same result is established more generally for proper (not necessarily birational) morphisms  π:X~→X , with  X~\r\n  smooth, satisfying  Rπ∗(OX~)=OX ."}],"type":"journal_article","publisher":"Cambridge University Press","corr_author":"1","department":[{"_id":"TaHa"}],"volume":11,"external_id":{"isi":["001041926700001"],"arxiv":["2212.06786"]},"date_created":"2023-08-27T22:01:16Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","scopus_import":"1","month":"08","_id":"14239","year":"2023","acknowledgement":"We thank Agnieszka Bodzenta-Skibińska, Paolo Cascini, Wahei Hara, Sándor Kovács, Alexander Kuznetsov, Mircea Musta  ă, Nebojsa Pavic, Pavel Sechin, and Michael Wemyss for discussions and e-mail correspondence. We also thank the anonymous referee for the helpful comments. M.M. was supported by the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 101034413. E.S. was partially supported by the EPSRC grant EP/T019379/1 “Derived categories and algebraic K-theory of singularities”, and by the ERC Synergy grant “Modern Aspects of Geometry: Categories, Cycles and Cohomology of Hyperkähler Varieties.”\r\n\r\n","article_type":"original","publication_identifier":{"eissn":["2050-5094"]},"ec_funded":1,"article_number":"e66","date_published":"2023-08-03T00:00:00Z","intvolume":"        11","oa":1,"file":[{"access_level":"open_access","date_created":"2023-09-05T06:43:11Z","file_name":"2023_ForumMathematics_Mauri.pdf","success":1,"creator":"dernst","file_size":280865,"checksum":"c36241750cc5cb06890aec0ecdfee626","content_type":"application/pdf","relation":"main_file","date_updated":"2023-09-05T06:43:11Z","file_id":"14266"}],"doi":"10.1017/fms.2023.65","day":"03","ddc":["510"],"project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"arxiv":1,"publication":"Forum of Mathematics, Sigma","oa_version":"Published Version","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2023-09-05T06:43:11Z","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:54:52Z","author":[{"first_name":"Mirko","last_name":"Mauri","full_name":"Mauri, Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130"},{"last_name":"Shinder","full_name":"Shinder, Evgeny","first_name":"Evgeny"}],"title":"Homological Bondal-Orlov localization conjecture for rational singularities"},{"type":"journal_article","abstract":[{"lang":"eng","text":"This paper introduces a novel method for simulating large bodies of water as a height field. At the start of each time step, we partition the waves into a bulk flow (which approximately satisfies the assumptions of the shallow water equations) and surface waves (which approximately satisfy the assumptions of Airy wave theory). We then solve the two wave regimes separately using appropriate state-of-the-art techniques, and re-combine the resulting wave velocities at the end of each step. This strategy leads to the first heightfield wave model capable of simulating complex interactions between both deep and shallow water effects, like the waves from a boat wake sloshing up onto a beach, or a dam break producing wave interference patterns and eddies. We also analyze the numerical dispersion created by our method and derive an exact correction factor for waves at a constant water depth, giving us a numerically perfect re-creation of theoretical water wave dispersion patterns."}],"citation":{"short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023).","mla":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 4, 83, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3592098\">10.1145/3592098</a>.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3592098\">https://doi.org/10.1145/3592098</a>.","ista":"Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 42(4), 83.","ama":"Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive surface waves. <i>ACM Transactions on Graphics</i>. 2023;42(4). doi:<a href=\"https://doi.org/10.1145/3592098\">10.1145/3592098</a>","ieee":"S. Jeschke and C. Wojtan, “Generalizing shallow water simulations with dispersive surface waves,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 4. Association for Computing Machinery, 2023.","apa":"Jeschke, S., &#38; Wojtan, C. (2023). Generalizing shallow water simulations with dispersive surface waves. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3592098\">https://doi.org/10.1145/3592098</a>"},"quality_controlled":"1","corr_author":"1","publisher":"Association for Computing Machinery","volume":42,"department":[{"_id":"ChWo"}],"external_id":{"isi":["001044671300049"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2023-08-27T22:01:17Z","month":"08","issue":"4","scopus_import":"1","_id":"14240","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"83","article_type":"original","year":"2023","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"acknowledgement":"We thank Georg Sperl for helping with early research for this paper, Mickael Ly and Yi-Lu Chen for proofreading, and members of the ISTA Visual Computing Group for general feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).\r\nThe motorboat and sailboat were modeled by Sergei and the palmtrees by YadroGames. The environment map was created by Emil Persson.","doi":"10.1145/3592098","day":"01","file":[{"file_id":"14704","date_updated":"2023-12-21T12:26:40Z","relation":"main_file","checksum":"1d178bb2f8011d9f5aedda6427e18c7a","content_type":"video/mp4","file_size":511572575,"creator":"sjeschke","file_name":"PaperVideo_final.mp4","success":1,"date_created":"2023-12-21T12:26:40Z","access_level":"open_access"},{"access_level":"open_access","success":1,"date_created":"2024-01-02T09:34:27Z","file_name":"2023_ACMToG_Jeschke.pdf","file_size":7469177,"creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"a49b2e744d5cd1276bb8b2e0ce6dc638","file_id":"14725","date_updated":"2024-01-02T09:34:27Z"}],"oa":1,"intvolume":"        42","date_published":"2023-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"ddc":["000"],"publication":"ACM Transactions on Graphics","isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2024-01-02T09:34:27Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546"}],"title":"Generalizing shallow water simulations with dispersive surface waves","date_updated":"2025-04-14T08:01:13Z"},{"date_created":"2023-08-27T22:01:17Z","publication_status":"published","external_id":{"arxiv":["2305.05944"],"isi":["001117690500020"]},"conference":{"start_date":"2023-08-06","location":"Los Angeles, CA, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2023-08-10"},"_id":"14241","scopus_import":"1","month":"07","quality_controlled":"1","citation":{"short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023.","mla":"Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” <i>SIGGRAPH 2023 Conference Proceedings</i>, 20, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3588432.3591542\">10.1145/3588432.3591542</a>.","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” In <i>SIGGRAPH 2023 Conference Proceedings</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3588432.3591542\">https://doi.org/10.1145/3588432.3591542</a>.","ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 20.","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity optimization as surface stylization,” in <i>SIGGRAPH 2023 Conference Proceedings</i>, Los Angeles, CA, United States, 2023.","apa":"Tojo, K., Shamir, A., Bickel, B., &#38; Umetani, N. (2023). Stealth shaper: Reflectivity optimization as surface stylization. In <i>SIGGRAPH 2023 Conference Proceedings</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3588432.3591542\">https://doi.org/10.1145/3588432.3591542</a>","ama":"Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization as surface stylization. In: <i>SIGGRAPH 2023 Conference Proceedings</i>. Association for Computing Machinery; 2023. doi:<a href=\"https://doi.org/10.1145/3588432.3591542\">10.1145/3588432.3591542</a>"},"abstract":[{"lang":"eng","text":"We present a technique to optimize the reflectivity of a surface while preserving its overall shape. The naïve optimization of the mesh vertices using the gradients of reflectivity simulations results in undesirable distortion. In contrast, our robust formulation optimizes the surface normal as an independent variable that bridges the reflectivity term with differential rendering, and the regularization term with as-rigid-as-possible elastic energy. We further adaptively subdivide the input mesh to improve the convergence. Consequently, our method can minimize the retroreflectivity of a wide range of input shapes, resulting in sharply creased shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by changing the reward for the direction of the outgoing light directions, our method can be applied to other reflectivity design tasks, such as the optimization of architectural walls to concentrate light in a specific region. We have tested the proposed method using light-transport simulations and real-world 3D-printed objects."}],"type":"conference","department":[{"_id":"BeBi"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.05944"}],"publisher":"Association for Computing Machinery","corr_author":"1","oa_version":"Preprint","date_updated":"2025-09-09T12:49:15Z","author":[{"first_name":"Kenji","last_name":"Tojo","full_name":"Tojo, Kenji"},{"full_name":"Shamir, Ariel","last_name":"Shamir","first_name":"Ariel"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"last_name":"Umetani","full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki"}],"title":"Stealth shaper: Reflectivity optimization as surface stylization","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_published":"2023-07-23T00:00:00Z","oa":1,"day":"23","doi":"10.1145/3588432.3591542","publication_identifier":{"isbn":["9798400701597"]},"acknowledgement":"The authors would like to thank Yuki Koyama and Takeo Igarashi for early discussions, and Yuta Yaguchi for support in 3D printing. This research is partially supported by the Israel Science Foundation grant number 1390/19.\r\n","year":"2023","article_number":"20","isi":1,"publication":"SIGGRAPH 2023 Conference Proceedings","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"volume":37,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.16187"}],"publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1","citation":{"short":"M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–14973.","mla":"Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, vol. 37, no. 12, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:<a href=\"https://doi.org/10.1609/aaai.v37i12.26747\">10.1609/aaai.v37i12.26747</a>.","chicago":"Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger, and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, 37:14964–73. Association for the Advancement of Artificial Intelligence, 2023. <a href=\"https://doi.org/10.1609/aaai.v37i12.26747\">https://doi.org/10.1609/aaai.v37i12.26747</a>.","ista":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 14964–14973.","apa":"Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., &#38; Rus, D. (2023). Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i> (Vol. 37, pp. 14964–14973). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v37i12.26747\">https://doi.org/10.1609/aaai.v37i12.26747</a>","ieee":"M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware interval bound propagation for training certifiably robust quantized neural networks,” in <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.","ama":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In: <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973. doi:<a href=\"https://doi.org/10.1609/aaai.v37i12.26747\">10.1609/aaai.v37i12.26747</a>"},"abstract":[{"text":"We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training algorithm computes the gradient of an abstract representation of the actual network. Unlike existing approaches, our method can handle the discrete semantics of QNNs. Based on QA-IBP, we also develop a complete verification procedure for verifying the adversarial robustness of QNNs, which is guaranteed to terminate and produce a correct answer. Compared to existing approaches, the key advantage of our verification procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate experimentally that our approach significantly outperforms existing methods and establish the new state-of-the-art for training and certifying the robustness of QNNs.","lang":"eng"}],"type":"conference","_id":"14242","issue":"12","scopus_import":"1","month":"06","date_created":"2023-08-27T22:01:17Z","publication_status":"published","external_id":{"arxiv":["2211.16187"]},"conference":{"end_date":"2023-02-14","location":"Washington, DC, United States","name":"AAAI: Conference on Artificial Intelligence","start_date":"2023-02-07"},"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_published":"2023-06-26T00:00:00Z","intvolume":"        37","oa":1,"doi":"10.1609/aaai.v37i12.26747","day":"26","year":"2023","publication_identifier":{"isbn":["9781577358800"]},"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research was sponsored by the United\r\nStates Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under Cooperative Agreement Number FA8750-19-2-\r\n1000. 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,\r\nof 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\r\nnotation herein. The research was also funded in part by the AI2050 program at Schmidt Futures (Grant G-22-63172) and Capgemini SE.","ec_funded":1,"page":"14964-14973","date_updated":"2025-03-31T16:01:08Z","author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rus","full_name":"Rus, Daniela","first_name":"Daniela"}],"title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint"},{"citation":{"apa":"Avni, G., Jecker, I. R., &#38; Zikelic, D. (2023). Bidding graph games with partially-observable budgets. In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i> (Vol. 37, pp. 5464–5471). Washington, DC, United States. <a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">https://doi.org/10.1609/aaai.v37i5.25679</a>","ieee":"G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable budgets,” in <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.","ama":"Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable budgets. In: <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>. Vol 37. ; 2023:5464-5471. doi:<a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">10.1609/aaai.v37i5.25679</a>","mla":"Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.” <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, vol. 37, no. 5, 2023, pp. 5464–71, doi:<a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">10.1609/aaai.v37i5.25679</a>.","ista":"Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 5464–5471.","chicago":"Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with Partially-Observable Budgets.” In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, 37:5464–71, 2023. <a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">https://doi.org/10.1609/aaai.v37i5.25679</a>.","short":"G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, 2023, pp. 5464–5471."},"type":"conference","abstract":[{"text":"Two-player zero-sum \"graph games\" are central in logic, verification, and multi-agent systems. The game proceeds by placing a token on a vertex of a graph, and allowing the players to move it to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In \"bidding games\", however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as full-information games. In this work we initiate the study of partial-information bidding games: we study bidding games in which a player's initial budget is drawn from a known probability distribution. We show that while for some bidding mechanisms and objectives, it is straightforward to adapt the results from the full-information setting to the partial-information setting, for others, the analysis is significantly more challenging, requires new techniques, and gives rise to interesting results. Specifically, we study games with \"mean-payoff\" objectives in combination with \"poorman\" bidding. We construct optimal strategies for a partially-informed player who plays against a fully-informed adversary. We show that, somewhat surprisingly, the \"value\" under pure strategies does not necessarily exist in such games.","lang":"eng"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1609/aaai.v37i5.25679"}],"volume":37,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"Washington, DC, United States","start_date":"2023-02-07","end_date":"2023-02-14"},"external_id":{"arxiv":["2211.13626"]},"publication_status":"published","date_created":"2023-08-27T22:01:18Z","month":"06","scopus_import":"1","issue":"5","_id":"14243","year":"2023","acknowledgement":"This research was supported in part by ISF grant no.1679/21, by the ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publication_identifier":{"isbn":["9781577358800"]},"ec_funded":1,"oa":1,"day":"27","doi":"10.1609/aaai.v37i5.25679","date_published":"2023-06-27T00:00:00Z","intvolume":"        37","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R","last_name":"Jecker"},{"first_name":"Dorde","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"title":"Bidding graph games with partially-observable budgets","page":"5464-5471","date_updated":"2025-03-31T16:01:08Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2023-08-27T22:01:18Z","external_id":{"isi":["001049312700001"],"arxiv":["1807.04057"]},"_id":"14244","month":"10","scopus_import":"1","issue":"4","citation":{"short":"T. Hausel, M.L. Wong, D. Wyss, Proceedings of the London Mathematical Society 127 (2023) 958–1027.","ama":"Hausel T, Wong ML, Wyss D. Arithmetic and metric aspects of open de Rham spaces. <i>Proceedings of the London Mathematical Society</i>. 2023;127(4):958-1027. doi:<a href=\"https://doi.org/10.1112/plms.12555\">10.1112/plms.12555</a>","ieee":"T. Hausel, M. L. Wong, and D. Wyss, “Arithmetic and metric aspects of open de Rham spaces,” <i>Proceedings of the London Mathematical Society</i>, vol. 127, no. 4. Wiley, pp. 958–1027, 2023.","apa":"Hausel, T., Wong, M. L., &#38; Wyss, D. (2023). Arithmetic and metric aspects of open de Rham spaces. <i>Proceedings of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/plms.12555\">https://doi.org/10.1112/plms.12555</a>","mla":"Hausel, Tamás, et al. “Arithmetic and Metric Aspects of Open de Rham Spaces.” <i>Proceedings of the London Mathematical Society</i>, vol. 127, no. 4, Wiley, 2023, pp. 958–1027, doi:<a href=\"https://doi.org/10.1112/plms.12555\">10.1112/plms.12555</a>.","chicago":"Hausel, Tamás, Michael Lennox Wong, and Dimitri Wyss. “Arithmetic and Metric Aspects of Open de Rham Spaces.” <i>Proceedings of the London Mathematical Society</i>. Wiley, 2023. <a href=\"https://doi.org/10.1112/plms.12555\">https://doi.org/10.1112/plms.12555</a>.","ista":"Hausel T, Wong ML, Wyss D. 2023. Arithmetic and metric aspects of open de Rham spaces. Proceedings of the London Mathematical Society. 127(4), 958–1027."},"type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we determine the motivic class — in particular, the weight polynomial and conjecturally the Poincaré polynomial — of the open de Rham space, defined and studied by Boalch, of certain moduli spaces of irregular meromorphic connections on the trivial rank \r\n bundle on P1. The computation is by motivic Fourier transform. We show that the result satisfies the purity conjecture, that is, it agrees with the pure part of the conjectured mixed Hodge polynomial of the corresponding wild character variety. We also identify the open de Rham spaces with quiver varieties with multiplicities of Yamakawa and Geiss–Leclerc–Schröer. We finish with constructing natural complete hyperkähler metrics on them, which in the four-dimensional cases are expected to be of type ALF."}],"quality_controlled":"1","volume":127,"department":[{"_id":"TaHa"}],"publisher":"Wiley","corr_author":"1","oa_version":"Published Version","title":"Arithmetic and metric aspects of open de Rham spaces","author":[{"orcid":"0000-0002-9582-2634","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamás","last_name":"Hausel","first_name":"Tamás"},{"first_name":"Michael Lennox","last_name":"Wong","full_name":"Wong, Michael Lennox"},{"first_name":"Dimitri","last_name":"Wyss","full_name":"Wyss, Dimitri"}],"date_updated":"2025-04-14T09:12:46Z","page":"958-1027","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-01-30T12:56:00Z","oa":1,"file":[{"date_updated":"2024-01-30T12:56:00Z","file_id":"14910","content_type":"application/pdf","checksum":"2af4d2d6a8ae42f7d3fba0188e79ae82","relation":"main_file","success":1,"file_name":"2023_ProcLondonMathSoc_Hausel.pdf","date_created":"2024-01-30T12:56:00Z","creator":"dernst","file_size":651335,"access_level":"open_access"}],"doi":"10.1112/plms.12555","day":"01","date_published":"2023-10-01T00:00:00Z","intvolume":"       127","acknowledgement":"We would like to thank Gergely Bérczy, Roger Bielawski, Philip Boalch, Sergey Cherkis, Andrew Dancer, Brent Doran, Eloïse Hamilton, Frances Kirwan, Bernard Leclerc, Emmanuel Letellier, Alessia Mandini, Maxence Mayrand, András Némethi, Szilárd Szabó, and Daisuke Yamakawa for discussions related to the paper. We especially thank the referee for an extensive list of very careful comments. At various stages of this project, the authors were supported by the Advanced Grant “Arithmetic and physics of Higgs moduli spaces” no. 320593 of the European Research Council, by grant no. 153627 and NCCR SwissMAP, both funded by the Swiss National Science Foundation as well as by EPF Lausanne and IST Austria. In the final stages of this project, MLW was supported by SFB/TR 45 “Periods, moduli and arithmetic of algebraic varieties,” subproject M08-10 “Moduli of vector bundles on higher-dimensional varieties.” DW was also supported by the Fondation Sciences Mathématiques de Paris, as well as public grants overseen by the Agence national de la recherche (ANR) of France as part of the Investissements d'avenir program, under reference numbers ANR-10-LABX-0098 and ANR-15-CE40-0008 (Défigéo).","year":"2023","publication_identifier":{"issn":["0024-6115"],"eissn":["1460-244X"]},"article_type":"original","ec_funded":1,"isi":1,"publication":"Proceedings of the London Mathematical Society","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","call_identifier":"FP7"},{"name":"Arithmetic quantization of character and quiver varities","_id":"25E6C798-B435-11E9-9278-68D0E5697425","grant_number":"153627"}],"ddc":["510"]},{"oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2023-09-05T07:26:17Z","author":[{"id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425","last_name":"Horesh","full_name":"Horesh, Tal","first_name":"Tal"},{"first_name":"Amos","full_name":"Nevo, Amos","last_name":"Nevo"}],"title":"Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution","page":"265-294","date_updated":"2024-10-09T21:06:46Z","acknowledgement":"The authors thank the referee for important comments which led to significant improvements is the presentation of several results in the paper. They also thank Ami Paz for preparing the figures for this paper. Horesh thanks Ami Paz and Yakov Karasik for helpful discussions. Nevo thanks John Parker and Rene Rühr for providing some very useful references. Nevo is supported by ISF Grant No. 2095/15.","article_type":"original","year":"2023","publication_identifier":{"issn":["0030-8730"],"eissn":["1945-5844"]},"file":[{"date_updated":"2023-09-05T07:26:17Z","file_id":"14267","content_type":"application/pdf","checksum":"a675b53cfb31fa46be1e879b7e77fe8c","relation":"main_file","file_name":"2023_PacificJourMaths_Horesh.pdf","date_created":"2023-09-05T07:26:17Z","success":1,"creator":"dernst","file_size":654895,"access_level":"open_access"}],"oa":1,"day":"26","doi":"10.2140/pjm.2023.324.265","date_published":"2023-07-26T00:00:00Z","intvolume":"       324","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"isi":1,"publication":"Pacific Journal of Mathematics","arxiv":1,"external_id":{"isi":["001047690500001"],"arxiv":["1612.08215"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2023-08-27T22:01:18Z","month":"07","scopus_import":"1","issue":"2","_id":"14245","citation":{"ieee":"T. Horesh and A. Nevo, “Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution,” <i>Pacific Journal of Mathematics</i>, vol. 324, no. 2. Mathematical Sciences Publishers, pp. 265–294, 2023.","apa":"Horesh, T., &#38; Nevo, A. (2023). Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pjm.2023.324.265\">https://doi.org/10.2140/pjm.2023.324.265</a>","ama":"Horesh T, Nevo A. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. <i>Pacific Journal of Mathematics</i>. 2023;324(2):265-294. doi:<a href=\"https://doi.org/10.2140/pjm.2023.324.265\">10.2140/pjm.2023.324.265</a>","chicago":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers, 2023. <a href=\"https://doi.org/10.2140/pjm.2023.324.265\">https://doi.org/10.2140/pjm.2023.324.265</a>.","ista":"Horesh T, Nevo A. 2023. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 324(2), 265–294.","mla":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” <i>Pacific Journal of Mathematics</i>, vol. 324, no. 2, Mathematical Sciences Publishers, 2023, pp. 265–94, doi:<a href=\"https://doi.org/10.2140/pjm.2023.324.265\">10.2140/pjm.2023.324.265</a>.","short":"T. Horesh, A. Nevo, Pacific Journal of Mathematics 324 (2023) 265–294."},"type":"journal_article","abstract":[{"lang":"eng","text":"We establish effective counting results for lattice points in families of domains in real, complex and quaternionic hyperbolic spaces of any dimension. The domains we focus on are defined as product sets with respect to an Iwasawa decomposition. Several natural diophantine problems can be reduced to counting lattice points in such domains. These include equidistribution of the ratio of the length of the shortest solution (x,y) to the gcd equation bx−ay=1 relative to the length of (a,b), where (a,b) ranges over primitive vectors in a disc whose radius increases, the natural analog of this problem in imaginary quadratic number fields, as well as equidistribution of integral solutions to the diophantine equation defined by an integral Lorentz form in three or more variables. We establish an effective rate of convergence for these equidistribution problems, depending on the size of the spectral gap associated with a suitable lattice subgroup in the isometry group of the relevant hyperbolic space. The main result underlying our discussion amounts to establishing effective joint equidistribution for the horospherical component and the radial component in the Iwasawa decomposition of lattice elements."}],"quality_controlled":"1","corr_author":"1","publisher":"Mathematical Sciences Publishers","volume":324,"department":[{"_id":"TiBr"}]},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2023-09-05T08:45:49Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-10-09T21:06:47Z","author":[{"last_name":"Brauneis","full_name":"Brauneis, Fabian","first_name":"Fabian"},{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg"},{"full_name":"Hammer, Hans-Werner","last_name":"Hammer","first_name":"Hans-Werner"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"title":"Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux","keyword":["General Physics and Astronomy"],"oa_version":"Published Version","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"arxiv":1,"publication":"Communications Physics","year":"2023","article_type":"original","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.\r\nWe would like to thank Jonas Jager for sharing his data with us in the early stages of this project. We thank Joachim Brand and Ray Yang for sharing with us data from Yang et al.46. This work has received funding from the DFG Project no. 413495248 [VO 2437/1-1] (F.B., H.-W.H., A.G.V.). We acknowledge support from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) and the Open Access Publishing Fund of the Technical University of Darmstadt.","publication_identifier":{"issn":["2399-3650"]},"article_number":"224","date_published":"2023-08-22T00:00:00Z","intvolume":"         6","oa":1,"file":[{"access_level":"open_access","success":1,"date_created":"2023-09-05T08:45:49Z","file_name":"2023_CommPhysics_Brauneis.pdf","creator":"dernst","file_size":855960,"checksum":"6edfc59b0ee7dc406d0968b05236e83d","content_type":"application/pdf","relation":"main_file","date_updated":"2023-09-05T08:45:49Z","file_id":"14268"}],"doi":"10.1038/s42005-023-01281-2","day":"22","scopus_import":"1","month":"08","_id":"14246","external_id":{"arxiv":["2301.10488"],"isi":["001052577500002"]},"date_created":"2023-08-28T12:36:49Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","corr_author":"1","publisher":"Springer Nature","department":[{"_id":"MiLe"}],"volume":6,"quality_controlled":"1","citation":{"mla":"Brauneis, Fabian, et al. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” <i>Communications Physics</i>, vol. 6, 224, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42005-023-01281-2\">10.1038/s42005-023-01281-2</a>.","ista":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. 2023. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 6, 224.","chicago":"Brauneis, Fabian, Areg Ghazaryan, Hans-Werner Hammer, and Artem Volosniev. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” <i>Communications Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42005-023-01281-2\">https://doi.org/10.1038/s42005-023-01281-2</a>.","apa":"Brauneis, F., Ghazaryan, A., Hammer, H.-W., &#38; Volosniev, A. (2023). Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-023-01281-2\">https://doi.org/10.1038/s42005-023-01281-2</a>","ieee":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, and A. Volosniev, “Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux,” <i>Communications Physics</i>, vol. 6. Springer Nature, 2023.","ama":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. <i>Communications Physics</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42005-023-01281-2\">10.1038/s42005-023-01281-2</a>","short":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (2023)."},"abstract":[{"text":"The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding of a coupling between gauge potentials and matter. The typical formulation of the model is based upon a single particle picture, and should be extended when interactions with other particles become relevant. Here, we illustrate such an extension for a particle in an Aharonov-Bohm ring subject to interactions with a weakly interacting Bose gas. We show that the ground state of the system can be described using the Bose-polaron concept—a particle dressed by interactions with a bosonic environment. We connect the energy spectrum to the effective mass of the polaron, and demonstrate how to change currents in the system by tuning boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform for studying coherence and few- to many-body crossover of quasi-particles that arise from an impurity immersed in a medium.","lang":"eng"}],"type":"journal_article"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"isi":1,"publication":"Nature Communications","article_number":"5231","year":"2023","acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","article_type":"original","publication_identifier":{"eissn":["2041-1723"]},"oa":1,"file":[{"relation":"main_file","checksum":"6ab8aab4e957f626a09a1c73db3388fb","content_type":"application/pdf","file_id":"14270","date_updated":"2023-09-06T06:50:07Z","access_level":"open_access","date_created":"2023-09-06T06:50:07Z","success":1,"file_name":"2023_NatureComm_Vierra.pdf","file_size":9412549,"creator":"dernst"}],"day":"26","doi":"10.1038/s41467-023-40930-6","date_published":"2023-08-26T00:00:00Z","intvolume":"        14","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2023-09-06T06:50:07Z","author":[{"full_name":"Vierra, Nicholas C.","last_name":"Vierra","first_name":"Nicholas C."},{"first_name":"Luisa","last_name":"Ribeiro-Silva","full_name":"Ribeiro-Silva, Luisa"},{"full_name":"Kirmiz, Michael","last_name":"Kirmiz","first_name":"Michael"},{"first_name":"Deborah","last_name":"Van Der List","full_name":"Van Der List, Deborah"},{"first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481"},{"first_name":"Olivia A.","last_name":"Mack","full_name":"Mack, Olivia A."},{"first_name":"James","last_name":"Carroll","full_name":"Carroll, James"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","last_name":"Le Monnier","full_name":"Le Monnier, Elodie","first_name":"Elodie"},{"full_name":"Aicher, Sue A.","last_name":"Aicher","first_name":"Sue A."},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Trimmer","full_name":"Trimmer, James S.","first_name":"James S."}],"title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","date_updated":"2025-09-09T12:50:49Z","oa_version":"Published Version","publisher":"Springer Nature","volume":14,"department":[{"_id":"RySh"}],"citation":{"apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>","ieee":"N. C. Vierra <i>et al.</i>, “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>","ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231.","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>.","mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>, vol. 14, 5231, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>.","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023)."},"pmid":1,"abstract":[{"lang":"eng","text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell."}],"type":"journal_article","quality_controlled":"1","month":"08","scopus_import":"1","_id":"14253","external_id":{"pmid":["37633939"],"isi":["001064563400013"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2023-09-03T22:01:14Z"},{"date_created":"2023-09-03T22:01:14Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"isi":["001071552300001"],"arxiv":["2303.04504"]},"_id":"14254","scopus_import":"1","issue":"10","month":"11","quality_controlled":"1","citation":{"short":"R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023).","mla":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>, vol. 285, no. 10, 110129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>.","chicago":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>.","ista":"Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 285(10), 110129.","ama":"Seiringer R, Solovej JP. A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. 2023;285(10). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>","apa":"Seiringer, R., &#38; Solovej, J. P. (2023). A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>","ieee":"R. Seiringer and J. P. Solovej, “A simple approach to Lieb-Thirring type inequalities,” <i>Journal of Functional Analysis</i>, vol. 285, no. 10. Elsevier, 2023."},"abstract":[{"lang":"eng","text":"In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a fermionic quantum system, with almost optimal (semi-classical) constant and a gradient correction term. We present a stronger version of this inequality, with a much simplified proof. As a corollary we obtain a simple proof of the original Lieb–Thirring inequality."}],"type":"journal_article","department":[{"_id":"RoSe"}],"volume":285,"publisher":"Elsevier","corr_author":"1","oa_version":"Published Version","date_updated":"2024-10-09T21:06:47Z","title":"A simple approach to Lieb-Thirring type inequalities","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Jan Philip","last_name":"Solovej","full_name":"Solovej, Jan Philip"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2024-01-30T14:15:16Z","language":[{"iso":"eng"}],"status":"public","date_published":"2023-11-15T00:00:00Z","intvolume":"       285","oa":1,"file":[{"checksum":"28e424ad91be6219e9d321054ce3a412","content_type":"application/pdf","relation":"main_file","date_updated":"2024-01-30T14:15:16Z","file_id":"14915","access_level":"open_access","creator":"dernst","file_size":232934,"file_name":"2023_JourFunctionalAnalysis_Seiringer.pdf","date_created":"2024-01-30T14:15:16Z","success":1}],"day":"15","doi":"10.1016/j.jfa.2023.110129","acknowledgement":"J.P.S. thanks the Institute of Science and Technology Austria for the hospitality and support during a visit where this work was done. J.P.S. was also partially supported by the VILLUM Centre of Excellence for the Mathematics of Quantum Theory (QMATH) (grant No. 10059).","year":"2023","article_type":"original","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"article_number":"110129","isi":1,"publication":"Journal of Functional Analysis","arxiv":1,"ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","citation":{"short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>","ieee":"J. Koch <i>et al.</i>, “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” <i>PLoS Pathogens</i>, vol. 19, no. 8. Public Library of Science, 2023.","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. 2023;19(8). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>.","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562.","chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>."},"pmid":1,"abstract":[{"lang":"eng","text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells."}],"type":"journal_article","publisher":"Public Library of Science","department":[{"_id":"FlSc"}],"volume":19,"external_id":{"isi":["001050846300004"],"pmid":["37578957"]},"date_created":"2023-09-03T22:01:14Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","issue":"8","scopus_import":"1","month":"08","_id":"14255","acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","article_type":"original","publication_identifier":{"issn":["1553-7366"],"eissn":["1553-7374"]},"year":"2023","article_number":"e1011562","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_published":"2023-08-14T00:00:00Z","intvolume":"        19","oa":1,"file":[{"date_updated":"2023-09-06T06:41:52Z","file_id":"14269","content_type":"application/pdf","checksum":"47ca3bb54b27f28b05644be0ad064bc6","relation":"main_file","date_created":"2023-09-06T06:41:52Z","success":1,"file_name":"2023_PloSPathogens_Koch.pdf","creator":"dernst","file_size":4458336,"access_level":"open_access"}],"doi":"10.1371/journal.ppat.1011562","day":"14","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF"}],"isi":1,"publication":"PLoS Pathogens","oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2023-09-06T06:41:52Z","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-04-15T08:24:50Z","author":[{"first_name":"Jana","full_name":"Koch, Jana","last_name":"Koch"},{"first_name":"Qilin","full_name":"Xin, Qilin","last_name":"Xin"},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr","orcid":"0000-0003-1756-6564","first_name":"Martin"},{"first_name":"Alicia","full_name":"Schäfer, Alicia","last_name":"Schäfer"},{"first_name":"Nina","last_name":"Rolfs","full_name":"Rolfs, Nina"},{"last_name":"Anagho","full_name":"Anagho, Holda A.","first_name":"Holda A."},{"first_name":"Aiste","full_name":"Kudulyte, Aiste","last_name":"Kudulyte"},{"first_name":"Lea","last_name":"Woltereck","full_name":"Woltereck, Lea"},{"last_name":"Kummer","full_name":"Kummer, Susann","first_name":"Susann"},{"full_name":"Campos, Joaquin","last_name":"Campos","first_name":"Joaquin"},{"first_name":"Zina M.","last_name":"Uckeley","full_name":"Uckeley, Zina M."},{"first_name":"Lesley","full_name":"Bell-Sakyi, Lesley","last_name":"Bell-Sakyi"},{"first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg","last_name":"Kräusslich"},{"first_name":"Florian Km","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian Km","orcid":"0000-0003-4790-8078"},{"last_name":"Acuna","full_name":"Acuna, Claudio","first_name":"Claudio"},{"last_name":"Lozach","full_name":"Lozach, Pierre Yves","first_name":"Pierre Yves"}],"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells"},{"date_updated":"2023-09-06T11:05:58Z","title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","author":[{"first_name":"S.","last_name":"Mathis","full_name":"Mathis, S."},{"first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-09-06T07:13:19Z","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","isi":1,"publication":"Astronomy and Astrophysics","arxiv":1,"ddc":["520"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2023-08-01T00:00:00Z","intvolume":"       676","oa":1,"file":[{"date_updated":"2023-09-06T07:13:19Z","file_id":"14271","content_type":"application/pdf","checksum":"7b30d26fb2b7bcb5b5be1414950615f9","relation":"main_file","file_name":"2023_AstronomyAstrophysics_Mathis.pdf","success":1,"date_created":"2023-09-06T07:13:19Z","creator":"dernst","file_size":458120,"access_level":"open_access"}],"day":"01","doi":"10.1051/0004-6361/202346832","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"article_type":"letter_note","year":"2023","acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions.","article_number":"L9","_id":"14256","scopus_import":"1","month":"08","date_created":"2023-09-03T22:01:15Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"isi":["001046037700007"],"arxiv":["2306.11587"]},"department":[{"_id":"LiBu"}],"volume":676,"publisher":"EDP Sciences","quality_controlled":"1","citation":{"short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).","apa":"Mathis, S., &#38; Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>","ieee":"S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” <i>Astronomy and Astrophysics</i>, vol. 676. EDP Sciences, 2023.","ama":"Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy and Astrophysics</i>. 2023;676. doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>","ista":"Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 676, L9.","chicago":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy and Astrophysics</i>. EDP Sciences, 2023. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>.","mla":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy and Astrophysics</i>, vol. 676, L9, EDP Sciences, 2023, doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>."},"abstract":[{"lang":"eng","text":"Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries."}],"type":"journal_article"},{"department":[{"_id":"MaRo"}],"volume":110,"publisher":"Elsevier","corr_author":"1","quality_controlled":"1","type":"journal_article","pmid":1,"abstract":[{"text":"There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data.","lang":"eng"}],"citation":{"short":"S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik, M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.","mla":"Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>, vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>.","ista":"Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson MR. 2023. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563.","chicago":"Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer, Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>.","ama":"Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. 2023;110(9):1549-1563. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>","ieee":"S. E. Ojavee <i>et al.</i>, “Genetic insights into the age-specific biological mechanisms governing human ovarian aging,” <i>American Journal of Human Genetics</i>, vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.","apa":"Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., … Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>"},"_id":"14258","scopus_import":"1","issue":"9","month":"09","date_created":"2023-09-03T22:01:15Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001074842500001"],"pmid":["37543033"]},"publication":"American Journal of Human Genetics","isi":1,"ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       110","date_published":"2023-09-07T00:00:00Z","day":"07","doi":"10.1016/j.ajhg.2023.07.006","oa":1,"file":[{"creator":"dernst","file_size":2551276,"file_name":"2023_AJHG_Ojavee.pdf","success":1,"date_created":"2024-01-30T13:20:35Z","access_level":"open_access","date_updated":"2024-01-30T13:20:35Z","file_id":"14912","checksum":"4108b031dc726ae6b4a5ae7e021ba188","content_type":"application/pdf","relation":"main_file"}],"article_type":"original","acknowledgement":"This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria. K.L. and R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank computations were performed in the High-Performance Computing Center, University of Tartu. We thank Triin Laisk for her valuable insights and comments that helped greatly. We would like to acknowledge the participants and investigators of UK Biobank and Estonian Biobank studies. This project uses UK Biobank data under project number 35520.","publication_identifier":{"eissn":["1537-6605"],"issn":["0002-9297"]},"year":"2023","page":"1549-1563","date_updated":"2025-09-09T12:51:20Z","title":"Genetic insights into the age-specific biological mechanisms governing human ovarian aging","author":[{"first_name":"Sven E.","last_name":"Ojavee","full_name":"Ojavee, Sven E."},{"first_name":"Liza","full_name":"Darrous, Liza","last_name":"Darrous"},{"last_name":"Patxot","full_name":"Patxot, Marion","first_name":"Marion"},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"first_name":"Krista","last_name":"Fischer","full_name":"Fischer, Krista"},{"first_name":"Reedik","full_name":"Mägi, Reedik","last_name":"Mägi"},{"first_name":"Zoltan","full_name":"Kutalik, Zoltan","last_name":"Kutalik"},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard"}],"file_date_updated":"2024-01-30T13:20:35Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version"},{"year":"2023","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","publication_identifier":{"isbn":["9783031377051"],"eissn":["1611-3349"],"issn":["0302-9743"]},"file":[{"creator":"dernst","file_size":428354,"date_created":"2023-09-06T08:25:50Z","success":1,"file_name":"2023_LNCS_CAV_Kretinsky.pdf","access_level":"open_access","date_updated":"2023-09-06T08:25:50Z","file_id":"14276","checksum":"ed66278b61bb869e1baba3d9b9081271","content_type":"application/pdf","relation":"main_file"}],"oa":1,"doi":"10.1007/978-3-031-37706-8_20","day":"17","date_published":"2023-07-17T00:00:00Z","intvolume":"     13964","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"isi":1,"publication":"35th International Conference on Computer Aided Verification ","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-09-06T08:25:50Z","author":[{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881"},{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias"},{"first_name":"Maximilian","last_name":"Prokop","full_name":"Prokop, Maximilian"},{"full_name":"Rieder, Sabine","last_name":"Rieder","first_name":"Sabine"}],"title":"Guessing winning policies in LTL synthesis by semantic learning","date_updated":"2025-09-09T12:52:34Z","page":"390-414","citation":{"short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:390-414. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>","ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 390–414.","apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., &#38; Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:390–414. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>.","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 390–414, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>."},"abstract":[{"lang":"eng","text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning."}],"type":"conference","quality_controlled":"1","publisher":"Springer Nature","volume":13964,"department":[{"_id":"KrCh"}],"conference":{"end_date":"2023-07-22","name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17"},"external_id":{"isi":["001310786500020"]},"alternative_title":["LNCS"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2023-09-03T22:01:16Z","month":"07","scopus_import":"1","_id":"14259"},{"oa":1,"file":[{"content_type":"application/pdf","checksum":"c346016393123a0a2338ad4d976f61bc","relation":"main_file","date_updated":"2023-09-06T08:16:25Z","file_id":"14275","access_level":"open_access","creator":"dernst","file_size":421408,"date_created":"2023-09-06T08:16:25Z","success":1,"file_name":"2023_LNCS_Koval.pdf"}],"day":"17","doi":"10.1007/978-3-031-37706-8_8","date_published":"2023-07-17T00:00:00Z","intvolume":"     13964","publication_identifier":{"isbn":["9783031377051"],"eissn":["1611-3349"],"issn":["0302-9743"]},"year":"2023","isi":1,"publication":"35th International Conference on Computer Aided Verification ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"oa_version":"Published Version","author":[{"full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita"},{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","full_name":"Fedorov, Alexander","first_name":"Alexander"},{"full_name":"Sokolova, Maria","last_name":"Sokolova","first_name":"Maria"},{"first_name":"Dmitry","full_name":"Tsitelov, Dmitry","last_name":"Tsitelov"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian"}],"title":"Lincheck: A practical framework for testing concurrent data structures on JVM","date_updated":"2025-09-09T12:51:52Z","related_material":{"record":[{"id":"14995","relation":"research_data","status":"public"}]},"page":"156-169","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2023-09-06T08:16:25Z","citation":{"short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 156–169.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 156–169.","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>."},"type":"conference","abstract":[{"lang":"eng","text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness."}],"quality_controlled":"1","volume":13964,"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2023-09-03T22:01:16Z","conference":{"start_date":"2023-07-17","name":"CAV: Computer Aided Verification","location":"Paris, France","end_date":"2023-07-22"},"alternative_title":["LNCS"],"external_id":{"isi":["001310786500008"]},"_id":"14260","month":"07","scopus_import":"1"},{"publisher":"American Chemical Society","volume":14,"department":[{"_id":"GradSch"}],"citation":{"short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>.","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>.","ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. 2023;14(33):7395-7403. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., &#38; Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>"},"pmid":1,"abstract":[{"text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","month":"08","issue":"33","scopus_import":"1","_id":"14261","external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2023-09-03T22:01:16Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["530","540"],"isi":1,"publication":"Journal of Physical Chemistry Letters","article_type":"original","year":"2023","acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","publication_identifier":{"eissn":["1948-7185"]},"oa":1,"file":[{"access_level":"open_access","success":1,"date_created":"2023-09-06T07:32:39Z","file_name":"2023_JourPhysChemistry_Gamper.pdf","file_size":4986859,"creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"637454e2b3a357498d8d622d241c4bf6","file_id":"14272","date_updated":"2023-09-06T07:32:39Z"}],"day":"11","doi":"10.1021/acs.jpclett.3c01707","date_published":"2023-08-11T00:00:00Z","intvolume":"        14","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2023-09-06T07:32:39Z","author":[{"last_name":"Gamper","full_name":"Gamper, Jakob","first_name":"Jakob"},{"first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl","full_name":"Kluibenschedl, Florian"},{"full_name":"Weiss, Alexander K.H.","last_name":"Weiss","first_name":"Alexander K.H."},{"first_name":"Thomas S.","full_name":"Hofer, Thomas S.","last_name":"Hofer"}],"title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","page":"7395-7403","date_updated":"2023-09-06T11:04:31Z","oa_version":"Published Version"},{"issue":"1","month":"07","_id":"14277","date_created":"2023-09-06T08:30:59Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"American Physical Society","corr_author":"1","department":[{"_id":"EdHa"}],"volume":1,"quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels."}],"citation":{"short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. 2023;1(1). doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>","apa":"Boocock, D. R., Hirashima, T., &#38; Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” <i>PRX Life</i>, vol. 1, no. 1. American Physical Society, 2023.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>.","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001."},"file_date_updated":"2023-09-15T06:30:50Z","has_accepted_license":"1","article_processing_charge":"Yes","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:52:27Z","title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","author":[{"full_name":"Boocock, Daniel R","last_name":"Boocock","id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","first_name":"Daniel R"},{"last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B"}],"oa_version":"Published Version","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"publication":"PRX Life","ec_funded":1,"article_type":"original","acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","publication_identifier":{"issn":["2835-8279"]},"year":"2023","article_number":"013001","intvolume":"         1","date_published":"2023-07-20T00:00:00Z","doi":"10.1103/prxlife.1.013001","day":"20","file":[{"date_created":"2023-09-15T06:30:50Z","success":1,"file_name":"2023_PRXLife_Boocock.pdf","creator":"dernst","file_size":2559520,"access_level":"open_access","date_updated":"2023-09-15T06:30:50Z","file_id":"14335","content_type":"application/pdf","checksum":"f881d98c89eb9f1aa136d7b781511553","relation":"main_file"}],"oa":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","date_created":"2023-09-06T08:39:25Z","status":"public","month":"07","has_accepted_license":"1","article_processing_charge":"No","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217","first_name":"Mehmet C"}],"related_material":{"record":[{"status":"public","id":"14274","relation":"used_in_publication"}]},"_id":"14279","date_updated":"2025-04-15T06:54:33Z","year":"2023","oa":1,"citation":{"mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.”</i> Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>.","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>","short":"M.C. Ucar, (2023)."},"day":"11","abstract":[{"text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.","lang":"eng"}],"type":"research_data_reference","doi":"10.5281/ZENODO.8133960","date_published":"2023-07-11T00:00:00Z","publisher":"Zenodo","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133960"}],"department":[{"_id":"EdHa"}]},{"oa_version":"None","page":"754-760","date_updated":"2023-11-07T12:42:09Z","author":[{"full_name":"Praetorius, Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"},{"first_name":"Philip J. Y.","full_name":"Leung, Philip J. Y.","last_name":"Leung"},{"first_name":"Maxx H.","full_name":"Tessmer, Maxx H.","last_name":"Tessmer"},{"last_name":"Broerman","full_name":"Broerman, Adam","first_name":"Adam"},{"first_name":"Cullen","last_name":"Demakis","full_name":"Demakis, Cullen"},{"full_name":"Dishman, Acacia F.","last_name":"Dishman","first_name":"Acacia F."},{"full_name":"Pillai, Arvind","last_name":"Pillai","first_name":"Arvind"},{"first_name":"Abbas","full_name":"Idris, Abbas","last_name":"Idris"},{"first_name":"David","full_name":"Juergens, David","last_name":"Juergens"},{"full_name":"Dauparas, Justas","last_name":"Dauparas","first_name":"Justas"},{"last_name":"Li","full_name":"Li, Xinting","first_name":"Xinting"},{"last_name":"Levine","full_name":"Levine, Paul M.","first_name":"Paul M."},{"full_name":"Lamb, Mila","last_name":"Lamb","first_name":"Mila"},{"first_name":"Ryanne K.","full_name":"Ballard, Ryanne K.","last_name":"Ballard"},{"last_name":"Gerben","full_name":"Gerben, Stacey R.","first_name":"Stacey R."},{"first_name":"Hannah","full_name":"Nguyen, Hannah","last_name":"Nguyen"},{"full_name":"Kang, Alex","last_name":"Kang","first_name":"Alex"},{"first_name":"Banumathi","full_name":"Sankaran, Banumathi","last_name":"Sankaran"},{"last_name":"Bera","full_name":"Bera, Asim K.","first_name":"Asim K."},{"first_name":"Brian F.","full_name":"Volkman, Brian F.","last_name":"Volkman"},{"first_name":"Jeff","full_name":"Nivala, Jeff","last_name":"Nivala"},{"first_name":"Stefan","full_name":"Stoll, Stefan","last_name":"Stoll"},{"first_name":"David","full_name":"Baker, David","last_name":"Baker"}],"title":"Design of stimulus-responsive two-state hinge proteins","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"intvolume":"       381","date_published":"2023-08-17T00:00:00Z","doi":"10.1126/science.adg7731","day":"17","year":"2023","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_type":"original","publication":"Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-06T12:04:23Z","publication_status":"published","external_id":{"pmid":["37590357"]},"_id":"14281","scopus_import":"1","issue":"6659","month":"08","quality_controlled":"1","extern":"1","abstract":[{"text":"In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.","lang":"eng"}],"pmid":1,"type":"journal_article","citation":{"short":"F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F. Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M. Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F. Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.","ama":"Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. 2023;381(6659):754-760. doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>","apa":"Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>","ieee":"F. M. Praetorius <i>et al.</i>, “Design of stimulus-responsive two-state hinge proteins,” <i>Science</i>, vol. 381, no. 6659. American Association for the Advancement of Science, pp. 754–760, 2023.","ista":"Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659), 754–760.","chicago":"Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>.","mla":"Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>, vol. 381, no. 6659, American Association for the Advancement of Science, 2023, pp. 754–60, doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>."},"volume":381,"publisher":"American Association for the Advancement of Science"},{"publication_status":"submitted","oa_version":"Preprint","date_created":"2023-09-06T12:31:49Z","language":[{"iso":"eng"}],"status":"public","month":"03","article_processing_charge":"No","author":[{"full_name":"Edman, Natasha I","last_name":"Edman","first_name":"Natasha I"},{"first_name":"Rachel L","last_name":"Redler","full_name":"Redler, Rachel L"},{"first_name":"Ashish","full_name":"Phal, Ashish","last_name":"Phal"},{"full_name":"Schlichthaerle, Thomas","last_name":"Schlichthaerle","first_name":"Thomas"},{"first_name":"Sanjay R","full_name":"Srivatsan, Sanjay R","last_name":"Srivatsan"},{"first_name":"Ali","last_name":"Etemadi","full_name":"Etemadi, Ali"},{"first_name":"Seong","full_name":"An, Seong","last_name":"An"},{"full_name":"Favor, Andrew","last_name":"Favor","first_name":"Andrew"},{"full_name":"Ehnes, Devon","last_name":"Ehnes","first_name":"Devon"},{"first_name":"Zhe","last_name":"Li","full_name":"Li, Zhe"},{"first_name":"Florian M","full_name":"Praetorius, Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Gordon","full_name":"Gordon, Max","first_name":"Max"},{"first_name":"Wei","last_name":"Yang","full_name":"Yang, Wei"},{"first_name":"Brian","full_name":"Coventry, Brian","last_name":"Coventry"},{"first_name":"Derrick R","full_name":"Hicks, Derrick R","last_name":"Hicks"},{"first_name":"Longxing","full_name":"Cao, Longxing","last_name":"Cao"},{"first_name":"Neville","last_name":"Bethel","full_name":"Bethel, Neville"},{"last_name":"Heine","full_name":"Heine, Piper","first_name":"Piper"},{"first_name":"Analisa N","last_name":"Murray","full_name":"Murray, Analisa N"},{"first_name":"Stacey","full_name":"Gerben, Stacey","last_name":"Gerben"},{"last_name":"Carter","full_name":"Carter, Lauren","first_name":"Lauren"},{"last_name":"Miranda","full_name":"Miranda, Marcos","first_name":"Marcos"},{"first_name":"Babak","last_name":"Negahdari","full_name":"Negahdari, Babak"},{"first_name":"Sangwon","full_name":"Lee, Sangwon","last_name":"Lee"},{"last_name":"Trapnell","full_name":"Trapnell, Cole","first_name":"Cole"},{"full_name":"Stewart, Lance","last_name":"Stewart","first_name":"Lance"},{"last_name":"Ekiert","full_name":"Ekiert, Damian C","first_name":"Damian C"},{"first_name":"Joseph","full_name":"Schlessinger, Joseph","last_name":"Schlessinger"},{"last_name":"Shendure","full_name":"Shendure, Jay","first_name":"Jay"},{"full_name":"Bhabha, Gira","last_name":"Bhabha","first_name":"Gira"},{"last_name":"Ruohola-Baker","full_name":"Ruohola-Baker, Hannele","first_name":"Hannele"},{"first_name":"David","last_name":"Baker","full_name":"Baker, David"}],"title":"Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies","_id":"14294","date_updated":"2023-11-07T12:21:58Z","year":"2023","oa":1,"citation":{"apa":"Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R., Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>","ama":"Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>","ieee":"N. I. Edman <i>et al.</i>, “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies,” <i>bioRxiv</i>. .","chicago":"Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>.","ista":"Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv, <a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","mla":"Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","short":"N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi, S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry, D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M. Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger, J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.)."},"type":"preprint","abstract":[{"lang":"eng","text":"Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways."}],"doi":"10.1101/2023.03.14.532666","day":"15","extern":"1","date_published":"2023-03-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2023.03.14.532666","open_access":"1"}],"publication":"bioRxiv"}]