[{"date_updated":"2025-09-10T09:55:10Z","author":[{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"issn":["0037-9484"],"eissn":["2102-622X"]},"oa_version":"None","fulldoi":"https://doi.org/10.24033/ast.1188","corr_author":"1","article_processing_charge":"No","department":[{"_id":"UlWa"}],"volume":438,"article_type":"original","doi":"10.24033/ast.1188","year":"2022","abstract":[{"text":"Expander graphs (sparse but highly connected graphs) have, since their inception, been the source of deep links between Mathematics and Computer Science as well as applications to other areas. In recent years, a fascinating theory of high-dimensional expanders has begun to emerge, which is still in a formative stage but has nonetheless already lead to a number of striking results. Unlike for graphs, in higher dimensions there is a rich array of non-equivalent notions of expansion (coboundary expansion, cosystolic expansion, topological expansion, spectral expansion, etc.), with differents strengths and applications. In this talk, we will survey this landscape of high-dimensional expansion, with a focus on two main results. First, we will present Gromov’s Topological Overlap Theorem, which asserts that coboundary expansion (a quantitative version of vanishing mod 2 cohomology) implies topological expansion (roughly, the property that for every map from a simplicial complex to a manifold of the same dimension, the images of a positive fraction of the simplices have a point in common). Second, we will outline a construction of bounded degree 2-dimensional topological expanders, due to Kaufman, Kazhdan, and Lubotzky.","lang":"eng"}],"scopus_import":"1","citation":{"short":"U. Wagner, Bulletin de La Societe Mathematique de France 438 (2022) 281–294.","mla":"Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” <i>Bulletin de La Societe Mathematique de France</i>, vol. 438, Societe Mathematique de France, 2022, pp. 281–94, doi:<a href=\"https://doi.org/10.24033/ast.1188\">10.24033/ast.1188</a>.","chicago":"Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” <i>Bulletin de La Societe Mathematique de France</i>. Societe Mathematique de France, 2022. <a href=\"https://doi.org/10.24033/ast.1188\">https://doi.org/10.24033/ast.1188</a>.","apa":"Wagner, U. (2022). High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). <i>Bulletin de La Societe Mathematique de France</i>. Societe Mathematique de France. <a href=\"https://doi.org/10.24033/ast.1188\">https://doi.org/10.24033/ast.1188</a>","ama":"Wagner U. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). <i>Bulletin de la Societe Mathematique de France</i>. 2022;438:281-294. doi:<a href=\"https://doi.org/10.24033/ast.1188\">10.24033/ast.1188</a>","ista":"Wagner U. 2022. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). Bulletin de la Societe Mathematique de France. 438, 281–294.","ieee":"U. Wagner, “High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others),” <i>Bulletin de la Societe Mathematique de France</i>, vol. 438. Societe Mathematique de France, pp. 281–294, 2022."},"external_id":{"isi":["000958364400007"]},"intvolume":"       438","status":"public","type":"journal_article","title":"High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others)","quality_controlled":"1","month":"01","date_published":"2022-01-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-10-01T22:01:14Z","publisher":"Societe Mathematique de France","publication_status":"published","page":"281-294","day":"01","_id":"14381","publication":"Bulletin de la Societe Mathematique de France"},{"article_processing_charge":"No","issue":"7941","department":[{"_id":"MaIb"}],"volume":612,"article_type":"letter_note","doi":"10.1038/d41586-022-04447-0","year":"2022","abstract":[{"text":"Future LEDs could be based on lead halide perovskites. A breakthrough in preparing device-compatible solids composed of nanoscale perovskite crystals overcomes a long-standing hurdle in making blue perovskite LEDs.","lang":"eng"}],"scopus_import":"1","citation":{"chicago":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>.","short":"H. Utzat, M. Ibáñez, Nature 612 (2022) 638–639.","mla":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>, vol. 612, no. 7941, Springer Nature, 2022, pp. 638–39, doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>.","ieee":"H. Utzat and M. Ibáñez, “Molecular engineering enables bright blue LEDs,” <i>Nature</i>, vol. 612, no. 7941. Springer Nature, pp. 638–639, 2022.","apa":"Utzat, H., &#38; Ibáñez, M. (2022). Molecular engineering enables bright blue LEDs. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>","ama":"Utzat H, Ibáñez M. Molecular engineering enables bright blue LEDs. <i>Nature</i>. 2022;612(7941):638-639. doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>","ista":"Utzat H, Ibáñez M. 2022. Molecular engineering enables bright blue LEDs. Nature. 612(7941), 638–639."},"author":[{"last_name":"Utzat","first_name":"Hendrik","full_name":"Utzat, Hendrik"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"date_updated":"2025-09-10T09:55:51Z","language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"isi":1,"fulldoi":"https://doi.org/10.1038/d41586-022-04447-0","oa_version":"None","corr_author":"1","date_published":"2022-12-21T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-10-17T11:14:43Z","publisher":"Springer Nature","publication_status":"published","keyword":["Multidisciplinary"],"day":"21","page":"638-639","_id":"14437","publication":"Nature","external_id":{"isi":["000934065100010"],"pmid":["36543947"]},"intvolume":"       612","status":"public","type":"journal_article","title":"Molecular engineering enables bright blue LEDs","quality_controlled":"1","month":"12"},{"citation":{"chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>.","mla":"Zemlicka, Martin, et al. <i>Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022).","ieee":"M. Zemlicka <i>et al.</i>, “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>.","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., &#38; Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>"},"_id":"14520","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses\" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request."}],"year":"2022","related_material":{"record":[{"relation":"used_in_publication","id":"14517","status":"public"}]},"doi":"10.5281/ZENODO.8408897","ddc":["530"],"day":"28","publisher":"Zenodo","department":[{"_id":"JoFi"}],"date_published":"2022-06-28T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8408897"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-11-13T08:09:10Z","article_processing_charge":"No","month":"06","license":"https://creativecommons.org/publicdomain/zero/1.0/","fulldoi":"https://doi.org/10.5281/ZENODO.8408897","corr_author":"1","oa_version":"Published Version","type":"research_data_reference","title":"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses","status":"public","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"oa":1,"has_accepted_license":"1","date_updated":"2026-06-03T07:16:02Z","author":[{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin","full_name":"Zemlicka, Martin","orcid":"0009-0005-0878-3032"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena"},{"last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"full_name":"Trioni, Andrea","first_name":"Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}]},{"ec_funded":1,"article_number":"2210.05308","oa_version":"Preprint","fulldoi":"https://doi.org/10.48550/ARXIV.2210.05308","corr_author":"1","language":[{"iso":"eng"}],"author":[{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"date_updated":"2026-04-07T13:27:56Z","oa":1,"year":"2022","abstract":[{"text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold $p\\in[0,1]$ over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on $3$ stochastic non-linear reinforcement learning tasks.","lang":"eng"}],"arxiv":1,"doi":"10.48550/ARXIV.2210.05308","citation":{"mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>ArXiv</i>, 2210.05308, doi:<a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>.","short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, ArXiv (n.d.).","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">https://doi.org/10.48550/ARXIV.2210.05308</a>.","ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. arXiv, 2210.05308.","apa":"Zikelic, D., Lechner, M., Henzinger, T. A., &#38; Chatterjee, K. (n.d.). Learning control policies for stochastic systems with reach-avoid guarantees. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">https://doi.org/10.48550/ARXIV.2210.05308</a>","ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” <i>arXiv</i>. ."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2210.05308"}],"article_processing_charge":"No","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"type":"preprint","title":"Learning control policies for stochastic systems with reach-avoid guarantees","status":"public","license":"https://creativecommons.org/licenses/by-sa/4.0/","month":"11","external_id":{"arxiv":["2210.05308"]},"tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"related_material":{"record":[{"status":"public","id":"14830","relation":"later_version"},{"id":"14539","status":"public","relation":"dissertation_contains"}]},"day":"29","OA_place":"repository","_id":"14600","publication":"arXiv","date_published":"2022-11-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-11-24T13:10:09Z","publication_status":"draft"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14539"}]},"day":"24","_id":"14601","publication":"arXiv","OA_place":"repository","date_published":"2022-05-24T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-11-24T13:22:30Z","publication_status":"draft","status":"public","type":"preprint","title":"Learning stabilizing policies in stochastic control systems","month":"05","external_id":{"arxiv":["2205.11991"]},"doi":"10.48550/arXiv.2205.11991","abstract":[{"text":"In this work, we address the problem of learning provably stable neural\r\nnetwork policies for stochastic control systems. While recent work has\r\ndemonstrated the feasibility of certifying given policies using martingale\r\ntheory, the problem of how to learn such policies is little explored. Here, we\r\nstudy the effectiveness of jointly learning a policy together with a martingale\r\ncertificate that proves its stability using a single learning algorithm. We\r\nobserve that the joint optimization problem becomes easily stuck in local\r\nminima when starting from a randomly initialized policy. Our results suggest\r\nthat some form of pre-training of the policy is required for the joint\r\noptimization to repair and verify the policy successfully.","lang":"eng"}],"year":"2022","arxiv":1,"citation":{"ieee":"D. Zikelic, M. Lechner, K. Chatterjee, and T. A. Henzinger, “Learning stabilizing policies in stochastic control systems,” <i>arXiv</i>. .","ista":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. arXiv, 2205.11991.","ama":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>","apa":"Zikelic, D., Lechner, M., Chatterjee, K., &#38; Henzinger, T. A. (n.d.). Learning stabilizing policies in stochastic control systems. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">https://doi.org/10.48550/arXiv.2205.11991</a>","chicago":"Zikelic, Dorde, Mathias Lechner, Krishnendu Chatterjee, and Thomas A Henzinger. “Learning Stabilizing Policies in Stochastic Control Systems.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">https://doi.org/10.48550/arXiv.2205.11991</a>.","mla":"Zikelic, Dorde, et al. “Learning Stabilizing Policies in Stochastic Control Systems.” <i>ArXiv</i>, 2205.11991, doi:<a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>.","short":"D. Zikelic, M. Lechner, K. Chatterjee, T.A. Henzinger, ArXiv (n.d.)."},"main_file_link":[{"url":"https://arxiv.org/abs/2205.11991","open_access":"1"}],"article_processing_charge":"No","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"article_number":"2205.11991","ec_funded":1,"fulldoi":"https://doi.org/10.48550/arXiv.2205.11991","corr_author":"1","oa_version":"Preprint","date_updated":"2026-04-07T13:27:56Z","author":[{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde"},{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"language":[{"iso":"eng"}],"oa":1},{"status":"public","type":"preprint","title":"On the size of chromatic Delaunay mosaics","month":"12","external_id":{"arxiv":["2212.03121"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"later_version","id":"20456","status":"public"},{"id":"15094","status":"public","relation":"dissertation_contains"}]},"day":"06","_id":"15090","publication":"arXiv","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-12-06T00:00:00Z","date_created":"2024-03-08T09:54:20Z","publication_status":"draft","article_number":"2212.03121","ec_funded":1,"corr_author":"1","oa_version":"Preprint","author":[{"full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas"},{"full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano"},{"full_name":"Draganov, Ondrej","orcid":"0000-0003-0464-3823","first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","full_name":"Saghafian, Morteza"}],"date_updated":"2026-04-07T12:58:47Z","language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"Given a locally finite set A⊆Rd and a coloring χ:A→{0,1,…,s}, we introduce the chromatic Delaunay mosaic of χ, which is a Delaunay mosaic in Rs+d that represents how points of different colors mingle. Our main results are bounds on the size of the chromatic Delaunay mosaic, in which we assume that d and s are constants. For example, if A is finite with n=#A, and the coloring is random, then the chromatic Delaunay mosaic has O(n⌈d/2⌉) cells in expectation. In contrast, for Delone sets and Poisson point processes in Rd, the expected number of cells within a closed ball is only a constant times the number of points in this ball. Furthermore, in R2 all colorings of a dense set of n points have chromatic Delaunay mosaics of size O(n). This encourages the use of chromatic Delaunay mosaics in applications.","lang":"eng"}],"year":"2022","arxiv":1,"citation":{"apa":"Biswas, R., Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). On the size of chromatic Delaunay mosaics. <i>arXiv</i>.","ama":"Biswas R, Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. On the size of chromatic Delaunay mosaics. <i>arXiv</i>.","ista":"Biswas R, Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. On the size of chromatic Delaunay mosaics. arXiv, 2212.03121.","ieee":"R. Biswas, S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “On the size of chromatic Delaunay mosaics,” <i>arXiv</i>. .","short":"R. Biswas, S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","mla":"Biswas, Ranita, et al. “On the Size of Chromatic Delaunay Mosaics.” <i>ArXiv</i>, 2212.03121.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “On the Size of Chromatic Delaunay Mosaics.” <i>ArXiv</i>, n.d."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03121"}],"article_processing_charge":"No","department":[{"_id":"HeEd"}],"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"name":"Persistent Homology, Algorithms and Stochastic Geometry","grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF"}]},{"type":"journal_article","title":"Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior","status":"public","month":"01","quality_controlled":"1","external_id":{"pmid":["34414600"]},"intvolume":"        90","keyword":["Molecular Biology","Biochemistry","Structural Biology"],"day":"01","page":"258-269","_id":"15268","publication":"Proteins: Structure, Function, and Bioinformatics","date_published":"2022-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-04-03T07:49:53Z","publisher":"Wiley","publication_status":"published","publication_identifier":{"issn":["0887-3585"],"eissn":["1097-0134"]},"oa_version":"Preprint","fulldoi":"https://doi.org/10.1002/prot.26217","corr_author":"1","language":[{"iso":"eng"}],"author":[{"full_name":"Gisonno, Romina A.","first_name":"Romina A.","last_name":"Gisonno"},{"full_name":"Masson, Tomas","orcid":"0000-0002-2634-6283","first_name":"Tomas","last_name":"Masson","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207"},{"full_name":"Ramella, Nahuel A.","last_name":"Ramella","first_name":"Nahuel A."},{"full_name":"Barrera, Exequiel E.","last_name":"Barrera","first_name":"Exequiel E."},{"last_name":"Romanowski","first_name":"Víctor","full_name":"Romanowski, Víctor"},{"full_name":"Tricerri, M. Alejandra","first_name":"M. Alejandra","last_name":"Tricerri"}],"date_updated":"2024-10-09T21:08:44Z","pmid":1,"oa":1,"abstract":[{"text":"Apolipoprotein A‐I (apoA‐I) has a key function in the reverse cholesterol transport. However, aggregation of apoA‐I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural consequences introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA‐I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation‐prone regions (APRs) present in apoA‐I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA‐I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA‐I. Structural properties of full‐length apoA‐I models suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Compared to silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha‐helix bundle with the concomitant exposure of APR1 to the solvent, suggesting an insight into the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA‐I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region.","lang":"eng"}],"year":"2022","doi":"10.1002/prot.26217","citation":{"mla":"Gisonno, Romina A., et al. “Evolutionary and Structural Constraints Influencing Apolipoprotein A‐I Amyloid Behavior.” <i>Proteins: Structure, Function, and Bioinformatics</i>, vol. 90, no. 1, Wiley, 2022, pp. 258–69, doi:<a href=\"https://doi.org/10.1002/prot.26217\">10.1002/prot.26217</a>.","short":"R.A. Gisonno, T. Masson, N.A. Ramella, E.E. Barrera, V. Romanowski, M.A. Tricerri, Proteins: Structure, Function, and Bioinformatics 90 (2022) 258–269.","chicago":"Gisonno, Romina A., Tomas Masson, Nahuel A. Ramella, Exequiel E. Barrera, Víctor Romanowski, and M. Alejandra Tricerri. “Evolutionary and Structural Constraints Influencing Apolipoprotein A‐I Amyloid Behavior.” <i>Proteins: Structure, Function, and Bioinformatics</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/prot.26217\">https://doi.org/10.1002/prot.26217</a>.","ama":"Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA. Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. <i>Proteins: Structure, Function, and Bioinformatics</i>. 2022;90(1):258-269. doi:<a href=\"https://doi.org/10.1002/prot.26217\">10.1002/prot.26217</a>","ista":"Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA. 2022. Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. Proteins: Structure, Function, and Bioinformatics. 90(1), 258–269.","apa":"Gisonno, R. A., Masson, T., Ramella, N. A., Barrera, E. E., Romanowski, V., &#38; Tricerri, M. A. (2022). Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. <i>Proteins: Structure, Function, and Bioinformatics</i>. Wiley. <a href=\"https://doi.org/10.1002/prot.26217\">https://doi.org/10.1002/prot.26217</a>","ieee":"R. A. Gisonno, T. Masson, N. A. Ramella, E. E. Barrera, V. Romanowski, and M. A. Tricerri, “Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior,” <i>Proteins: Structure, Function, and Bioinformatics</i>, vol. 90, no. 1. Wiley, pp. 258–269, 2022."},"issue":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.09.18.304337","open_access":"1"}],"article_processing_charge":"No","volume":90,"article_type":"original","department":[{"_id":"MaJö"}]},{"date_updated":"2026-06-18T17:51:26Z","author":[{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"language":[{"iso":"eng"}],"oa":1,"isi":1,"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"article_number":"jcs259715","oa_version":"Published Version","fulldoi":"https://doi.org/10.1242/jcs.259715","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.259715"}],"article_processing_charge":"No","issue":"2","department":[{"_id":"MaLo"}],"volume":135,"doi":"10.1242/jcs.259715","ddc":["570"],"year":"2022","abstract":[{"lang":"eng","text":"Martin Loose studied chemistry at the University of Heidelberg, Germany. He then joined Petra Schwille's group at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, where he obtained his PhD degree in 2010 for work on self-organization and pattern formation in the bacterial Min protein system. He then moved to Tim Mitchison's lab at Harvard Medical School, Boston, USA for his postdoc, funded by Human Frontier Science Program (HSFP) and European Molecular Biology Organization (EMBO) long-term fellowships; there, he discovered that the bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Martin established his independent research group at the Institute of Science and Technology (IST) Austria in 2015, supported by an European Research Council (ERC) starting grant and HFSP Young Investigator Grant. His lab studies the self-organization of bacterial cell division and small GTPase networks."}],"citation":{"short":"M. Loose, Cell Scientist to Watch – Martin Loose, The Company of Biologists, 2022.","mla":"Loose, Martin. “Cell Scientist to Watch – Martin Loose.” <i>Journal of Cell Science</i>, vol. 135, no. 2, jcs259715, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.259715\">10.1242/jcs.259715</a>.","chicago":"Loose, Martin. <i>Cell Scientist to Watch – Martin Loose</i>. <i>Journal of Cell Science</i>. Vol. 135. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.259715\">https://doi.org/10.1242/jcs.259715</a>.","apa":"Loose, M. (2022). <i>Cell scientist to watch – Martin Loose</i>. <i>Journal of Cell Science</i> (Vol. 135). The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.259715\">https://doi.org/10.1242/jcs.259715</a>","ama":"Loose M. <i>Cell Scientist to Watch – Martin Loose</i>. Vol 135. The Company of Biologists; 2022. doi:<a href=\"https://doi.org/10.1242/jcs.259715\">10.1242/jcs.259715</a>","ista":"Loose M. 2022. Cell scientist to watch – Martin Loose, The Company of Biologists,p.","ieee":"M. Loose, <i>Cell scientist to watch – Martin Loose</i>, vol. 135, no. 2. The Company of Biologists, 2022."},"external_id":{"isi":["000762665200015"]},"intvolume":"       135","status":"public","type":"other_academic_publication","title":"Cell scientist to watch – Martin Loose","month":"01","quality_controlled":"1","date_published":"2022-01-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-05-28T13:28:30Z","publisher":"The Company of Biologists","publication_status":"published","day":"19","_id":"17057","publication":"Journal of Cell Science"},{"department":[{"_id":"DaAl"}],"volume":162,"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"article_processing_charge":"Yes","citation":{"apa":"Frantar, E., &#38; Alistarh, D.-A. (2022). SPDY: Accurate pruning with speedup guarantees. In <i>39th International Conference on Machine Learning</i> (Vol. 162, pp. 6726–6743). Baltimore, MD, United States: ML Research Press.","ista":"Frantar E, Alistarh D-A. 2022. SPDY: Accurate pruning with speedup guarantees. 39th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 162, 6726–6743.","ama":"Frantar E, Alistarh D-A. SPDY: Accurate pruning with speedup guarantees. In: <i>39th International Conference on Machine Learning</i>. Vol 162. ML Research Press; 2022:6726-6743.","ieee":"E. Frantar and D.-A. Alistarh, “SPDY: Accurate pruning with speedup guarantees,” in <i>39th International Conference on Machine Learning</i>, Baltimore, MD, United States, 2022, vol. 162, pp. 6726–6743.","short":"E. Frantar, D.-A. Alistarh, in:, 39th International Conference on Machine Learning, ML Research Press, 2022, pp. 6726–6743.","mla":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” <i>39th International Conference on Machine Learning</i>, vol. 162, ML Research Press, 2022, pp. 6726–43.","chicago":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” In <i>39th International Conference on Machine Learning</i>, 162:6726–43. ML Research Press, 2022."},"alternative_title":["PMLR"],"ddc":["000"],"scopus_import":"1","abstract":[{"lang":"eng","text":"The recent focus on the efficiency of deep neural networks (DNNs) has led to significant work on model compression approaches, of which weight pruning is one of the most popular. At the same time, there is rapidly-growing computational support for efficiently executing the unstructured-sparse models obtained via pruning. Yet, most existing pruning methods minimize just the number of remaining weights, i.e. the size of the model, rather than optimizing for inference time. We address this gap by introducing SPDY, a new compression method which automatically determines layer-wise sparsity targets achieving a desired inference speedup on a given system, while minimizing accuracy loss. SPDY is the composition of two new techniques. The first is an efficient and general dynamic programming algorithm for solving constrained layer-wise compression problems, given a set of layer-wise error scores. The second technique is a local search procedure for automatically determining such scores in an accurate and robust manner. Experiments across popular vision and language models show that SPDY guarantees speedups while recovering higher accuracy relative to existing strategies, both for one-shot and gradual pruning scenarios, and is compatible with most existing pruning approaches. We also extend our approach to the recently-proposed task of pruning with very little data, where we achieve the best known accuracy recovery when pruning to the GPU-supported 2:4 sparsity pattern."}],"year":"2022","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No 805223 ScaleML),\r\nas well as computational support from AWS EC2. We thank Eldar Kurtic for code and hyper-parameters for BERT pruning, and the Neural Magic Team, notably Michael Goin and\r\nMark Kurtz, for support with their software.","oa":1,"date_updated":"2025-04-14T07:49:14Z","author":[{"id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar","first_name":"Elias","full_name":"Frantar, Elias"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"language":[{"iso":"eng"}],"conference":{"location":"Baltimore, MD, United States","name":"ICML: International Conference on Machine Learning","start_date":"2022-07-17","end_date":"2022-07-23"},"oa_version":"Published Version","corr_author":"1","isi":1,"ec_funded":1,"file":[{"success":1,"relation":"main_file","file_size":615916,"creator":"dernst","checksum":"5179a1e4dfc0fbfab6674907299e414a","date_created":"2024-08-19T06:54:41Z","date_updated":"2024-08-19T06:54:41Z","access_level":"open_access","file_id":"17440","file_name":"2022_PMLR_Frantar.pdf","content_type":"application/pdf"}],"publication_status":"published","publisher":"ML Research Press","date_created":"2024-05-28T13:45:20Z","date_published":"2022-07-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"39th International Conference on Machine Learning","_id":"17059","day":"20","page":"6726-6743","intvolume":"       162","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000922378801029"]},"has_accepted_license":"1","quality_controlled":"1","month":"07","status":"public","title":"SPDY: Accurate pruning with speedup guarantees","file_date_updated":"2024-08-19T06:54:41Z","type":"conference"},{"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"KrPi"}],"ddc":["000"],"doi":"10.1145/3558535.3559775","arxiv":1,"scopus_import":"1","acknowledgement":"This work was supported partially by ERC Starting Grant QIP–805241, by the Vienna business agency (Wirtschaftsagentur) through the Vienna Cybersecurity and Privacy Research Center\r\n(ViSP) and by the Austrian Science Fund (FWF) project I 4800-N (ADVISE).\r\nThe first author would like to thank Daniel Dadush for suggesting the use of discrepancy techniques to solve the transaction aggregation problem.","year":"2022","abstract":[{"lang":"eng","text":"Payment channel networks (PCNs) are one of the most prominent solutions to the limited transaction throughput of blockchains. Nevertheless, PCNs suffer themselves from a throughput limitation due to the capital constraints of their channels. A similar dependence on high capital is also found in inter-bank payment settlements, where the so-called netting technique is used to mitigate liquidity demands.\r\nIn this work, we alleviate this limitation by introducing the notion of transaction aggregation: instead of executing transactions sequentially through a PCN, we enable senders to aggregate multiple transactions and execute them simultaneously to benefit from several amounts that may \"cancel out\". Two direct advantages of our proposal is the decrease in intermediary fees paid by senders as well as the obfuscation of the transaction data from the intermediaries.\r\nWe formulate the transaction aggregation as a computational problem, a generalization of the Bank Clearing Problem. We present a generic framework for the transaction aggregation execution, and thereafter we propose Wiser as an implementation of this framework in a specific hub-based setting. To overcome the NP-hardness of the transaction aggregation problem, in Wiser we propose a fixed-parameter linear algorithm for a special case of transaction aggregation as well as the Bank Clearing Problem. Wiser can also be seen as a modern variant of the Hawala money transfer system, as well as a decentralized implementation of the overseas remittance service of Wise."}],"citation":{"mla":"Tiwari, Samarth, et al. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>, Association for Computing Machinery, 2022, pp. 217–31, doi:<a href=\"https://doi.org/10.1145/3558535.3559775\">10.1145/3558535.3559775</a>.","short":"S. Tiwari, M.X. Yeo, Z. Avarikioti, I. Salem, K.Z. Pietrzak, S. Schmid, in:, Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Association for Computing Machinery, 2022, pp. 217–231.","chicago":"Tiwari, Samarth, Michelle X Yeo, Zeta Avarikioti, Iosif Salem, Krzysztof Z Pietrzak, and Stefan Schmid. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” In <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>, 217–31. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3558535.3559775\">https://doi.org/10.1145/3558535.3559775</a>.","ista":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. 2022. Wiser: Increasing throughput in payment channel networks with transaction aggregation. Proceedings of the 4th ACM Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, 217–231.","ama":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. Wiser: Increasing throughput in payment channel networks with transaction aggregation. In: <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>. Association for Computing Machinery; 2022:217-231. doi:<a href=\"https://doi.org/10.1145/3558535.3559775\">10.1145/3558535.3559775</a>","apa":"Tiwari, S., Yeo, M. X., Avarikioti, Z., Salem, I., Pietrzak, K. Z., &#38; Schmid, S. (2022). Wiser: Increasing throughput in payment channel networks with transaction aggregation. In <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i> (pp. 217–231). Cambridge, MA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558535.3559775\">https://doi.org/10.1145/3558535.3559775</a>","ieee":"S. Tiwari, M. X. Yeo, Z. Avarikioti, I. Salem, K. Z. Pietrzak, and S. Schmid, “Wiser: Increasing throughput in payment channel networks with transaction aggregation,” in <i>Proceedings of the 4th ACM Conference on Advances in Financial Technologies</i>, Cambridge, MA, United States, 2022, pp. 217–231."},"author":[{"first_name":"Samarth","last_name":"Tiwari","full_name":"Tiwari, Samarth"},{"full_name":"Yeo, Michelle X","orcid":"0009-0001-3676-4809","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo"},{"last_name":"Avarikioti","first_name":"Zeta","full_name":"Avarikioti, Zeta"},{"first_name":"Iosif","last_name":"Salem","full_name":"Salem, Iosif"},{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"date_updated":"2025-09-10T09:57:48Z","language":[{"iso":"eng"}],"conference":{"end_date":"2022-09-21","start_date":"2022-09-19","name":"AFT: Conference on Advances in Financial Technologies","location":"Cambridge, MA, United States"},"oa":1,"publication_identifier":{"isbn":["9781450398619"]},"isi":1,"file":[{"success":1,"relation":"main_file","file_size":574728,"creator":"dernst","date_updated":"2024-08-19T06:45:21Z","access_level":"open_access","checksum":"54a7d405f8e57dba24728599ca63818c","date_created":"2024-08-19T06:45:21Z","content_type":"application/pdf","file_name":"2022_AFT_Tiwari.pdf","file_id":"17439"}],"fulldoi":"https://doi.org/10.1145/3558535.3559775","oa_version":"Published Version","date_created":"2024-05-28T13:58:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2022-09-19T00:00:00Z","publication_status":"published","publisher":"Association for Computing Machinery","day":"19","page":"217-231","publication":"Proceedings of the 4th ACM Conference on Advances in Financial Technologies","_id":"17060","has_accepted_license":"1","external_id":{"arxiv":["2205.11597"],"isi":["001041852800015"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","title":"Wiser: Increasing throughput in payment channel networks with transaction aggregation","type":"conference","file_date_updated":"2024-08-19T06:45:21Z","month":"09","quality_controlled":"1"},{"status":"public","title":"Evolutionary instability of selfish learning in repeated games","file_date_updated":"2024-08-06T07:33:30Z","type":"journal_article","month":"09","quality_controlled":"1","external_id":{"pmid":["36714856"],"arxiv":["2105.06199"]},"has_accepted_license":"1","intvolume":"         1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","related_material":{"link":[{"url":"https://github.com/alexmcavoy/fmtl/","relation":"software"}]},"publication":"PNAS Nexus","_id":"17061","date_created":"2024-05-28T14:23:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-09-01T00:00:00Z","publication_status":"published","publisher":"Oxford University Press","article_number":"pgac141","publication_identifier":{"issn":["2752-6542"]},"file":[{"success":1,"relation":"main_file","file_size":2410962,"creator":"dernst","date_updated":"2024-08-06T07:33:30Z","access_level":"open_access","checksum":"79a8e3e4be7e8a2b407b4efddd65f3f3","date_created":"2024-08-06T07:33:30Z","content_type":"application/pdf","file_name":"2022_PNASNexus_McAvoy.pdf","file_id":"17400"}],"ec_funded":1,"oa_version":"Published Version","fulldoi":"https://doi.org/10.1093/pnasnexus/pgac141","author":[{"last_name":"McAvoy","first_name":"Alex","full_name":"McAvoy, Alex"},{"full_name":"Kates-Harbeck, Julian","last_name":"Kates-Harbeck","first_name":"Julian"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"date_updated":"2025-06-11T13:54:20Z","language":[{"iso":"eng"}],"oa":1,"pmid":1,"doi":"10.1093/pnasnexus/pgac141","ddc":["000"],"scopus_import":"1","arxiv":1,"year":"2022","acknowledgement":"The authors are grateful to Jörg Oechssler for many helpful comments. A.M. was supported by a Simons Postdoctoral Fellowship (Math+X) at the University of Pennsylvania; K.C. was supported by the European Research Council Consolidator Grant 863818 (ForM-SMArt); and C.H. was supported by the European Research Council Starting Grant 850529 (E-DIRECT).","abstract":[{"text":"Across many domains of interaction, both natural and artificial, individuals use past experience to shape future behaviors. The results of such learning processes depend on what individuals wish to maximize. A natural objective is one’s own success. However, when two such “selfish” learners interact with each other, the outcome can be detrimental to both, especially when there are conflicts of interest. Here, we explore how a learner can align incentives with a selfish opponent. Moreover, we consider the dynamics that arise when learning rules themselves are subject to evolutionary pressure. By combining extensive simulations and analytical techniques, we demonstrate that selfish learning is unstable in most classical two-player repeated games. If evolution operates on the level of long-run payoffs, selection instead favors learning rules that incorporate social (other-regarding) preferences. To further corroborate these results, we analyze data from a repeated prisoner’s dilemma experiment. We find that selfish learning is insufficient to explain human behavior when there is a trade-off between payoff maximization and fairness.","lang":"eng"}],"citation":{"chicago":"McAvoy, Alex, Julian Kates-Harbeck, Krishnendu Chatterjee, and Christian Hilbe. “Evolutionary Instability of Selfish Learning in Repeated Games.” <i>PNAS Nexus</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">https://doi.org/10.1093/pnasnexus/pgac141</a>.","short":"A. McAvoy, J. Kates-Harbeck, K. Chatterjee, C. Hilbe, PNAS Nexus 1 (2022).","mla":"McAvoy, Alex, et al. “Evolutionary Instability of Selfish Learning in Repeated Games.” <i>PNAS Nexus</i>, vol. 1, no. 4, pgac141, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">10.1093/pnasnexus/pgac141</a>.","ieee":"A. McAvoy, J. Kates-Harbeck, K. Chatterjee, and C. Hilbe, “Evolutionary instability of selfish learning in repeated games,” <i>PNAS Nexus</i>, vol. 1, no. 4. Oxford University Press, 2022.","apa":"McAvoy, A., Kates-Harbeck, J., Chatterjee, K., &#38; Hilbe, C. (2022). Evolutionary instability of selfish learning in repeated games. <i>PNAS Nexus</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">https://doi.org/10.1093/pnasnexus/pgac141</a>","ista":"McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. 2022. Evolutionary instability of selfish learning in repeated games. PNAS Nexus. 1(4), pgac141.","ama":"McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. Evolutionary instability of selfish learning in repeated games. <i>PNAS Nexus</i>. 2022;1(4). doi:<a href=\"https://doi.org/10.1093/pnasnexus/pgac141\">10.1093/pnasnexus/pgac141</a>"},"article_processing_charge":"Yes","issue":"4","department":[{"_id":"KrCh"}],"article_type":"original","volume":1,"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}]},{"citation":{"ama":"Zhao H, Willsey M, Zhu A, et al. Co-optimization of design and fabrication plans for carpentry. <i>ACM Transactions on Graphics</i>. 2022;41(3). doi:<a href=\"https://doi.org/10.1145/3508499\">10.1145/3508499</a>","ista":"Zhao H, Willsey M, Zhu A, Nandi C, Tatlock Z, Solomon J, Schulz A. 2022. Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. 41(3), 32.","apa":"Zhao, H., Willsey, M., Zhu, A., Nandi, C., Tatlock, Z., Solomon, J., &#38; Schulz, A. (2022). Co-optimization of design and fabrication plans for carpentry. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3508499\">https://doi.org/10.1145/3508499</a>","ieee":"H. Zhao <i>et al.</i>, “Co-optimization of design and fabrication plans for carpentry,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 3. Association for Computing Machinery, 2022.","mla":"Zhao, Haisen, et al. “Co-Optimization of Design and Fabrication Plans for Carpentry.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 3, 32, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3508499\">10.1145/3508499</a>.","short":"H. Zhao, M. Willsey, A. Zhu, C. Nandi, Z. Tatlock, J. Solomon, A. Schulz, ACM Transactions on Graphics 41 (2022).","chicago":"Zhao, Haisen, Max Willsey, Amy Zhu, Chandrakana Nandi, Zachary Tatlock, Justin Solomon, and Adriana Schulz. “Co-Optimization of Design and Fabrication Plans for Carpentry.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3508499\">https://doi.org/10.1145/3508499</a>."},"doi":"10.1145/3508499","abstract":[{"text":"Past work on optimizing fabrication plans given a carpentry design can provide Pareto-optimal plans trading off between material waste, fabrication time, precision, and other considerations. However, when developing fabrication plans, experts rarely restrict to a single design, instead considering families of design variations, sometimes adjusting designs to simplify fabrication. Jointly exploring the design and fabrication plan spaces for each design is intractable using current techniques. We present a new approach to jointly optimize design and fabrication plans for carpentered objects. To make this bi-level optimization tractable, we adapt recent work from program synthesis based on equality graphs (e-graphs), which encode sets of equivalent programs. Our insight is that subproblems within our bi-level problem share significant substructures. By representing both designs and fabrication plans in a new bag of parts (BOP) e-graph, we amortize the cost of optimizing design components shared among multiple candidates. Even using BOP e-graphs, the optimization space grows quickly in practice. Hence, we also show how a feedback-guided search strategy dubbed Iterative Contraction and Expansion on E-graphs (ICEE) can keep the size of the e-graph manageable and direct the search towards promising candidates. We illustrate the advantages of our pipeline through examples from the carpentry domain.","lang":"eng"}],"year":"2022","acknowledgement":"The authors would like to thank anonymous reviewers for their helpful feedback; Haomiao Wu for her contribution to the algorithm development in the early stage of the project; Elias Baldwin, David Tsay, Alexander Lefort, and Qiyang Tan for helping the experiments.","scopus_import":"1","arxiv":1,"department":[{"_id":"BeBi"}],"volume":41,"article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.12265"}],"article_processing_charge":"No","issue":"3","oa_version":"Preprint","fulldoi":"https://doi.org/10.1145/3508499","article_number":"32","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"oa":1,"author":[{"last_name":"Zhao","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","first_name":"Haisen","full_name":"Zhao, Haisen","orcid":"0000-0002-6389-1045"},{"full_name":"Willsey, Max","last_name":"Willsey","first_name":"Max"},{"full_name":"Zhu, Amy","last_name":"Zhu","first_name":"Amy"},{"first_name":"Chandrakana","last_name":"Nandi","full_name":"Nandi, Chandrakana"},{"last_name":"Tatlock","first_name":"Zachary","full_name":"Tatlock, Zachary"},{"last_name":"Solomon","first_name":"Justin","full_name":"Solomon, Justin"},{"last_name":"Schulz","first_name":"Adriana","full_name":"Schulz, Adriana"}],"date_updated":"2024-08-06T07:03:14Z","language":[{"iso":"eng"}],"_id":"17065","publication":"ACM Transactions on Graphics","day":"09","publisher":"Association for Computing Machinery","publication_status":"published","date_published":"2022-03-09T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-05-29T06:09:23Z","month":"03","quality_controlled":"1","status":"public","type":"journal_article","title":"Co-optimization of design and fabrication plans for carpentry","intvolume":"        41","external_id":{"arxiv":["2107.12265"]}},{"has_accepted_license":"1","external_id":{"pmid":["36201522"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        20","title":"A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans","file_date_updated":"2024-08-06T07:07:52Z","type":"journal_article","status":"public","quality_controlled":"1","month":"10","date_created":"2024-05-29T06:09:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-10-06T00:00:00Z","publication_status":"published","publisher":"Public Library of Science","day":"06","publication":"PLOS Biology","_id":"17066","language":[{"iso":"eng"}],"date_updated":"2024-08-06T07:08:54Z","author":[{"full_name":"Sethi, Aditya","first_name":"Aditya","last_name":"Sethi"},{"first_name":"Hai","last_name":"Wei","full_name":"Wei, Hai"},{"full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","first_name":"Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","last_name":"Mishra"},{"first_name":"Ioannis","last_name":"Segos","full_name":"Segos, Ioannis"},{"first_name":"Eric J.","last_name":"Lambie","full_name":"Lambie, Eric J."},{"first_name":"Esther","last_name":"Zanin","full_name":"Zanin, Esther"},{"first_name":"Barbara","last_name":"Conradt","full_name":"Conradt, Barbara"}],"pmid":1,"oa":1,"file":[{"date_updated":"2024-08-06T07:07:52Z","access_level":"open_access","date_created":"2024-08-06T07:07:52Z","creator":"dernst","checksum":"a7b46460b7819c196028481cc18a7c85","file_size":2515388,"file_name":"2022_PlosBio_Sethi.pdf","file_id":"17399","content_type":"application/pdf","success":1,"relation":"main_file"}],"article_number":"e3001786","publication_identifier":{"issn":["1545-7885"]},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1371/journal.pbio.3001786","issue":"10","article_processing_charge":"Yes","volume":20,"article_type":"original","department":[{"_id":"CaHe"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"A cell’s size affects the likelihood that it will die. But how is cell size controlled in this context and how does cell size impact commitment to the cell death fate? We present evidence that the caspase CED-3 interacts with the RhoGEF ECT-2 in Caenorhabditis elegans neuroblasts that generate “unwanted” cells. We propose that this interaction promotes polar actomyosin contractility, which leads to unequal neuroblast division and the generation of a daughter cell that is below the critical “lethal” size threshold. Furthermore, we find that hyperactivation of ECT-2 RhoGEF reduces the sizes of unwanted cells. Importantly, this suppresses the “cell death abnormal” phenotype caused by the partial loss of ced-3 caspase and therefore increases the likelihood that unwanted cells die. A putative null mutation of ced-3 caspase, however, is not suppressed, which indicates that cell size affects CED-3 caspase activation and/or activity. Therefore, we have uncovered novel sequential and reciprocal interactions between the apoptosis pathway and cell size that impact a cell’s commitment to the cell death fate."}],"year":"2022","acknowledgement":"We thank members of the Conradt, Lambie, and Hajnal labs for discussions and comments on the manuscript. We thank M. Bauer, L. Jocham, N. Lebedeva, and L. McGuinness for excellent technical support; A. Hajnal and T. Kohlbrenner (University of Zurich, Switzerland) for allele zh135; and H.R. Horvitz (Massachusetts of Technology, USA) for plasmid pET-CED-3.\r\nSome strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (https://orip.nih.gov/) (P40 OD010440). This work was supported by UCL (Capital Equipment Fund, CEF2), a predoctoral fellowship from the China Scholarship Council (https://www.csc.edu.cn/) to HW, a predoctoral fellowship from the Studienstiftung des Deutschen Volkes (https://www.studienstiftung.de/) to NM, a Wolfson Fellowship from the Royal Society (https://royalsociety.org/) to BC (RSWF\\R1\\180008), the Deutsche Forschungsgemeinschaft (https://www.dfg.de/en/index.jsp) (ZA619/3-1 and ZA619/3-2 to EZ; C0204/10-1 and EXC114 to BC), and the Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1 to BC). ","doi":"10.1371/journal.pbio.3001786","ddc":["570"],"citation":{"apa":"Sethi, A., Wei, H., Mishra, N., Segos, I., Lambie, E. J., Zanin, E., &#38; Conradt, B. (2022). A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. <i>PLOS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001786\">https://doi.org/10.1371/journal.pbio.3001786</a>","ista":"Sethi A, Wei H, Mishra N, Segos I, Lambie EJ, Zanin E, Conradt B. 2022. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. 20(10), e3001786.","ama":"Sethi A, Wei H, Mishra N, et al. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. <i>PLOS Biology</i>. 2022;20(10). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001786\">10.1371/journal.pbio.3001786</a>","ieee":"A. Sethi <i>et al.</i>, “A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans,” <i>PLOS Biology</i>, vol. 20, no. 10. Public Library of Science, 2022.","short":"A. Sethi, H. Wei, N. Mishra, I. Segos, E.J. Lambie, E. Zanin, B. Conradt, PLOS Biology 20 (2022).","mla":"Sethi, Aditya, et al. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” <i>PLOS Biology</i>, vol. 20, no. 10, e3001786, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001786\">10.1371/journal.pbio.3001786</a>.","chicago":"Sethi, Aditya, Hai Wei, Nikhil Mishra, Ioannis Segos, Eric J. Lambie, Esther Zanin, and Barbara Conradt. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” <i>PLOS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001786\">https://doi.org/10.1371/journal.pbio.3001786</a>."}},{"article_type":"original","volume":168,"department":[{"_id":"SiHi"}],"article_processing_charge":"Yes","citation":{"apa":"Stouffer, M. A., Khalaf-Nazzal, R., Cifuentes-Diaz, C., Albertini, G., Bandet, E., Grannec, G., … Francis, F. (2022). Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. <i>Neurobiology of Disease</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nbd.2022.105702\">https://doi.org/10.1016/j.nbd.2022.105702</a>","ista":"Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, Albertini G, Bandet E, Grannec G, Lavilla V, Deleuze J-F, Olaso R, Nosten-Bertrand M, Francis F. 2022. Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. Neurobiology of Disease. 168, 105702.","ama":"Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, et al. Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. <i>Neurobiology of Disease</i>. 2022;168. doi:<a href=\"https://doi.org/10.1016/j.nbd.2022.105702\">10.1016/j.nbd.2022.105702</a>","ieee":"M. A. Stouffer <i>et al.</i>, “Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells,” <i>Neurobiology of Disease</i>, vol. 168. Elsevier, 2022.","short":"M.A. Stouffer, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini, E. Bandet, G. Grannec, V. Lavilla, J.-F. Deleuze, R. Olaso, M. Nosten-Bertrand, F. Francis, Neurobiology of Disease 168 (2022).","mla":"Stouffer, Melissa A., et al. “Doublecortin Mutation Leads to Persistent Defects in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal Cells.” <i>Neurobiology of Disease</i>, vol. 168, 105702, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.nbd.2022.105702\">10.1016/j.nbd.2022.105702</a>.","chicago":"Stouffer, Melissa A, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini, E. Bandet, G. Grannec, V. Lavilla, et al. “Doublecortin Mutation Leads to Persistent Defects in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal Cells.” <i>Neurobiology of Disease</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.nbd.2022.105702\">https://doi.org/10.1016/j.nbd.2022.105702</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Human doublecortin (DCX) mutations are associated with severe brain malformations leading to aberrant neuron positioning (heterotopia), intellectual disability and epilepsy. DCX is a microtubule-associated protein which plays a key role during neurodevelopment in neuronal migration and differentiation. Dcx knockout (KO) mice show disorganized hippocampal pyramidal neurons. The CA2/CA3 pyramidal cell layer is present as two abnormal layers and disorganized CA3 KO pyramidal neurons are also more excitable than wild-type (WT) cells. To further identify abnormalities, we characterized Dcx KO hippocampal neurons at subcellular, molecular and ultrastructural levels. Severe defects were observed in mitochondria, affecting number and distribution. Also, the Golgi apparatus was visibly abnormal, increased in volume and abnormally organized. Transcriptome analyses from laser microdissected hippocampal tissue at postnatal day 60 (P60) highlighted organelle abnormalities. Ultrastructural studies of CA3 cells performed in P60 (young adult) and > 9 months (mature) tissue showed that organelle defects are persistent throughout life. Locomotor activity and fear memory of young and mature adults were also abnormal: Dcx KO mice consistently performed less well than WT littermates, with defects becoming more severe with age. Thus, we show that disruption of a neurodevelopmentally-regulated gene can lead to permanent organelle anomalies contributing to abnormal adult behavior."}],"acknowledgement":"We thank Sylvie Dumont for initial aid with laser microdissection and G. Martinez-Lorenzana for experimental help with electron microscopy. We thank the animal experimentation facility and cellular and tissue imaging platforms at the Institut du Fer à Moulin, supported also by the Région Ile de France and the FRC Rotary. The Francis lab was associated with the BioPsy Labex project and the Ecole des Neurosciences de Paris Ile-de-France (ENP) network. Our salaries and lab were supported by Inserm, the Centre national de la recherche scientifique (CNRS) and Sorbonne University. The Francis group obtained the following funding contributing to this project: the European Union (EU- HEALTH-2013, DESIRE, N° 60253), the JTC 2015 Neurodevelopmental Disorders affiliated with the French Agence National de la Recherche (for \r\nNEURON8-Full- 815-006 STEM-MCD, to FF), E-Rare-3, the ERA-Net for Research on Rare Diseases affiliated with the French ANR (ERARE18-049), the European Cooperation on Science and Technology (COST Action CA16118).","year":"2022","doi":"10.1016/j.nbd.2022.105702","ddc":["570"],"pmid":1,"oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-08-06T06:57:39Z","author":[{"full_name":"Stouffer, Melissa A","first_name":"Melissa A","last_name":"Stouffer","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"R.","last_name":"Khalaf-Nazzal","full_name":"Khalaf-Nazzal, R."},{"full_name":"Cifuentes-Diaz, C.","first_name":"C.","last_name":"Cifuentes-Diaz"},{"full_name":"Albertini, G.","first_name":"G.","last_name":"Albertini"},{"last_name":"Bandet","first_name":"E.","full_name":"Bandet, E."},{"first_name":"G.","last_name":"Grannec","full_name":"Grannec, G."},{"first_name":"V.","last_name":"Lavilla","full_name":"Lavilla, V."},{"first_name":"J.-F.","last_name":"Deleuze","full_name":"Deleuze, J.-F."},{"first_name":"R.","last_name":"Olaso","full_name":"Olaso, R."},{"full_name":"Nosten-Bertrand, M.","last_name":"Nosten-Bertrand","first_name":"M."},{"last_name":"Francis","first_name":"F.","full_name":"Francis, F."}],"fulldoi":"https://doi.org/10.1016/j.nbd.2022.105702","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_id":"17398","file_name":"2022_NeurobioDisease_Stouffer.pdf","date_created":"2024-08-06T06:54:24Z","file_size":8890818,"date_updated":"2024-08-06T06:54:24Z","checksum":"b705d3d23d0b424ba29920be7ab64c23","access_level":"open_access","creator":"dernst","relation":"main_file","success":1}],"article_number":"105702","publication_identifier":{"issn":["0969-9961"]},"publication_status":"published","publisher":"Elsevier","date_created":"2024-05-29T06:10:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-15T00:00:00Z","publication":"Neurobiology of Disease","_id":"17067","day":"15","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"       168","external_id":{"pmid":["35339680"]},"has_accepted_license":"1","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"06","title":"Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells","type":"journal_article","file_date_updated":"2024-08-06T06:54:24Z","status":"public"},{"oa":1,"pmid":1,"date_updated":"2024-08-05T10:27:03Z","author":[{"first_name":"Fernando","last_name":"Navarrete","full_name":"Navarrete, Fernando"},{"last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"full_name":"Kornienko, Aleksandra E.","first_name":"Aleksandra E.","last_name":"Kornienko"},{"last_name":"Saado","first_name":"Indira","full_name":"Saado, Indira"},{"first_name":"Mamoona","last_name":"Khan","full_name":"Khan, Mamoona"},{"last_name":"Chia","first_name":"Khong-Sam","full_name":"Chia, Khong-Sam"},{"first_name":"Martin A.","last_name":"Darino","full_name":"Darino, Martin A."},{"full_name":"Bindics, Janos","first_name":"Janos","last_name":"Bindics"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.xplc.2021.100269","oa_version":"Published Version","article_number":"100269","publication_identifier":{"issn":["2590-3462"]},"file":[{"relation":"main_file","success":1,"content_type":"application/pdf","file_id":"17393","file_name":"2022_PlantComm_Navarrete.pdf","checksum":"1eeb6ee65419e4aa34627fea6857f343","file_size":3216686,"date_created":"2024-08-05T10:26:29Z","access_level":"open_access","creator":"dernst","date_updated":"2024-08-05T10:26:29Z"}],"department":[{"_id":"JiFr"}],"article_type":"original","volume":3,"article_processing_charge":"Yes","issue":"2","citation":{"chicago":"Navarrete, Fernando, Michelle C Gallei, Aleksandra E. Kornienko, Indira Saado, Mamoona Khan, Khong-Sam Chia, Martin A. Darino, Janos Bindics, and Armin Djamei. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” <i>Plant Communications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">https://doi.org/10.1016/j.xplc.2021.100269</a>.","short":"F. Navarrete, M.C. Gallei, A.E. Kornienko, I. Saado, M. Khan, K.-S. Chia, M.A. Darino, J. Bindics, A. Djamei, Plant Communications 3 (2022).","mla":"Navarrete, Fernando, et al. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” <i>Plant Communications</i>, vol. 3, no. 2, 100269, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">10.1016/j.xplc.2021.100269</a>.","ieee":"F. Navarrete <i>et al.</i>, “TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1,” <i>Plant Communications</i>, vol. 3, no. 2. Elsevier, 2022.","apa":"Navarrete, F., Gallei, M. C., Kornienko, A. E., Saado, I., Khan, M., Chia, K.-S., … Djamei, A. (2022). TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">https://doi.org/10.1016/j.xplc.2021.100269</a>","ista":"Navarrete F, Gallei MC, Kornienko AE, Saado I, Khan M, Chia K-S, Darino MA, Bindics J, Djamei A. 2022. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. 3(2), 100269.","ama":"Navarrete F, Gallei MC, Kornienko AE, et al. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. <i>Plant Communications</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">10.1016/j.xplc.2021.100269</a>"},"doi":"10.1016/j.xplc.2021.100269","ddc":["580"],"scopus_import":"1","acknowledgement":"The research leading to these results received funding from the European Research Council under the European Union Seventh Framework Programme ERC-2013-STG grant agreement \r\n335691; the Austrian Science Fund (FWF) P27818-B22,I 3033-B22; the Austrian Academy of Sciences (OEAW); and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2070-390732324.\r\nWe would like to thank the GMI/IMBA/IMP core facilities for excellent technical support, especially the BioOptics and Molecular Biology Services. We thank the Plant Sciences and Next Generation Sequencing Facilities at the Vienna BioCenter Core Facilities GmbH (VBCF). We are grateful to the Jirí Friml and Jürgen Kleine-Vehn laboratories for providing useful A. thaliana lines. We thank Mathias Madalinski for peptide synthesis and Dr. J. Matthew Watson for proofreading and valuable feedback on the manuscript. The authors declare no competing interests.","year":"2022","abstract":[{"text":"In plants, the antagonism between growth and defense is hardwired by hormonal signaling. The perception of pathogen-associated molecular patterns (PAMPs) from invading microorganisms inhibits auxin signaling and plant growth. Conversely, pathogens manipulate auxin signaling to promote disease, but how this hormone inhibits immunity is not fully understood. Ustilago maydis is a maize pathogen that induces auxin signaling in its host. We characterized a U. maydis effector protein, Naked1 (Nkd1), that is translocated into the host nucleus. Through its native ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, Nkd1 binds to the transcriptional co-repressors TOPLESS/TOPLESS-related (TPL/TPRs) and prevents the recruitment of a transcriptional repressor involved in hormonal signaling, leading to the de-repression of auxin and jasmonate signaling and thereby promoting susceptibility to (hemi)biotrophic pathogens. A moderate upregulation of auxin signaling inhibits the PAMP-triggered reactive oxygen species (ROS) burst, an early defense response. Thus, our findings establish a clear mechanism for auxin-induced pathogen susceptibility. Engineered Nkd1 variants with increased expression or increased EAR-mediated TPL/TPR binding trigger typical salicylic-acid-mediated defense reactions, leading to pathogen resistance. This implies that moderate binding of Nkd1 to TPL is a result of a balancing evolutionary selection process to enable TPL manipulation while avoiding host recognition.","lang":"eng"}],"intvolume":"         3","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"external_id":{"pmid":["35529945"]},"has_accepted_license":"1","month":"03","quality_controlled":"1","status":"public","title":"TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1","file_date_updated":"2024-08-05T10:26:29Z","type":"journal_article","publication_status":"published","publisher":"Elsevier","date_created":"2024-05-29T06:10:22Z","date_published":"2022-03-14T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Plant Communications","_id":"17068","day":"14"},{"fulldoi":"https://doi.org/10.1126/science.abl4683","oa_version":"Submitted Version","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"oa":1,"pmid":1,"date_updated":"2025-04-24T11:39:46Z","author":[{"last_name":"Zhong","first_name":"Sheng","full_name":"Zhong, Sheng"},{"full_name":"Li, Ling","first_name":"Ling","last_name":"Li"},{"first_name":"Zhijuan","last_name":"Wang","full_name":"Wang, Zhijuan"},{"first_name":"Zengxiang","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","last_name":"Ge","orcid":"0000-0001-9381-3577","full_name":"Ge, Zengxiang"},{"last_name":"Li","first_name":"Qiyun","full_name":"Li, Qiyun"},{"full_name":"Bleckmann, Andrea","first_name":"Andrea","last_name":"Bleckmann"},{"first_name":"Jizong","last_name":"Wang","full_name":"Wang, Jizong"},{"first_name":"Zihan","last_name":"Song","full_name":"Song, Zihan"},{"first_name":"Yihao","last_name":"Shi","full_name":"Shi, Yihao"},{"full_name":"Liu, Tianxu","first_name":"Tianxu","last_name":"Liu"},{"last_name":"Li","first_name":"Luhan","full_name":"Li, Luhan"},{"last_name":"Zhou","first_name":"Huabin","full_name":"Zhou, Huabin"},{"first_name":"Yanyan","last_name":"Wang","full_name":"Wang, Yanyan"},{"first_name":"Li","last_name":"Zhang","full_name":"Zhang, Li"},{"last_name":"Wu","first_name":"Hen-Ming","full_name":"Wu, Hen-Ming"},{"first_name":"Luhua","last_name":"Lai","full_name":"Lai, Luhua"},{"full_name":"Gu, Hongya","last_name":"Gu","first_name":"Hongya"},{"first_name":"Juan","last_name":"Dong","full_name":"Dong, Juan"},{"full_name":"Cheung, Alice Y.","last_name":"Cheung","first_name":"Alice Y."},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"},{"full_name":"Qu, Li-Jia","last_name":"Qu","first_name":"Li-Jia"}],"language":[{"iso":"eng"}],"citation":{"chicago":"Zhong, Sheng, Ling Li, Zhijuan Wang, Zengxiang Ge, Qiyun Li, Andrea Bleckmann, Jizong Wang, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abl4683\">https://doi.org/10.1126/science.abl4683</a>.","mla":"Zhong, Sheng, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” <i>Science</i>, vol. 375, no. 6578, American Association for the Advancement of Science, 2022, pp. 290–96, doi:<a href=\"https://doi.org/10.1126/science.abl4683\">10.1126/science.abl4683</a>.","short":"S. Zhong, L. Li, Z. Wang, Z. Ge, Q. Li, A. Bleckmann, J. Wang, Z. Song, Y. Shi, T. Liu, L. Li, H. Zhou, Y. Wang, L. Zhang, H.-M. Wu, L. Lai, H. Gu, J. Dong, A.Y. Cheung, T. Dresselhaus, L.-J. Qu, Science 375 (2022) 290–296.","ieee":"S. Zhong <i>et al.</i>, “RALF peptide signaling controls the polytubey block in Arabidopsis,” <i>Science</i>, vol. 375, no. 6578. American Association for the Advancement of Science, pp. 290–296, 2022.","ama":"Zhong S, Li L, Wang Z, et al. RALF peptide signaling controls the polytubey block in Arabidopsis. <i>Science</i>. 2022;375(6578):290-296. doi:<a href=\"https://doi.org/10.1126/science.abl4683\">10.1126/science.abl4683</a>","ista":"Zhong S, Li L, Wang Z, Ge Z, Li Q, Bleckmann A, Wang J, Song Z, Shi Y, Liu T, Li L, Zhou H, Wang Y, Zhang L, Wu H-M, Lai L, Gu H, Dong J, Cheung AY, Dresselhaus T, Qu L-J. 2022. RALF peptide signaling controls the polytubey block in Arabidopsis. Science. 375(6578), 290–296.","apa":"Zhong, S., Li, L., Wang, Z., Ge, Z., Li, Q., Bleckmann, A., … Qu, L.-J. (2022). RALF peptide signaling controls the polytubey block in Arabidopsis. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abl4683\">https://doi.org/10.1126/science.abl4683</a>"},"doi":"10.1126/science.abl4683","scopus_import":"1","acknowledgement":"We thank D. Ye for providing fer-4 and myb97 myb101 myb120 mutant seeds; L. Smith for sharing anj, herk1, anj herk1, and fer anj herk1 mutant seeds; J. F. Harper for providing aca9 mutant seeds; and C. Li and Q. Duan for sharing fer+/− mutant seeds.\r\nL.-J.Q. was funded by the National Natural Science Foundation of China (grant nos. 31991202, 31830004, 31620103903, and 31621001), S.Z. was supported by the Young Elite Scientists Sponsorship Program by the China Association of Science and Technology (2019QNRC001), Z.G. was supported by a NSFC Young Scientists Fund (31900161), A.Y.C. was funded by the US Natural Science Foundation (IOS-1645854, MCB-1715764, and MCB-0955910), J.D. was funded by the National Institute of Health (R01GM109080), and T.D. was supported by the German Research Foundation DFG (SFB924).","year":"2022","abstract":[{"lang":"eng","text":"Fertilization of an egg by multiple sperm (polyspermy) leads to lethal genome imbalance and chromosome segregation defects. In Arabidopsis thaliana, the block to polyspermy is facilitated by a mechanism that prevents polytubey (the arrival of multiple pollen tubes to one ovule). We show here that FERONIA, ANJEA, and HERCULES RECEPTOR KINASE 1 receptor-like kinases located at the septum interact with pollen tube–specific RALF6, 7, 16, 36, and 37 peptide ligands to establish this polytubey block. The same combination of RALF (rapid alkalinization factor) peptides and receptor complexes controls pollen tube reception and rupture inside the targeted ovule. Pollen tube rupture releases the polytubey block at the septum, which allows the emergence of secondary pollen tubes upon fertilization failure. Thus, orchestrated steps in the fertilization process in Arabidopsis are coordinated by the same signaling components to guarantee and optimize reproductive success."}],"department":[{"_id":"JiFr"}],"article_type":"original","volume":375,"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9040003","open_access":"1"}],"issue":"6578","month":"01","quality_controlled":"1","status":"public","title":"RALF peptide signaling controls the polytubey block in Arabidopsis","type":"journal_article","intvolume":"       375","external_id":{"pmid":["35050671"]},"publication":"Science","_id":"17069","OA_place":"repository","page":"290-296","day":"20","publication_status":"published","publisher":"American Association for the Advancement of Science","date_created":"2024-05-29T06:11:10Z","date_published":"2022-01-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green"},{"language":[{"iso":"eng"}],"date_updated":"2024-07-31T12:14:55Z","author":[{"last_name":"Mistakidis","first_name":"S I","full_name":"Mistakidis, S I"},{"first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis","full_name":"Koutentakis, Georgios"},{"full_name":"Grusdt, F","last_name":"Grusdt","first_name":"F"},{"full_name":"Schmelcher, P","first_name":"P","last_name":"Schmelcher"},{"last_name":"Sadeghpour","first_name":"H R","full_name":"Sadeghpour, H R"}],"oa":1,"file":[{"relation":"main_file","success":1,"content_type":"application/pdf","file_id":"17358","file_name":"2022_NewJournPhysics_Mistakidis.pdf","date_updated":"2024-07-31T12:13:16Z","access_level":"open_access","date_created":"2024-07-31T12:13:16Z","creator":"dernst","checksum":"85776a9d3abe163b33b322c8e346752a","file_size":4201283}],"article_number":"083030","publication_identifier":{"issn":["1367-2630"]},"fulldoi":"https://doi.org/10.1088/1367-2630/ac836c","oa_version":"Published Version","issue":"8","article_processing_charge":"Yes","volume":24,"article_type":"original","department":[{"_id":"MiLe"}],"year":"2022","abstract":[{"text":"We investigate the formation of magnetic Bose polaron, an impurity atom dressed by spin-wave excitations, in a one-dimensional spinor Bose gas. Within an effective potential model, the impurity is strongly confined by the host excitations which can even overcome the impurity-medium repulsion leading to a self-localized quasi-particle state. The phase diagram of the attractive and self-bound repulsive magnetic polaron, repulsive non-magnetic (Fröhlich-type) polaron and impurity-medium phase-separation regimes is explored with respect to the Rabi-coupling between the spin components, spin–spin interactions and impurity-medium coupling. The residue of such magnetic polarons decreases substantially in both strong attractive and repulsive branches with strong impurity-spin interactions, illustrating significant dressing of the impurity. The impurity can be used to probe and maneuver the spin polarization of the magnetic medium while suppressing ferromagnetic spin–spin correlations. It is shown that mean-field theory fails as the spinor gas approaches immiscibility since the generated spin-wave excitations are prominent. Our findings illustrate that impurities can be utilized to generate controllable spin–spin correlations and magnetic polaron states which can be realized with current cold atom setups.","lang":"eng"}],"scopus_import":"1","arxiv":1,"ddc":["530"],"doi":"10.1088/1367-2630/ac836c","citation":{"ieee":"S. I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, and H. R. Sadeghpour, “Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron,” <i>New Journal of Physics</i>, vol. 24, no. 8. IOP Publishing, 2022.","apa":"Mistakidis, S. I., Koutentakis, G., Grusdt, F., Schmelcher, P., &#38; Sadeghpour, H. R. (2022). Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac836c\">https://doi.org/10.1088/1367-2630/ac836c</a>","ama":"Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. <i>New Journal of Physics</i>. 2022;24(8). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac836c\">10.1088/1367-2630/ac836c</a>","ista":"Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. 2022. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. 24(8), 083030.","chicago":"Mistakidis, S I, Georgios Koutentakis, F Grusdt, P Schmelcher, and H R Sadeghpour. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” <i>New Journal of Physics</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1367-2630/ac836c\">https://doi.org/10.1088/1367-2630/ac836c</a>.","short":"S.I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, H.R. Sadeghpour, New Journal of Physics 24 (2022).","mla":"Mistakidis, S. I., et al. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” <i>New Journal of Physics</i>, vol. 24, no. 8, 083030, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac836c\">10.1088/1367-2630/ac836c</a>."},"has_accepted_license":"1","external_id":{"arxiv":["2204.10960"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        24","type":"journal_article","file_date_updated":"2024-07-31T12:13:16Z","title":"Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron","status":"public","quality_controlled":"1","month":"09","date_published":"2022-09-08T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-05-29T06:11:35Z","publisher":"IOP Publishing","publication_status":"published","day":"08","_id":"17070","publication":"New Journal of Physics"},{"title":"AI-based structure prediction empowers integrative structural analysis of human nuclear pores","type":"journal_article","status":"public","quality_controlled":"1","month":"06","external_id":{"pmid":["35679397"]},"intvolume":"       376","day":"10","publication":"Science","_id":"17071","date_created":"2024-05-29T06:12:02Z","date_published":"2022-06-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"American Association for the Advancement of Science","article_number":"abm9506","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"fulldoi":"https://doi.org/10.1126/science.abm9506","oa_version":"None","language":[{"iso":"eng"}],"author":[{"last_name":"Mosalaganti","first_name":"Shyamal","full_name":"Mosalaganti, Shyamal"},{"full_name":"Obarska-Kosinska, Agnieszka","last_name":"Obarska-Kosinska","first_name":"Agnieszka"},{"first_name":"Marc","last_name":"Siggel","full_name":"Siggel, Marc"},{"full_name":"Taniguchi, Reiya","last_name":"Taniguchi","first_name":"Reiya"},{"last_name":"Turoňová","first_name":"Beata","full_name":"Turoňová, Beata"},{"full_name":"Zimmerli, Christian E.","first_name":"Christian E.","last_name":"Zimmerli"},{"last_name":"Buczak","first_name":"Katarzyna","full_name":"Buczak, Katarzyna"},{"first_name":"Florian","last_name":"Schmidt","id":"A2EF226A-AF19-11E9-924C-0525E6697425","full_name":"Schmidt, Florian"},{"last_name":"Margiotta","first_name":"Erica","full_name":"Margiotta, Erica"},{"full_name":"Mackmull, Marie-Therese","last_name":"Mackmull","first_name":"Marie-Therese"},{"first_name":"Wim J. H.","last_name":"Hagen","full_name":"Hagen, Wim J. H."},{"full_name":"Hummer, Gerhard","first_name":"Gerhard","last_name":"Hummer"},{"first_name":"Jan","last_name":"Kosinski","full_name":"Kosinski, Jan"},{"full_name":"Beck, Martin","first_name":"Martin","last_name":"Beck"}],"date_updated":"2024-07-31T12:10:32Z","pmid":1,"scopus_import":"1","year":"2022","acknowledgement":"We acknowledge support from the Electron Microscopy Core Facility (EMCF) and IT services of European Molecular Biology Laboratory (EMBL) Heidelberg. We thank S. Welsch at the Central Electron Microscopy Facility of the Max Planck Institute of Biophysics for technical expertise. We thank T. Hoffman and R. Alves for help with the AlphaFold installation.\r\nFunding: M.B. acknowledges funding by EMBL, the Max Planck Society, and the European Research Council (ComplexAssembly 724349). J.K. acknowledges funding from the Federal Ministry of Education and Research of Germany (FKZ 031L0100). The work by M.S. and G.H. on computer simulations was supported by the Max Planck Society. M.S. was supported by the EMBL Interdisciplinary Postdoc Programme under Marie Curie COFUND actions. M.S. and G.H. were supported by the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) DynaMem program of the State of Hessen.","abstract":[{"lang":"eng","text":"The eukaryotic nucleus pro­tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the larg­est protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaf­fold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conforma­tional breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial chal­lenge for structural biologists.\r\nConsiderable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integra­tive modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous struc­tural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaf­fold is interconnected by a set of intrinsically disordered linker NUPs that are not straight­forwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topol­ogy and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination.\r\nIn this study, we used artificial intelligence (AI)–based prediction to generate an exten­sive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharac­terized. Benchmarking against previous and unpublished x-ray and cryo–electron micros­copy structures revealed unprecedented accu­racy. We obtained well-resolved cryo–electron tomographic maps of both the constricted and dilated conformational states of the hu­man NPC. Using integrative modeling, we fit­ted the structural models of individual NUPs into the cryo–electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaf­fold. We elucidated in great detail how mem­brane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane en­vironment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension\r\nOur 70-MDa atomically re­solved model covers &gt;90% of the human NPC scaffold. It captures conforma­tional changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dy­namic model of the NPC. Our study exempli­fies how AI-based structure prediction may accelerate the elucidation of subcellular ar­chitecture at atomic resolution."}],"doi":"10.1126/science.abm9506","citation":{"ieee":"S. Mosalaganti <i>et al.</i>, “AI-based structure prediction empowers integrative structural analysis of human nuclear pores,” <i>Science</i>, vol. 376, no. 6598. American Association for the Advancement of Science, 2022.","apa":"Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., … Beck, M. (2022). AI-based structure prediction empowers integrative structural analysis of human nuclear pores. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abm9506\">https://doi.org/10.1126/science.abm9506</a>","ista":"Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt F, Margiotta E, Mackmull M-T, Hagen WJH, Hummer G, Kosinski J, Beck M. 2022. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 376(6598), abm9506.","ama":"Mosalaganti S, Obarska-Kosinska A, Siggel M, et al. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. <i>Science</i>. 2022;376(6598). doi:<a href=\"https://doi.org/10.1126/science.abm9506\">10.1126/science.abm9506</a>","chicago":"Mosalaganti, Shyamal, Agnieszka Obarska-Kosinska, Marc Siggel, Reiya Taniguchi, Beata Turoňová, Christian E. Zimmerli, Katarzyna Buczak, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abm9506\">https://doi.org/10.1126/science.abm9506</a>.","short":"S. Mosalaganti, A. Obarska-Kosinska, M. Siggel, R. Taniguchi, B. Turoňová, C.E. Zimmerli, K. Buczak, F. Schmidt, E. Margiotta, M.-T. Mackmull, W.J.H. Hagen, G. Hummer, J. Kosinski, M. Beck, Science 376 (2022).","mla":"Mosalaganti, Shyamal, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” <i>Science</i>, vol. 376, no. 6598, abm9506, American Association for the Advancement of Science, 2022, doi:<a href=\"https://doi.org/10.1126/science.abm9506\">10.1126/science.abm9506</a>."},"issue":"6598","article_processing_charge":"No","volume":376,"article_type":"original","department":[{"_id":"MaJö"}]},{"fulldoi":"https://doi.org/10.1126/sciadv.abl6293","oa_version":"Published Version","file":[{"relation":"main_file","success":1,"file_name":"2022_ScienceAdv_Naqvi.pdf","file_id":"17357","content_type":"application/pdf","checksum":"9511579306cce7e04107d3d6389ed614","date_created":"2024-07-31T12:01:51Z","access_level":"open_access","date_updated":"2024-07-31T12:01:51Z","file_size":2404150,"creator":"dernst"}],"publication_identifier":{"issn":["2375-2548"]},"article_number":"eabl6293","pmid":1,"oa":1,"language":[{"iso":"eng"}],"author":[{"last_name":"Naqvi","first_name":"Mohsin M.","full_name":"Naqvi, Mohsin M."},{"first_name":"Mario","last_name":"Avellaneda Sarrió","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","orcid":"0000-0001-6406-524X","full_name":"Avellaneda Sarrió, Mario"},{"first_name":"Andrew","last_name":"Roth","full_name":"Roth, Andrew"},{"first_name":"Eline J.","last_name":"Koers","full_name":"Koers, Eline J."},{"last_name":"Roland","first_name":"Antoine","full_name":"Roland, Antoine"},{"full_name":"Sunderlikova, Vanda","last_name":"Sunderlikova","first_name":"Vanda"},{"first_name":"Günter","last_name":"Kramer","full_name":"Kramer, Günter"},{"full_name":"Rye, Hays S.","last_name":"Rye","first_name":"Hays S."},{"last_name":"Tans","first_name":"Sander J.","full_name":"Tans, Sander J."}],"date_updated":"2024-08-05T08:30:29Z","citation":{"short":"M.M. Naqvi, M. Avellaneda Sarrió, A. Roth, E.J. Koers, A. Roland, V. Sunderlikova, G. Kramer, H.S. Rye, S.J. Tans, Science Advances 8 (2022).","mla":"Naqvi, Mohsin M., et al. “Protein Chain Collapse Modulation and Folding Stimulation by GroEL-ES.” <i>Science Advances</i>, vol. 8, no. 9, eabl6293, American Association for the Advancement of Science, 2022, doi:<a href=\"https://doi.org/10.1126/sciadv.abl6293\">10.1126/sciadv.abl6293</a>.","chicago":"Naqvi, Mohsin M., Mario Avellaneda Sarrió, Andrew Roth, Eline J. Koers, Antoine Roland, Vanda Sunderlikova, Günter Kramer, Hays S. Rye, and Sander J. Tans. “Protein Chain Collapse Modulation and Folding Stimulation by GroEL-ES.” <i>Science Advances</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/sciadv.abl6293\">https://doi.org/10.1126/sciadv.abl6293</a>.","apa":"Naqvi, M. M., Avellaneda Sarrió, M., Roth, A., Koers, E. J., Roland, A., Sunderlikova, V., … Tans, S. J. (2022). Protein chain collapse modulation and folding stimulation by GroEL-ES. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abl6293\">https://doi.org/10.1126/sciadv.abl6293</a>","ista":"Naqvi MM, Avellaneda Sarrió M, Roth A, Koers EJ, Roland A, Sunderlikova V, Kramer G, Rye HS, Tans SJ. 2022. Protein chain collapse modulation and folding stimulation by GroEL-ES. Science Advances. 8(9), eabl6293.","ama":"Naqvi MM, Avellaneda Sarrió M, Roth A, et al. Protein chain collapse modulation and folding stimulation by GroEL-ES. <i>Science Advances</i>. 2022;8(9). doi:<a href=\"https://doi.org/10.1126/sciadv.abl6293\">10.1126/sciadv.abl6293</a>","ieee":"M. M. Naqvi <i>et al.</i>, “Protein chain collapse modulation and folding stimulation by GroEL-ES,” <i>Science Advances</i>, vol. 8, no. 9. American Association for the Advancement of Science, 2022."},"year":"2022","abstract":[{"text":"The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding of proteins by strengthening their collapse. GroEL induces contractile forces in substrate chains, which draws them into the cavity and triggers a general compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL and is aided by GroES binding to the cavity rim and by the amphiphilic C-terminal tails at the cavity bottom. Collapse modulation is distinct from other proposed GroEL-ES folding acceleration mechanisms, including steric confinement and misfold unfolding. Given the prevalence of collapse throughout the proteome, we conjecture that collapse modulation is more generally relevant within the protein quality control machinery.","lang":"eng"}],"acknowledgement":"We thank A. L. Horwich, K. Chakraborty, and B. Schuler for providing plasmids, and R. van Leeuwen, M. Mayer, J. van Zon, W. Noorduin, and P. R. ten Wolde for comments and critical reading of the manuscript. Work in the group of S.J.T. was supported by the Netherlands Organization for Scientific Research (NWO). Work in the group of H.S.R. was supported by a grant from the NIH (R01GM114405).","scopus_import":"1","ddc":["570"],"doi":"10.1126/sciadv.abl6293","volume":8,"article_type":"original","department":[{"_id":"MiSi"}],"issue":"9","article_processing_charge":"Yes","quality_controlled":"1","month":"03","type":"journal_article","file_date_updated":"2024-07-31T12:01:51Z","title":"Protein chain collapse modulation and folding stimulation by GroEL-ES","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"         8","has_accepted_license":"1","external_id":{"pmid":["35245117"]},"_id":"17072","publication":"Science Advances","day":"01","publisher":"American Association for the Advancement of Science","publication_status":"published","date_published":"2022-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-05-29T06:12:19Z"},{"edition":"2","status":"public","place":"Cham","title":"Amino Acid Transport Defects","type":"book_chapter","month":"02","quality_controlled":"1","day":"22","page":"291-312","publication":"Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases","_id":"17075","date_created":"2024-05-29T06:13:04Z","date_published":"2022-02-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","publication_identifier":{"eisbn":["9783030677275"],"isbn":["9783030677268"]},"editor":[{"full_name":"Blau, Nenad","last_name":"Blau","first_name":"Nenad"},{"full_name":"Vici, Carlo Dionisi","first_name":"Carlo Dionisi","last_name":"Vici"},{"full_name":"Ferreira, Carlos R. ","last_name":"Ferreira","first_name":"Carlos R. "},{"full_name":"Vianey-Saban, Christine","first_name":"Christine","last_name":"Vianey-Saban"},{"last_name":"van Karnebeek","first_name":"Clara D.M.","full_name":"van Karnebeek, Clara D.M."}],"fulldoi":"https://doi.org/10.1007/978-3-030-67727-5_18","oa_version":"None","author":[{"first_name":"Manuel","last_name":"Palacín","full_name":"Palacín, Manuel"},{"first_name":"Stefan","last_name":"Bröer","full_name":"Bröer, Stefan"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"date_updated":"2024-07-31T11:45:50Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-67727-5_18","scopus_import":"1","abstract":[{"text":"Disorders associated with the malfunction of amino acid transporters mainly affect the function of the intestine, kidney, brain, and liver. Mutations of brain amino acid transporters, for example, alter neuronal excitability (e.g., episodic ataxia due to SLC1A3 (EAAT1) defect and hyperekplexia due to SLC6A5 (GLYT2) deficiency) or brain development (SLC1A1 (EAAT3), SLC3A2/SLC7A5 (CD98hc/LAT1), and SLC1A4 (ASCT1) deficiencies). Mutations of renal and intestinal amino acid transporters SLC3A1/SLC7A9 (rBAT/b0,+AT) and SLC1A1 (EAAT3) cause renal problems (cystinuria and dicarboxylic aminoaciduria, respectively) and malabsorption that can affect whole-body homoeostasis (Hartnup disorder SLC6A19 (B0AT1), lysinuric protein intolerance SLC3A2/SLC7A7 (CD98hc/y+LAT1), and hyperdibasic aminoaciduria type 1). Mutations in the neuronal system A amino acid transporter SLC38A8 (SNAT8) cause eye developmental and visual defects. Inborn errors associated with mitochondrial SLC25 family members such as SLC25A12 (neuronal- and muscle-specific mitochondrial aspartate/glutamate transporter 1; AGC1) (global cerebral hypomyelination), SLC25A13 (aspartate/glutamate transporter 2) (citrin deficiency), SLC25A15 (ornithine-citrulline carrier 2) (homocitrullinuria, hyperornithinemia, and hyperammonemia syndrome), and SLC25A22 (mitochondrial glutamate/H+ symporter 1, GC1) (neonatal myoclonic epilepsy) will be dealt within Chap. 43 (defects of mitochondrial carriers).","lang":"eng"}],"acknowledgement":"The authors thank Dr. Christian Lueck (Canberra Hospital) for clarification of differential diagnosis in cases of episodic ataxia. The authors thank Dr. Rafael Artuch (Hospital San Joan de Deu, Barcelona) for reference values of plasma amino acid concentration. The authors also thank Lisa Kraus (Institute of Science and Technology-Austria) and Dr. Susanna Bodoy (IRB-Barcelona) that helped in preparing tables and bibliography.","year":"2022","citation":{"ieee":"M. Palacín, S. Bröer, and G. Novarino, “Amino Acid Transport Defects,” in <i>Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases</i>, 2nd ed., N. Blau, C. D. Vici, C. R. Ferreira, C. Vianey-Saban, and C. D. M. van Karnebeek, Eds. Cham: Springer Nature, 2022, pp. 291–312.","apa":"Palacín, M., Bröer, S., &#38; Novarino, G. (2022). Amino Acid Transport Defects. In N. Blau, C. D. Vici, C. R. Ferreira, C. Vianey-Saban, &#38; C. D. M. van Karnebeek (Eds.), <i>Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases</i> (2nd ed., pp. 291–312). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67727-5_18\">https://doi.org/10.1007/978-3-030-67727-5_18</a>","ama":"Palacín M, Bröer S, Novarino G. Amino Acid Transport Defects. In: Blau N, Vici CD, Ferreira CR, Vianey-Saban C, van Karnebeek CDM, eds. <i>Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases</i>. 2nd ed. Cham: Springer Nature; 2022:291-312. doi:<a href=\"https://doi.org/10.1007/978-3-030-67727-5_18\">10.1007/978-3-030-67727-5_18</a>","ista":"Palacín M, Bröer S, Novarino G. 2022.Amino Acid Transport Defects. In: Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases. , 291–312.","chicago":"Palacín, Manuel, Stefan Bröer, and Gaia Novarino. “Amino Acid Transport Defects.” In <i>Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases</i>, edited by Nenad Blau, Carlo Dionisi Vici, Carlos R.  Ferreira, Christine Vianey-Saban, and Clara D.M. van Karnebeek, 2nd ed., 291–312. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-67727-5_18\">https://doi.org/10.1007/978-3-030-67727-5_18</a>.","short":"M. Palacín, S. Bröer, G. Novarino, in:, N. Blau, C.D. Vici, C.R. Ferreira, C. Vianey-Saban, C.D.M. van Karnebeek (Eds.), Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, 2nd ed., Springer Nature, Cham, 2022, pp. 291–312.","mla":"Palacín, Manuel, et al. “Amino Acid Transport Defects.” <i>Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases</i>, edited by Nenad Blau et al., 2nd ed., Springer Nature, 2022, pp. 291–312, doi:<a href=\"https://doi.org/10.1007/978-3-030-67727-5_18\">10.1007/978-3-030-67727-5_18</a>."},"article_processing_charge":"No","department":[{"_id":"GaNo"}]}]