[{"title":"Generalizing shallow water simulations with dispersive surface waves","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.","isi":1,"date_published":"2023-08-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","acknowledged_ssus":[{"_id":"ScienComp"}],"volume":42,"month":"08","external_id":{"isi":["001044671300049"]},"date_updated":"2025-04-14T08:01:13Z","quality_controlled":"1","publisher":"Association for Computing Machinery","oa_version":"Published Version","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":{"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>.","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>","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023).","ista":"Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 42(4), 83.","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>.","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.","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>"},"article_number":"83","scopus_import":"1","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"type":"journal_article","status":"public","date_created":"2023-08-27T22:01:17Z","article_type":"original","year":"2023","doi":"10.1145/3592098","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"file":[{"date_created":"2023-12-21T12:26:40Z","file_id":"14704","success":1,"creator":"sjeschke","checksum":"1d178bb2f8011d9f5aedda6427e18c7a","access_level":"open_access","file_name":"PaperVideo_final.mp4","file_size":511572575,"date_updated":"2023-12-21T12:26:40Z","relation":"main_file","content_type":"video/mp4"},{"creator":"dernst","checksum":"a49b2e744d5cd1276bb8b2e0ce6dc638","access_level":"open_access","file_name":"2023_ACMToG_Jeschke.pdf","date_created":"2024-01-02T09:34:27Z","file_id":"14725","success":1,"file_size":7469177,"relation":"main_file","date_updated":"2024-01-02T09:34:27Z","content_type":"application/pdf"}],"publication_status":"published","oa":1,"intvolume":"        42","file_date_updated":"2024-01-02T09:34:27Z","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"ddc":["000"],"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"4","department":[{"_id":"ChWo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14240","corr_author":"1","publication":"ACM Transactions on Graphics","day":"01"},{"conference":{"location":"Los Angeles, CA, United States","start_date":"2023-08-06","end_date":"2023-08-10","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"department":[{"_id":"BeBi"}],"_id":"14241","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"23","publication":"SIGGRAPH 2023 Conference Proceedings","corr_author":"1","year":"2023","date_created":"2023-08-27T22:01:17Z","author":[{"last_name":"Tojo","first_name":"Kenji","full_name":"Tojo, Kenji"},{"last_name":"Shamir","first_name":"Ariel","full_name":"Shamir, Ariel"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki","last_name":"Umetani"}],"language":[{"iso":"eng"}],"doi":"10.1145/3588432.3591542","publication_status":"published","oa":1,"oa_version":"Preprint","scopus_import":"1","citation":{"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>","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.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023.","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.","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>.","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>"},"abstract":[{"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.","lang":"eng"}],"article_number":"20","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.05944","open_access":"1"}],"publisher":"Association for Computing Machinery","status":"public","publication_identifier":{"isbn":["9798400701597"]},"type":"conference","isi":1,"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","article_processing_charge":"No","date_published":"2023-07-23T00:00:00Z","arxiv":1,"title":"Stealth shaper: Reflectivity optimization as surface stylization","quality_controlled":"1","date_updated":"2025-09-09T12:49:15Z","external_id":{"isi":["001117690500020"],"arxiv":["2305.05944"]},"month":"07"},{"status":"public","type":"conference","publication_identifier":{"isbn":["9781577358800"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.16187","open_access":"1"}],"publisher":"Association for the Advancement of Artificial Intelligence","scopus_import":"1","citation":{"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.","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>.","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>","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>","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."},"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"}],"oa_version":"Preprint","month":"06","date_updated":"2025-03-31T16:01:08Z","quality_controlled":"1","external_id":{"arxiv":["2211.16187"]},"article_processing_charge":"No","arxiv":1,"date_published":"2023-06-26T00:00:00Z","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.","title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","volume":37,"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","day":"26","page":"14964-14973","_id":"14242","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ec_funded":1,"conference":{"name":"AAAI: Conference on Artificial Intelligence","end_date":"2023-02-14","start_date":"2023-02-07","location":"Washington, DC, United States"},"issue":"12","intvolume":"        37","oa":1,"publication_status":"published","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"doi":"10.1609/aaai.v37i12.26747","language":[{"iso":"eng"}],"author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias"},{"orcid":"0000-0002-4681-1699","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"}],"date_created":"2023-08-27T22:01:17Z","year":"2023"},{"status":"public","type":"journal_article","publication_identifier":{"issn":["0024-6115"],"eissn":["1460-244X"]},"citation":{"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.","short":"T. Hausel, M.L. Wong, D. Wyss, Proceedings of the London Mathematical Society 127 (2023) 958–1027.","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.","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>.","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>"},"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."}],"scopus_import":"1","oa_version":"Published Version","publisher":"Wiley","date_updated":"2025-04-14T09:12:46Z","quality_controlled":"1","external_id":{"arxiv":["1807.04057"],"isi":["001049312700001"]},"month":"10","volume":127,"article_processing_charge":"Yes (via OA deal)","date_published":"2023-10-01T00:00:00Z","arxiv":1,"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).","isi":1,"title":"Arithmetic and metric aspects of open de Rham spaces","day":"01","publication":"Proceedings of the London Mathematical Society","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14244","department":[{"_id":"TaHa"}],"issue":"4","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","page":"958-1027","ddc":["510"],"language":[{"iso":"eng"}],"author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamás","last_name":"Hausel","first_name":"Tamás","orcid":"0000-0002-9582-2634"},{"full_name":"Wong, Michael Lennox","last_name":"Wong","first_name":"Michael Lennox"},{"last_name":"Wyss","first_name":"Dimitri","full_name":"Wyss, Dimitri"}],"file_date_updated":"2024-01-30T12:56:00Z","intvolume":"       127","oa":1,"publication_status":"published","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces"},{"_id":"25E6C798-B435-11E9-9278-68D0E5697425","grant_number":"153627","name":"Arithmetic quantization of character and quiver varities"}],"file":[{"file_size":651335,"content_type":"application/pdf","date_updated":"2024-01-30T12:56:00Z","relation":"main_file","date_created":"2024-01-30T12:56:00Z","success":1,"file_id":"14910","checksum":"2af4d2d6a8ae42f7d3fba0188e79ae82","creator":"dernst","file_name":"2023_ProcLondonMathSoc_Hausel.pdf","access_level":"open_access"}],"doi":"10.1112/plms.12555","year":"2023","article_type":"original","date_created":"2023-08-27T22:01:18Z"},{"year":"2023","date_created":"2023-08-28T12:36:49Z","article_type":"original","file_date_updated":"2023-09-05T08:45:49Z","author":[{"last_name":"Brauneis","first_name":"Fabian","full_name":"Brauneis, Fabian"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","first_name":"Areg"},{"last_name":"Hammer","first_name":"Hans-Werner","full_name":"Hammer, Hans-Werner"},{"orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530"],"language":[{"iso":"eng"}],"doi":"10.1038/s42005-023-01281-2","file":[{"file_size":855960,"content_type":"application/pdf","relation":"main_file","date_updated":"2023-09-05T08:45:49Z","creator":"dernst","checksum":"6edfc59b0ee7dc406d0968b05236e83d","access_level":"open_access","file_name":"2023_CommPhysics_Brauneis.pdf","date_created":"2023-09-05T08:45:49Z","file_id":"14268","success":1}],"publication_status":"published","oa":1,"intvolume":"         6","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14246","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"22","corr_author":"1","publication":"Communications Physics","volume":6,"title":"Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux","isi":1,"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.","article_processing_charge":"Yes (via OA deal)","arxiv":1,"date_published":"2023-08-22T00:00:00Z","external_id":{"arxiv":["2301.10488"],"isi":["001052577500002"]},"date_updated":"2024-10-09T21:06:47Z","quality_controlled":"1","month":"08","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"article_number":"224","scopus_import":"1","citation":{"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>","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>","short":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (2023).","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.","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>."},"keyword":["General Physics and Astronomy"],"publisher":"Springer Nature","publication_identifier":{"issn":["2399-3650"]},"type":"journal_article","status":"public"},{"external_id":{"pmid":["37633939"],"isi":["001064563400013"]},"quality_controlled":"1","date_updated":"2025-09-09T12:50:49Z","month":"08","volume":14,"title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","isi":1,"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.).","date_published":"2023-08-26T00:00:00Z","article_processing_charge":"Yes","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","status":"public","oa_version":"Published Version","scopus_import":"1","citation":{"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.","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).","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>.","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>.","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>","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>","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."},"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."}],"article_number":"5231","publisher":"Springer Nature","file_date_updated":"2023-09-06T06:50:07Z","author":[{"last_name":"Vierra","first_name":"Nicholas C.","full_name":"Vierra, Nicholas C."},{"full_name":"Ribeiro-Silva, Luisa","first_name":"Luisa","last_name":"Ribeiro-Silva"},{"first_name":"Michael","last_name":"Kirmiz","full_name":"Kirmiz, Michael"},{"full_name":"Van Der List, Deborah","first_name":"Deborah","last_name":"Van Der List"},{"orcid":"0000-0003-0863-4481","first_name":"Pradeep","last_name":"Bhandari","full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mack","first_name":"Olivia A.","full_name":"Mack, Olivia A."},{"full_name":"Carroll, James","last_name":"Carroll","first_name":"James"},{"first_name":"Elodie","last_name":"Le Monnier","full_name":"Le Monnier, Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sue A.","last_name":"Aicher","full_name":"Aicher, Sue A."},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"last_name":"Trimmer","first_name":"James S.","full_name":"Trimmer, James S."}],"language":[{"iso":"eng"}],"ddc":["570"],"file":[{"file_name":"2023_NatureComm_Vierra.pdf","access_level":"open_access","checksum":"6ab8aab4e957f626a09a1c73db3388fb","creator":"dernst","success":1,"file_id":"14270","date_created":"2023-09-06T06:50:07Z","date_updated":"2023-09-06T06:50:07Z","relation":"main_file","content_type":"application/pdf","file_size":9412549}],"doi":"10.1038/s41467-023-40930-6","publication_status":"published","oa":1,"intvolume":"        14","year":"2023","date_created":"2023-09-03T22:01:14Z","article_type":"original","day":"26","publication":"Nature Communications","department":[{"_id":"RySh"}],"_id":"14253","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"volume":285,"title":"A simple approach to Lieb-Thirring type inequalities","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).","isi":1,"date_published":"2023-11-15T00:00:00Z","arxiv":1,"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001071552300001"],"arxiv":["2303.04504"]},"date_updated":"2024-10-09T21:06:47Z","quality_controlled":"1","month":"11","oa_version":"Published Version","scopus_import":"1","citation":{"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>","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.","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>.","short":"R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023).","ista":"Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 285(10), 110129.","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>","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>."},"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."}],"article_number":"110129","publisher":"Elsevier","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"type":"journal_article","status":"public","year":"2023","date_created":"2023-09-03T22:01:14Z","article_type":"original","file_date_updated":"2024-01-30T14:15:16Z","author":[{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"},{"first_name":"Jan Philip","last_name":"Solovej","full_name":"Solovej, Jan Philip"}],"ddc":["510"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","date_updated":"2024-01-30T14:15:16Z","relation":"main_file","file_size":232934,"success":1,"file_id":"14915","date_created":"2024-01-30T14:15:16Z","file_name":"2023_JourFunctionalAnalysis_Seiringer.pdf","access_level":"open_access","checksum":"28e424ad91be6219e9d321054ce3a412","creator":"dernst"}],"doi":"10.1016/j.jfa.2023.110129","publication_status":"published","oa":1,"intvolume":"       285","department":[{"_id":"RoSe"}],"issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14254","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"15","corr_author":"1","publication":"Journal of Functional Analysis"},{"day":"14","publication":"PLoS Pathogens","pmid":1,"department":[{"_id":"FlSc"}],"issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14255","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Jana","last_name":"Koch","full_name":"Koch, Jana"},{"first_name":"Qilin","last_name":"Xin","full_name":"Xin, Qilin"},{"last_name":"Obr","first_name":"Martin","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin"},{"full_name":"Schäfer, Alicia","first_name":"Alicia","last_name":"Schäfer"},{"last_name":"Rolfs","first_name":"Nina","full_name":"Rolfs, Nina"},{"full_name":"Anagho, Holda A.","first_name":"Holda A.","last_name":"Anagho"},{"last_name":"Kudulyte","first_name":"Aiste","full_name":"Kudulyte, Aiste"},{"full_name":"Woltereck, Lea","first_name":"Lea","last_name":"Woltereck"},{"first_name":"Susann","last_name":"Kummer","full_name":"Kummer, Susann"},{"full_name":"Campos, Joaquin","first_name":"Joaquin","last_name":"Campos"},{"full_name":"Uckeley, Zina M.","last_name":"Uckeley","first_name":"Zina M."},{"full_name":"Bell-Sakyi, Lesley","first_name":"Lesley","last_name":"Bell-Sakyi"},{"full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg","last_name":"Kräusslich"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian Km","last_name":"Schur","first_name":"Florian Km","orcid":"0000-0003-4790-8078"},{"last_name":"Acuna","first_name":"Claudio","full_name":"Acuna, Claudio"},{"last_name":"Lozach","first_name":"Pierre Yves","full_name":"Lozach, Pierre Yves"}],"language":[{"iso":"eng"}],"ddc":["570"],"file_date_updated":"2023-09-06T06:41:52Z","intvolume":"        19","doi":"10.1371/journal.ppat.1011562","file":[{"checksum":"47ca3bb54b27f28b05644be0ad064bc6","creator":"dernst","file_name":"2023_PloSPathogens_Koch.pdf","access_level":"open_access","date_created":"2023-09-06T06:41:52Z","success":1,"file_id":"14269","file_size":4458336,"date_updated":"2023-09-06T06:41:52Z","relation":"main_file","content_type":"application/pdf"}],"project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"publication_status":"published","oa":1,"year":"2023","article_type":"original","date_created":"2023-09-03T22:01:14Z","status":"public","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"type":"journal_article","oa_version":"Published Version","citation":{"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>","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>","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>.","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.","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)."},"article_number":"e1011562","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"publisher":"Public Library of Science","date_updated":"2025-04-15T08:24:50Z","quality_controlled":"1","external_id":{"isi":["001050846300004"],"pmid":["37578957"]},"month":"08","acknowledged_ssus":[{"_id":"EM-Fac"}],"volume":19,"isi":1,"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_processing_charge":"Yes","date_published":"2023-08-14T00:00:00Z","title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells"},{"publication_identifier":{"eissn":["1537-6605"],"issn":["0002-9297"]},"type":"journal_article","status":"public","publisher":"Elsevier","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"scopus_import":"1","citation":{"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.","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>","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>.","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>","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.","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>."},"month":"09","external_id":{"isi":["001074842500001"],"pmid":["37543033"]},"quality_controlled":"1","date_updated":"2025-09-09T12:51:20Z","title":"Genetic insights into the age-specific biological mechanisms governing human ovarian aging","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.","isi":1,"date_published":"2023-09-07T00:00:00Z","article_processing_charge":"Yes (via OA deal)","volume":110,"corr_author":"1","publication":"American Journal of Human Genetics","day":"07","page":"1549-1563","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"9","department":[{"_id":"MaRo"}],"_id":"14258","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"file":[{"file_id":"14912","success":1,"date_created":"2024-01-30T13:20:35Z","access_level":"open_access","file_name":"2023_AJHG_Ojavee.pdf","checksum":"4108b031dc726ae6b4a5ae7e021ba188","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_updated":"2024-01-30T13:20:35Z","file_size":2551276}],"doi":"10.1016/j.ajhg.2023.07.006","oa":1,"publication_status":"published","intvolume":"       110","file_date_updated":"2024-01-30T13:20:35Z","author":[{"full_name":"Ojavee, Sven E.","first_name":"Sven E.","last_name":"Ojavee"},{"full_name":"Darrous, Liza","first_name":"Liza","last_name":"Darrous"},{"first_name":"Marion","last_name":"Patxot","full_name":"Patxot, Marion"},{"first_name":"Kristi","last_name":"Läll","full_name":"Läll, Kristi"},{"full_name":"Fischer, Krista","first_name":"Krista","last_name":"Fischer"},{"full_name":"Mägi, Reedik","first_name":"Reedik","last_name":"Mägi"},{"full_name":"Kutalik, Zoltan","last_name":"Kutalik","first_name":"Zoltan"},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"ddc":["570"],"language":[{"iso":"eng"}],"date_created":"2023-09-03T22:01:15Z","article_type":"original","year":"2023"},{"type":"journal_article","publication_identifier":{"eissn":["1948-7185"]},"status":"public","publisher":"American Chemical Society","scopus_import":"1","abstract":[{"lang":"eng","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."}],"citation":{"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>","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>.","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>.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","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."},"oa_version":"Published Version","month":"08","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"date_updated":"2023-09-06T11:04:31Z","quality_controlled":"1","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","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-08-11T00:00:00Z","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.","isi":1,"volume":14,"publication":"Journal of Physical Chemistry Letters","day":"11","page":"7395-7403","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"14261","department":[{"_id":"GradSch"}],"issue":"33","pmid":1,"publication_status":"published","oa":1,"file":[{"file_id":"14272","success":1,"date_created":"2023-09-06T07:32:39Z","access_level":"open_access","file_name":"2023_JourPhysChemistry_Gamper.pdf","checksum":"637454e2b3a357498d8d622d241c4bf6","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_updated":"2023-09-06T07:32:39Z","file_size":4986859}],"doi":"10.1021/acs.jpclett.3c01707","intvolume":"        14","file_date_updated":"2023-09-06T07:32:39Z","language":[{"iso":"eng"}],"ddc":["530","540"],"author":[{"first_name":"Jakob","last_name":"Gamper","full_name":"Gamper, Jakob"},{"full_name":"Kluibenschedl, Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","last_name":"Kluibenschedl"},{"full_name":"Weiss, Alexander K.H.","first_name":"Alexander K.H.","last_name":"Weiss"},{"full_name":"Hofer, Thomas S.","first_name":"Thomas S.","last_name":"Hofer"}],"date_created":"2023-09-03T22:01:16Z","article_type":"original","year":"2023"},{"_id":"14277","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"issue":"1","department":[{"_id":"EdHa"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","day":"20","publication":"PRX Life","corr_author":"1","year":"2023","article_type":"original","date_created":"2023-09-06T08:30:59Z","ddc":["570"],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-1585-2631","last_name":"Boocock","first_name":"Daniel R","full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hirashima","first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"}],"file_date_updated":"2023-09-15T06:30:50Z","intvolume":"         1","publication_status":"published","oa":1,"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"doi":"10.1103/prxlife.1.013001","file":[{"content_type":"application/pdf","date_updated":"2023-09-15T06:30:50Z","relation":"main_file","file_size":2559520,"success":1,"file_id":"14335","date_created":"2023-09-15T06:30:50Z","file_name":"2023_PRXLife_Boocock.pdf","access_level":"open_access","creator":"dernst","checksum":"f881d98c89eb9f1aa136d7b781511553"}],"article_number":"013001","citation":{"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>.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","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>","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>.","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>","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."},"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."}],"oa_version":"Published Version","publisher":"American Physical Society","status":"public","type":"journal_article","publication_identifier":{"issn":["2835-8279"]},"volume":1,"article_processing_charge":"Yes","date_published":"2023-07-20T00:00:00Z","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.","title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","date_updated":"2025-04-14T07:52:27Z","quality_controlled":"1","month":"07"},{"author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217"}],"date_updated":"2026-06-18T17:34:48Z","ddc":["570"],"month":"07","doi":"10.5281/ZENODO.8133960","oa":1,"year":"2023","date_created":"2023-09-06T08:39:25Z","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","article_processing_charge":"No","date_published":"2023-07-11T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14274"}]},"day":"11","corr_author":"1","type":"research_data_reference","status":"public","department":[{"_id":"EdHa"}],"_id":"14279","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","citation":{"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.","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>.","short":"M.C. Ucar, (2023).","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>.","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>"},"abstract":[{"lang":"eng","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."}],"publisher":"Zenodo","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}]},{"quality_controlled":"1","date_updated":"2023-11-07T12:42:09Z","external_id":{"pmid":["37590357"]},"month":"08","volume":381,"article_processing_charge":"No","date_published":"2023-08-17T00:00:00Z","title":"Design of stimulus-responsive two-state hinge proteins","status":"public","type":"journal_article","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"citation":{"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.","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>","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>.","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>","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.","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.","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>."},"scopus_import":"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"}],"oa_version":"None","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"author":[{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M"},{"first_name":"Philip J. Y.","last_name":"Leung","full_name":"Leung, Philip J. Y."},{"full_name":"Tessmer, Maxx H.","last_name":"Tessmer","first_name":"Maxx H."},{"full_name":"Broerman, Adam","first_name":"Adam","last_name":"Broerman"},{"last_name":"Demakis","first_name":"Cullen","full_name":"Demakis, Cullen"},{"first_name":"Acacia F.","last_name":"Dishman","full_name":"Dishman, Acacia F."},{"full_name":"Pillai, Arvind","first_name":"Arvind","last_name":"Pillai"},{"first_name":"Abbas","last_name":"Idris","full_name":"Idris, Abbas"},{"full_name":"Juergens, David","first_name":"David","last_name":"Juergens"},{"last_name":"Dauparas","first_name":"Justas","full_name":"Dauparas, Justas"},{"full_name":"Li, Xinting","last_name":"Li","first_name":"Xinting"},{"full_name":"Levine, Paul M.","last_name":"Levine","first_name":"Paul M."},{"full_name":"Lamb, Mila","last_name":"Lamb","first_name":"Mila"},{"last_name":"Ballard","first_name":"Ryanne K.","full_name":"Ballard, Ryanne K."},{"last_name":"Gerben","first_name":"Stacey R.","full_name":"Gerben, Stacey R."},{"first_name":"Hannah","last_name":"Nguyen","full_name":"Nguyen, Hannah"},{"full_name":"Kang, Alex","first_name":"Alex","last_name":"Kang"},{"last_name":"Sankaran","first_name":"Banumathi","full_name":"Sankaran, Banumathi"},{"first_name":"Asim K.","last_name":"Bera","full_name":"Bera, Asim K."},{"full_name":"Volkman, Brian F.","first_name":"Brian F.","last_name":"Volkman"},{"first_name":"Jeff","last_name":"Nivala","full_name":"Nivala, Jeff"},{"full_name":"Stoll, Stefan","first_name":"Stefan","last_name":"Stoll"},{"first_name":"David","last_name":"Baker","full_name":"Baker, David"}],"intvolume":"       381","extern":"1","publication_status":"published","doi":"10.1126/science.adg7731","year":"2023","article_type":"original","date_created":"2023-09-06T12:04:23Z","day":"17","publication":"Science","pmid":1,"_id":"14281","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6659","page":"754-760"},{"extern":"1","oa":1,"publication_status":"submitted","month":"03","doi":"10.1101/2023.03.14.532666","language":[{"iso":"eng"}],"author":[{"full_name":"Edman, Natasha I","first_name":"Natasha I","last_name":"Edman"},{"full_name":"Redler, Rachel L","last_name":"Redler","first_name":"Rachel L"},{"full_name":"Phal, Ashish","last_name":"Phal","first_name":"Ashish"},{"full_name":"Schlichthaerle, Thomas","first_name":"Thomas","last_name":"Schlichthaerle"},{"full_name":"Srivatsan, Sanjay R","last_name":"Srivatsan","first_name":"Sanjay R"},{"full_name":"Etemadi, Ali","first_name":"Ali","last_name":"Etemadi"},{"full_name":"An, Seong","last_name":"An","first_name":"Seong"},{"first_name":"Andrew","last_name":"Favor","full_name":"Favor, Andrew"},{"full_name":"Ehnes, Devon","last_name":"Ehnes","first_name":"Devon"},{"full_name":"Li, Zhe","first_name":"Zhe","last_name":"Li"},{"first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"full_name":"Gordon, Max","last_name":"Gordon","first_name":"Max"},{"first_name":"Wei","last_name":"Yang","full_name":"Yang, Wei"},{"first_name":"Brian","last_name":"Coventry","full_name":"Coventry, Brian"},{"full_name":"Hicks, Derrick R","first_name":"Derrick R","last_name":"Hicks"},{"full_name":"Cao, Longxing","last_name":"Cao","first_name":"Longxing"},{"full_name":"Bethel, Neville","first_name":"Neville","last_name":"Bethel"},{"full_name":"Heine, Piper","first_name":"Piper","last_name":"Heine"},{"full_name":"Murray, Analisa N","first_name":"Analisa N","last_name":"Murray"},{"full_name":"Gerben, Stacey","last_name":"Gerben","first_name":"Stacey"},{"full_name":"Carter, Lauren","last_name":"Carter","first_name":"Lauren"},{"full_name":"Miranda, Marcos","last_name":"Miranda","first_name":"Marcos"},{"full_name":"Negahdari, Babak","first_name":"Babak","last_name":"Negahdari"},{"full_name":"Lee, Sangwon","first_name":"Sangwon","last_name":"Lee"},{"full_name":"Trapnell, Cole","last_name":"Trapnell","first_name":"Cole"},{"full_name":"Stewart, Lance","last_name":"Stewart","first_name":"Lance"},{"last_name":"Ekiert","first_name":"Damian C","full_name":"Ekiert, Damian C"},{"full_name":"Schlessinger, Joseph","first_name":"Joseph","last_name":"Schlessinger"},{"first_name":"Jay","last_name":"Shendure","full_name":"Shendure, Jay"},{"full_name":"Bhabha, Gira","first_name":"Gira","last_name":"Bhabha"},{"last_name":"Ruohola-Baker","first_name":"Hannele","full_name":"Ruohola-Baker, Hannele"},{"full_name":"Baker, David","last_name":"Baker","first_name":"David"}],"date_updated":"2023-11-07T12:21:58Z","article_processing_charge":"No","date_published":"2023-03-15T00:00:00Z","title":"Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies","date_created":"2023-09-06T12:31:49Z","year":"2023","publication":"bioRxiv","status":"public","type":"preprint","day":"15","main_file_link":[{"url":"https://doi.org/10.1101/2023.03.14.532666","open_access":"1"}],"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."}],"citation":{"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>.","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.).","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>.","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>.","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>. ."},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14294"},{"day":"01","corr_author":"1","publication":"Current Opinion in Plant Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"14313","issue":"10","department":[{"_id":"JiFr"}],"pmid":1,"has_accepted_license":"1","file_date_updated":"2023-11-02T17:03:20Z","ddc":["580"],"language":[{"iso":"eng"}],"author":[{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","first_name":"Lukas","last_name":"Fiedler"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"oa":1,"publication_status":"published","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2023-11-02T17:03:20Z","file_size":737872,"success":1,"file_id":"14482","date_created":"2023-11-02T17:03:20Z","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","access_level":"open_access","checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","creator":"amally"}],"doi":"10.1016/j.pbi.2023.102443","intvolume":"        75","year":"2023","date_created":"2023-09-10T22:01:11Z","article_type":"review","type":"journal_article","publication_identifier":{"issn":["1369-5266"]},"status":"public","citation":{"ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. 2023;75(10). doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10. Elsevier, 2023.","mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10, 102443, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>.","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","apa":"Fiedler, L., &#38; Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>","chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>."},"article_number":"102443","abstract":[{"lang":"eng","text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling."}],"scopus_import":"1","oa_version":"Submitted Version","publisher":"Elsevier","external_id":{"isi":["001080095300001"],"pmid":["37666097"]},"date_updated":"2025-09-09T12:54:16Z","quality_controlled":"1","month":"10","volume":75,"title":"Rapid auxin signaling: Unknowns old and new","article_processing_charge":"No","date_published":"2023-10-01T00:00:00Z","isi":1,"acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology."},{"corr_author":"1","publication":"Cell Reports","day":"26","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JoCs"}],"issue":"9","ec_funded":1,"_id":"14314","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"file":[{"file_name":"2023_CellPress_Nardin.pdf","access_level":"open_access","checksum":"ca77a304fb813c292550b8604b0fb41d","creator":"dernst","success":1,"file_id":"14337","date_created":"2023-09-15T07:12:46Z","relation":"main_file","date_updated":"2023-09-15T07:12:46Z","content_type":"application/pdf","file_size":4879455}],"doi":"10.1016/j.celrep.2023.113015","project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616","call_identifier":"FP7","name":"inter-and intracellular signalling in schizophrenia"}],"publication_status":"published","oa":1,"intvolume":"        42","file_date_updated":"2023-09-15T07:12:46Z","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570"},{"last_name":"Käfer","first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico","last_name":"Stella","first_name":"Federico","orcid":"0000-0001-9439-3148"},{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"ddc":["570"],"date_created":"2023-09-10T22:01:11Z","article_type":"original","year":"2023","publication_identifier":{"eissn":["2211-1247"]},"type":"journal_article","status":"public","publisher":"Elsevier","oa_version":"Published Version","article_number":"113015","citation":{"ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. 2023;42(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” <i>Cell Reports</i>, vol. 42, no. 9. Elsevier, 2023.","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>, vol. 42, no. 9, 113015, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>.","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","apa":"Nardin, M., Käfer, K., Stella, F., &#38; Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>","chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>."},"abstract":[{"lang":"eng","text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations."}],"scopus_import":"1","month":"09","external_id":{"isi":["001068779200001"],"pmid":["37632747"]},"date_updated":"2025-09-09T12:53:32Z","quality_controlled":"1","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","isi":1,"acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","article_processing_charge":"Yes","date_published":"2023-09-26T00:00:00Z","volume":42},{"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"department":[{"_id":"MaHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14315","publication":"eLife","corr_author":"1","day":"04","article_type":"original","date_created":"2023-09-10T22:01:11Z","year":"2023","intvolume":"        12","file":[{"file_id":"14336","success":1,"date_created":"2023-09-15T06:59:10Z","access_level":"open_access","file_name":"2023_eLife_Cho.pdf","creator":"dernst","checksum":"db24bf3d595507387b48d3799c33e289","date_updated":"2023-09-15T06:59:10Z","relation":"main_file","content_type":"application/pdf","file_size":3703097}],"doi":"10.7554/eLife.89066","publication_status":"published","oa":1,"author":[{"full_name":"Cho, Ukrae H.","first_name":"Ukrae H.","last_name":"Cho"},{"full_name":"Hetzer, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"Hetzer","first_name":"Martin W"}],"ddc":["570"],"language":[{"iso":"eng"}],"file_date_updated":"2023-09-15T06:59:10Z","publisher":"eLife Sciences Publications","oa_version":"Published Version","citation":{"ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>.","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","short":"U.H. Cho, M. Hetzer, ELife 12 (2023).","apa":"Cho, U. H., &#38; Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>."},"abstract":[{"text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.","lang":"eng"}],"scopus_import":"1","article_number":"RP89066","status":"public","publication_identifier":{"eissn":["2050-084X"]},"type":"journal_article","acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","article_processing_charge":"Yes","date_published":"2023-09-04T00:00:00Z","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","volume":12,"month":"09","quality_controlled":"1","date_updated":"2024-10-09T21:06:57Z","external_id":{"pmid":["37665327"]}},{"pmid":1,"department":[{"_id":"DaSi"}],"issue":"17","_id":"14316","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Journal of Cell Science","day":"01","article_type":"original","date_created":"2023-09-10T22:01:12Z","year":"2023","intvolume":"       136","doi":"10.1242/jcs.261448","oa":1,"publication_status":"published","author":[{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"first_name":"Kaito","last_name":"Aoshima","full_name":"Aoshima, Kaito"},{"full_name":"Shimamura, Hiroki","first_name":"Hiroki","last_name":"Shimamura"},{"orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Junko Y.","last_name":"Toshima","full_name":"Toshima, Junko Y."},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.27.534325"}],"publisher":"The Company of Biologists","oa_version":"Preprint","article_number":"jcs261448","abstract":[{"text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.","lang":"eng"}],"scopus_import":"1","citation":{"ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. 2023;136(17). doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>","ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” <i>Journal of Cell Science</i>, vol. 136, no. 17. The Company of Biologists, 2023.","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448.","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>.","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>.","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &#38; Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>"},"status":"public","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"type":"journal_article","isi":1,"date_published":"2023-09-01T00:00:00Z","article_processing_charge":"No","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","volume":136,"month":"09","date_updated":"2025-09-09T12:56:46Z","quality_controlled":"1","external_id":{"pmid":["37539494"],"isi":["001112832300005"]}},{"publisher":"Springer Nature","oa_version":"Published Version","scopus_import":"1","citation":{"chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112.","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>"},"abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]},"type":"conference","status":"public","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","isi":1,"acknowledgement":"This work was supported in part 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 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","date_published":"2023-07-17T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","volume":13966,"month":"07","external_id":{"isi":["001310805600005"]},"quality_controlled":"1","date_updated":"2025-09-09T12:56:00Z","page":"86-112","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"conference":{"location":"Paris, France","name":"CAV: Computer Aided Verification","end_date":"2023-07-22","start_date":"2023-07-17"},"department":[{"_id":"KrCh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"14317","publication":"International Conference on Computer Aided Verification","day":"17","date_created":"2023-09-10T22:01:12Z","alternative_title":["LNCS"],"year":"2023","file":[{"file_name":"2023_LNCS_Akshay.pdf","access_level":"open_access","creator":"dernst","checksum":"f143c8eedf609f20f2aad2eeb496d53f","success":1,"file_id":"14349","date_created":"2023-09-20T08:46:43Z","relation":"main_file","content_type":"application/pdf","date_updated":"2023-09-20T08:46:43Z","file_size":531745}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"doi":"10.1007/978-3-031-37709-9_5","publication_status":"published","oa":1,"intvolume":"     13966","file_date_updated":"2023-09-20T08:46:43Z","author":[{"last_name":"Akshay","first_name":"S.","full_name":"Akshay, S."},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","first_name":"Tobias","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165"},{"first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"ddc":["000"],"language":[{"iso":"eng"}]},{"volume":13966,"article_processing_charge":"Yes (in subscription journal)","date_published":"2023-07-17T00:00:00Z","acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","isi":1,"title":"Automated tail bound analysis for probabilistic recurrence relations","quality_controlled":"1","date_updated":"2025-09-09T12:55:28Z","external_id":{"isi":["001310805600002"]},"month":"07","citation":{"ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 16–39.","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: <i>Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:16-39. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In <i>Computer Aided Verification</i>, 13966:16–39. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>.","apa":"Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In <i>Computer Aided Verification</i> (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” <i>Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice."}],"oa_version":"Published Version","publisher":"Springer Nature","related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"status":"public","type":"conference","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]},"year":"2023","alternative_title":["LNCS"],"date_created":"2023-09-10T22:01:12Z","ddc":["000"],"language":[{"iso":"eng"}],"author":[{"full_name":"Sun, Yican","first_name":"Yican","last_name":"Sun"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-09-20T08:24:47Z","intvolume":"     13966","publication_status":"published","oa":1,"file":[{"file_size":624647,"relation":"main_file","date_updated":"2023-09-20T08:24:47Z","content_type":"application/pdf","date_created":"2023-09-20T08:24:47Z","success":1,"file_id":"14348","checksum":"42917e086f8c7699f3bccf84f74fe000","creator":"dernst","file_name":"2023_LNCS_Sun.pdf","access_level":"open_access"}],"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"doi":"10.1007/978-3-031-37709-9_2","_id":"14318","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"start_date":"2023-07-17","name":"CAV: Computer Aided Verification","end_date":"2023-07-22","location":"Paris, France"},"department":[{"_id":"KrCh"}],"ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","page":"16-39","day":"17","publication":"Computer Aided Verification"}]