[{"oa":1,"publisher":"Association for Computing Machinery","publication_identifier":{"isbn":["9798400705250"]},"conference":{"location":"Denver, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2024-08-01","start_date":"2024-07-28"},"quality_controlled":"1","type":"conference","external_id":{"isi":["001282218200091"]},"month":"07","citation":{"apa":"Chen, Y.-L., Ly, M., &#38; Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Denver, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>.","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Denver, United States, 2024.","ista":"Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>."},"file":[{"success":1,"relation":"main_file","date_updated":"2024-07-10T11:03:14Z","file_size":47309472,"access_level":"open_access","file_id":"17215","file_name":"sig24_friction_authors.pdf","checksum":"b8b203ed09e3995ba0d7e6a76288663a","content_type":"application/pdf","date_created":"2024-07-10T11:03:14Z","creator":"yichen"},{"file_name":"sig24_friction_supplementary.pdf","checksum":"89d81b397b4b6469d828808a68b70820","file_id":"17216","creator":"yichen","content_type":"application/pdf","date_created":"2024-07-10T11:03:12Z","relation":"main_file","success":1,"date_updated":"2024-07-10T11:03:12Z","access_level":"open_access","file_size":10518286},{"date_created":"2024-07-10T11:03:51Z","content_type":"video/mp4","creator":"yichen","file_id":"17217","file_name":"friction_paper_extra_video_finished.mp4","checksum":"7123deed34a5456810e7b5336a31c657","date_updated":"2024-07-10T11:03:51Z","file_size":71789192,"access_level":"open_access","success":1,"relation":"main_file"},{"creator":"yichen","date_created":"2024-07-10T11:03:58Z","content_type":"video/mp4","file_name":"friction_paper_video_finished.mp4","checksum":"e606fc1ae8f2610ce3b4421566800b45","file_id":"17218","file_size":280610763,"access_level":"open_access","date_updated":"2024-07-10T11:03:58Z","relation":"main_file","success":1}],"project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"title":"Primal-dual non-smooth friction for rigid body animation","ddc":["621","531","006"],"abstract":[{"text":"Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.","lang":"eng"}],"status":"public","publication_status":"published","publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","oa_version":"Published Version","date_updated":"2025-09-08T08:54:38Z","day":"01","date_published":"2024-07-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","author":[{"id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","last_name":"Chen","full_name":"Chen, Yi-Lu","first_name":"Yi-Lu"},{"last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","full_name":"Ly, Mickaël","first_name":"Mickaël"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"date_created":"2024-07-10T11:06:20Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"acknowledgement":"We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","scopus_import":"1","_id":"17214","doi":"10.1145/3641519.3657485","has_accepted_license":"1","corr_author":"1","file_date_updated":"2024-07-10T11:03:58Z","language":[{"iso":"eng"}],"keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2024"},{"title":"Multi-material mesh-based surface tracking with implicit topology changes","ddc":["004"],"abstract":[{"lang":"eng","text":"We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles."}],"status":"public","publication_status":"published","publication":"ACM Transactions on Graphics","article_processing_charge":"Yes (via OA deal)","date_published":"2024-07-01T00:00:00Z","oa_version":"Published Version","day":"01","date_updated":"2026-04-07T13:02:36Z","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"OA_place":"publisher","intvolume":"        43","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"oa":1,"publisher":"Association for Computing Machinery","volume":43,"external_id":{"isi":["001289270900021"]},"type":"journal_article","month":"07","quality_controlled":"1","citation":{"apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., &#38; Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>","ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>.","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024).","ieee":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","chicago":"Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>.","ista":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54."},"file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2024-07-23T06:35:15Z","file_name":"2024_ACMToG_HeissSynak.pdf","checksum":"1917067d4b52d7729019b03560004e43","file_id":"17317","date_updated":"2024-07-23T06:35:15Z","file_size":48763368,"access_level":"open_access","relation":"main_file","success":1},{"relation":"main_file","success":1,"date_updated":"2024-07-10T12:23:44Z","file_size":48021463,"access_level":"open_access","checksum":"a4f0e293184bfa034c0c585848806b17","file_name":"sdtopofixer_final.mp4","file_id":"17221","creator":"akalinov","content_type":"video/mp4","date_created":"2024-07-10T12:23:44Z"},{"content_type":"application/pdf","date_created":"2025-11-11T09:50:52Z","creator":"akalinov","file_id":"20633","title":"Authors' version of the text","file_name":"SuperDuperTopoFixer.pdf","checksum":"18fc310a78ec91651148c45a8b89fa44","access_level":"open_access","file_size":48639581,"date_updated":"2025-11-11T09:50:52Z","relation":"preprint"}],"article_type":"original","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"file_date_updated":"2025-11-11T09:50:52Z","corr_author":"1","OA_type":"hybrid","language":[{"iso":"eng"}],"keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"related_material":{"record":[{"id":"19630","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"18301","status":"public"}]},"year":"2024","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_number":"54","date_created":"2024-07-10T12:24:00Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"author":[{"first_name":"Peter","full_name":"Synak, Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak"},{"id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","full_name":"Kalinov, Aleksei","first_name":"Aleksei","orcid":"0000-0003-2189-3904"},{"last_name":"Strugaru","id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","full_name":"Strugaru, Irina-Malina","first_name":"Irina-Malina"},{"first_name":"Arian","full_name":"Etemadihaghighi, Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","last_name":"Etemadihaghighi"},{"last_name":"Yang","full_name":"Yang, Huidong","first_name":"Huidong"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"scopus_import":"1","issue":"4","acknowledgement":"Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses.  This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","doi":"10.1145/3658223","has_accepted_license":"1","_id":"17219"},{"abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) uses a quantum computer\r\nto implement a variational method with $2p$ layers of alternating unitary\r\noperators, optimized by a classical computer to minimize a cost function. While\r\nrigorous performance guarantees exist for the QAOA at small depths $p$, the\r\nbehavior at large depths remains less clear, though simulations suggest\r\nexponentially fast convergence for certain problems. In this work, we gain\r\ninsights into the deep QAOA using an analytic expansion of the cost function\r\naround transition states. Transition states are constructed in a recursive\r\nmanner: from the local minima of the QAOA with $p$ layers we obtain transition\r\nstates of the QAOA with $p+1$ layers, which are stationary points characterized\r\nby a unique direction of negative curvature. We construct an analytic estimate\r\nof the negative curvature and the corresponding direction in parameter space at\r\neach transition state. The expansion of the QAOA cost function along the\r\nnegative direction to the quartic order gives a lower bound of the QAOA cost\r\nfunction improvement. We provide physical intuition behind the analytic\r\nexpressions for the local curvature and quartic expansion coefficient. Our\r\nnumerical study confirms the accuracy of our approximations and reveals that\r\nthe obtained bound and the true value of the QAOA cost function gain have a\r\ncharacteristic exponential decrease with the number of layers $p$, with the\r\nbound decreasing more rapidly. Our study establishes an analytical method for\r\nrecursively studying the QAOA that is applicable in the regime of high circuit\r\ndepth."}],"arxiv":1,"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.10125","open_access":"1"}],"title":"A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm","corr_author":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2405.10125","date_updated":"2026-04-07T12:43:22Z","day":"16","date_published":"2024-05-16T00:00:00Z","article_processing_charge":"No","year":"2024","related_material":{"record":[{"status":"public","id":"17208","relation":"dissertation_contains"}]},"status":"public","publication":"arXiv","publication_status":"draft","author":[{"id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","orcid":"0000-0002-5383-2869"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2405.10125"]},"department":[{"_id":"MaSe"}],"type":"preprint","date_created":"2024-07-10T13:12:09Z","month":"05","oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"repository","_id":"17222","doi":"10.48550/arXiv.2405.10125","citation":{"apa":"Medina Ramos, R. A., &#38; Serbyn, M. (n.d.). A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>","ama":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>","short":"R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.).","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>, 2405.10125, doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>.","chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>.","ista":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv, 2405.10125.","ieee":"R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm,” <i>arXiv</i>. ."}},{"year":"2024","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.3934/dcds.2024059"}],"corr_author":"1","OA_type":"free access","doi":"10.3934/dcds.2024059","_id":"17231","scopus_import":"1","issue":"11","date_created":"2024-07-14T22:01:10Z","department":[{"_id":"VaKa"}],"author":[{"first_name":"Corentin","last_name":"Fiorebe","id":"06619f18-9070-11eb-847d-d1ee780bd88b","full_name":"Fiorebe, Corentin"}],"article_processing_charge":"No","date_published":"2024-11-01T00:00:00Z","date_updated":"2026-06-18T17:54:16Z","day":"01","oa_version":"Published Version","publication_status":"published","status":"public","publication":"Discrete and Continuous Dynamical Systems- Series A","abstract":[{"lang":"eng","text":"In the class of projective billiards, which contains the usual billiards, we exhibit counter-examples to Ivrii's conjecture, which states that in any planar billiard with smooth boundary the set of periodic orbits has zero measure. The counter-examples are polygons admitting a 2-parameters family of n-periodic orbits, with n being either 3 or any even integer greater than 4."}],"ddc":["500"],"title":"Examples of projective billiards with open sets of periodic orbits","article_type":"original","citation":{"apa":"Fiorebe, C. (2024). Examples of projective billiards with open sets of periodic orbits. <i>Discrete and Continuous Dynamical Systems- Series A</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/dcds.2024059\">https://doi.org/10.3934/dcds.2024059</a>","ama":"Fiorebe C. Examples of projective billiards with open sets of periodic orbits. <i>Discrete and Continuous Dynamical Systems- Series A</i>. 2024;44(11):3287-3301. doi:<a href=\"https://doi.org/10.3934/dcds.2024059\">10.3934/dcds.2024059</a>","mla":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44, no. 11, American Institute of Mathematical Sciences, 2024, pp. 3287–301, doi:<a href=\"https://doi.org/10.3934/dcds.2024059\">10.3934/dcds.2024059</a>.","short":"C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024) 3287–3301.","ieee":"C. Fiorebe, “Examples of projective billiards with open sets of periodic orbits,” <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44, no. 11. American Institute of Mathematical Sciences, pp. 3287–3301, 2024.","ista":"Fiorebe C. 2024. Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. 44(11), 3287–3301.","chicago":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>. American Institute of Mathematical Sciences, 2024. <a href=\"https://doi.org/10.3934/dcds.2024059\">https://doi.org/10.3934/dcds.2024059</a>."},"type":"journal_article","month":"11","external_id":{"isi":["001230091000001"]},"page":"3287-3301","quality_controlled":"1","intvolume":"        44","publication_identifier":{"issn":["1078-0947"],"eissn":["1553-5231"]},"oa":1,"publisher":"American Institute of Mathematical Sciences","volume":44},{"date_created":"2024-07-14T22:01:10Z","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"author":[{"first_name":"Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"doi":"10.1016/j.xpro.2024.103168","has_accepted_license":"1","_id":"17232","scopus_import":"1","acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","issue":"3","language":[{"iso":"eng"}],"file_date_updated":"2025-01-09T12:16:53Z","corr_author":"1","OA_type":"gold","year":"2024","article_number":"103168","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","external_id":{"pmid":["38968076"]},"month":"09","quality_controlled":"1","intvolume":"         5","OA_place":"publisher","publication_identifier":{"eissn":["2666-1667"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"volume":5,"oa":1,"publisher":"Elsevier","project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"article_type":"original","file":[{"file_name":"2024_STARProtoc_Cheung2.pdf","checksum":"464f52ecc6ec92f509552823bb82bf79","file_id":"18810","creator":"dernst","date_created":"2025-01-09T12:16:53Z","content_type":"application/pdf","relation":"main_file","success":1,"file_size":6445556,"access_level":"open_access","date_updated":"2025-01-09T12:16:53Z"}],"pmid":1,"citation":{"mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>"},"abstract":[{"lang":"eng","text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1"}],"ddc":["570"],"title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","date_published":"2024-09-20T00:00:00Z","article_processing_charge":"Yes","date_updated":"2025-12-30T10:54:12Z","day":"20","APC_amount":"804 EUR","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"oa_version":"Published Version","status":"public","publication_status":"published","publication":"STAR Protocols"},{"pmid":1,"citation":{"ama":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-protocol</i>. 2024;14(13). doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>","apa":"LI, Z., Huard, J., Bayer, E. M., &#38; Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-Protocol</i>. Bio-Protocol. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>","ista":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. 2024. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 14(13), e5029.","chicago":"LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>. Bio-Protocol, 2024. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>.","ieee":"Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” <i>Bio-protocol</i>, vol. 14, no. 13. Bio-Protocol, 2024.","short":"Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024).","mla":"LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>."},"file":[{"content_type":"application/pdf","date_created":"2024-07-16T06:16:11Z","creator":"dernst","file_id":"17242","checksum":"c8671c0ad483da6407cb16cc3fef1990","file_name":"2024_BioProtocol_Li.pdf","date_updated":"2024-07-16T06:16:11Z","access_level":"open_access","file_size":2896048,"success":1,"relation":"main_file"}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Bio-Protocol","oa":1,"volume":14,"publication_identifier":{"eissn":["2331-8325"]},"intvolume":"        14","quality_controlled":"1","month":"07","type":"journal_article","external_id":{"pmid":["39007160"]},"publication":"Bio-protocol","publication_status":"published","status":"public","oa_version":"Published Version","date_updated":"2025-03-06T10:28:18Z","day":"05","article_processing_charge":"Yes","date_published":"2024-07-05T00:00:00Z","title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis","ddc":["570"],"abstract":[{"lang":"eng","text":"CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene."}],"issue":"13","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING to E.M.B.).","scopus_import":"1","_id":"17233","has_accepted_license":"1","doi":"10.21769/BioProtoc.5029","author":[{"first_name":"Ziqiang","full_name":"Li, Ziqiang","last_name":"Li","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3"},{"first_name":"Jennifer","last_name":"Huard","full_name":"Huard, Jennifer"},{"full_name":"Bayer, Emmanuelle M.","last_name":"Bayer","first_name":"Emmanuelle M."},{"first_name":"Valérie","full_name":"Wattelet-Boyer, Valérie","last_name":"Wattelet-Boyer"}],"date_created":"2024-07-14T22:01:11Z","department":[{"_id":"MiSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e5029","year":"2024","file_date_updated":"2024-07-16T06:16:11Z","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"file_date_updated":"2024-07-16T06:24:29Z","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_number":"L13","department":[{"_id":"JoMa"}],"date_created":"2024-07-14T22:01:11Z","author":[{"first_name":"Bingjie","full_name":"Wang, Bingjie","last_name":"Wang"},{"full_name":"Leja, Joel","last_name":"Leja","first_name":"Joel"},{"first_name":"Anna","last_name":"De Graaff","full_name":"De Graaff, Anna"},{"first_name":"Gabriel B.","full_name":"Brammer, Gabriel B.","last_name":"Brammer"},{"first_name":"Andrea","last_name":"Weibel","full_name":"Weibel, Andrea"},{"first_name":"Pieter","full_name":"Van Dokkum, Pieter","last_name":"Van Dokkum"},{"last_name":"Baggen","full_name":"Baggen, Josephine F.W.","first_name":"Josephine F.W."},{"last_name":"Suess","full_name":"Suess, Katherine A.","first_name":"Katherine A."},{"last_name":"Greene","full_name":"Greene, Jenny E.","first_name":"Jenny E."},{"full_name":"Bezanson, Rachel","last_name":"Bezanson","first_name":"Rachel"},{"full_name":"Cleri, Nikko J.","last_name":"Cleri","first_name":"Nikko J."},{"first_name":"Michaela","full_name":"Hirschmann, Michaela","last_name":"Hirschmann"},{"last_name":"Labbé","full_name":"Labbé, Ivo","first_name":"Ivo"},{"orcid":"0000-0003-2871-127X","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"Ian","last_name":"Mcconachie","full_name":"Mcconachie, Ian"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"full_name":"Nelson, Erica","last_name":"Nelson","first_name":"Erica"},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"last_name":"Setton","full_name":"Setton, David J.","first_name":"David J."},{"first_name":"Christina C.","full_name":"Williams, Christina C.","last_name":"Williams"}],"has_accepted_license":"1","doi":"10.3847/2041-8213/ad55f7","_id":"17234","DOAJ_listed":"1","scopus_import":"1","issue":"1","acknowledgement":"We thank the anonymous referee for the helpful comments. B.W. and J.L. acknowledge support from JWST-GO04233.009-A. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project No. 562 (First Light at Cosmic Dawn: Exploiting the James Webb Space Telescope Revolution). This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The JWST data presented in this Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed can be accessed via doi:10.17909/3a4n-9p88. Computations for this research were performed on the Pennsylvania State University’s Institute for Computational and Data Sciences’ Roar supercomputer. This publication made use of the NASA Astrophysical Data System for bibliographic information. \r\nFacilities: HST (ACS, WFC3), JWST (NIRCam, NIRSpec). Software: Astropy (Astropy Collaboration et al. 2013, 2018, 2022), dynesty (Speagle 2020), EAzY (Brammer et al. 2008),\r\nemcee (Foreman-Mackey et al. 2013), Matplotlib (Hunter 2007), msaexp (Brammer 2023b), msafit (de Graaff et al. 2024a), NumPy (Harris et al. 2020), Prospector (Johnson et al. 2021), Python-FSPS (Johnson et al. 2023).","abstract":[{"lang":"eng","text":"The identification of red, apparently massive galaxies at z > 7 in early James Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line compared to standard models of galaxy growth. A major uncertainty in the interpretation is whether the red colors are caused by evolved stellar populations, dust, or other effects such as emission lines or active galactic nuclei (AGNs). Here we show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4 μm and require formation histories extending hundreds of millions of years into the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies also show broad Balmer lines, with Hβ FWHM > 2500 km s−1, suggesting that dust-reddened AGNs contribute to, or even dominate, the spectral energy distributions of these galaxies at λrest ≳ 0.6 μm. All three galaxies have relatively narrow [O iii] lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically relaxed, inclined disks. Yet the inferred masses also remain highly uncertain. We model the high-quality spectra using Prospector to decompose the continuum into stellar and AGN components and explore limiting cases in stellar/AGN contribution. This produces a wide range of possible stellar masses, spanning M⋆ ∼ 109−1011M⊙. Nevertheless, all fits suggest a very early and rapid formation, most of which follow with a truncation in star formation. Potential origins and evolutionary tracks for these objects are discussed, from the cores of massive galaxies to low-mass galaxies with overmassive black holes. Intriguingly, we find all of these explanations to be incomplete; deeper and redder data are needed to understand the physics of these systems."}],"arxiv":1,"title":"RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec","ddc":["520"],"article_processing_charge":"Yes","date_published":"2024-07-01T00:00:00Z","oa_version":"Published Version","day":"01","date_updated":"2025-09-08T08:10:21Z","publication_status":"published","status":"public","publication":"Astrophysical Journal Letters","month":"07","external_id":{"arxiv":["2405.01473"],"isi":["001257903200001"]},"type":"journal_article","quality_controlled":"1","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"intvolume":"       969","oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"IOP Publishing","volume":969,"article_type":"original","citation":{"ama":"Wang B, Leja J, De Graaff A, et al. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. <i>Astrophysical Journal Letters</i>. 2024;969(1). doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>","apa":"Wang, B., Leja, J., De Graaff, A., Brammer, G. B., Weibel, A., Van Dokkum, P., … Williams, C. C. (2024). RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>","chicago":"Wang, Bingjie, Joel Leja, Anna De Graaff, Gabriel B. Brammer, Andrea Weibel, Pieter Van Dokkum, Josephine F.W. Baggen, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” <i>Astrophysical Journal Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>.","ista":"Wang B, Leja J, De Graaff A, Brammer GB, Weibel A, Van Dokkum P, Baggen JFW, Suess KA, Greene JE, Bezanson R, Cleri NJ, Hirschmann M, Labbé I, Matthee JJ, Mcconachie I, Naidu RP, Nelson E, Oesch PA, Setton DJ, Williams CC. 2024. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 969(1), L13.","ieee":"B. Wang <i>et al.</i>, “RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1. IOP Publishing, 2024.","short":"B. Wang, J. Leja, A. De Graaff, G.B. Brammer, A. Weibel, P. Van Dokkum, J.F.W. Baggen, K.A. Suess, J.E. Greene, R. Bezanson, N.J. Cleri, M. Hirschmann, I. Labbé, J.J. Matthee, I. Mcconachie, R.P. Naidu, E. Nelson, P.A. Oesch, D.J. Setton, C.C. Williams, Astrophysical Journal Letters 969 (2024).","mla":"Wang, Bingjie, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1, L13, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>."},"file":[{"file_id":"17243","checksum":"bb1a6725586df12e745d091b5778bb2b","file_name":"2024_AstrophysicalJourn_Wang.pdf","content_type":"application/pdf","date_created":"2024-07-16T06:24:29Z","creator":"dernst","success":1,"relation":"main_file","date_updated":"2024-07-16T06:24:29Z","access_level":"open_access","file_size":3273303}]},{"file":[{"checksum":"32a5cdf0ea9c937f806b6039f3219917","file_name":"2024_APLMaterial_Kohopaa.pdf","file_id":"17244","creator":"dernst","content_type":"application/pdf","date_created":"2024-07-16T06:30:30Z","relation":"main_file","success":1,"date_updated":"2024-07-16T06:30:30Z","access_level":"open_access","file_size":9408198}],"citation":{"mla":"Kohopää, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>.","short":"K. Kohopää, A. Ronzani, R.N. Jabdaraghi, A. Bera, M. Ribeiro, D. Hazra, J.L. Senior, M. Prunnila, J. Govenius, J.S. Lehtinen, A. Kemppinen, APL Materials 12 (2024).","ieee":"K. Kohopää <i>et al.</i>, “Effect of ion irradiation on superconducting thin films,” <i>APL Materials</i>, vol. 12, no. 7. AIP Publishing, 2024.","chicago":"Kohopää, Katja, Alberto Ronzani, Robab Najafi Jabdaraghi, Arijit Bera, Mário Ribeiro, Dibyendu Hazra, Jorden L Senior, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>.","ista":"Kohopää K, Ronzani A, Jabdaraghi RN, Bera A, Ribeiro M, Hazra D, Senior JL, Prunnila M, Govenius J, Lehtinen JS, Kemppinen A. 2024. Effect of ion irradiation on superconducting thin films. APL Materials. 12(7), 071101.","apa":"Kohopää, K., Ronzani, A., Jabdaraghi, R. N., Bera, A., Ribeiro, M., Hazra, D., … Kemppinen, A. (2024). Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>","ama":"Kohopää K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. 2024;12(7). doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>"},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_type":"original","intvolume":"        12","publication_identifier":{"eissn":["2166-532X"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"publisher":"AIP Publishing","volume":12,"month":"07","external_id":{"isi":["001260942200003"]},"type":"journal_article","quality_controlled":"1","status":"public","publication_status":"published","publication":"APL Materials","article_processing_charge":"Yes","date_published":"2024-07-01T00:00:00Z","date_updated":"2025-09-08T08:10:58Z","day":"01","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"ddc":["530"],"title":"Effect of ion irradiation on superconducting thin films","abstract":[{"text":"We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors.","lang":"eng"}],"ec_funded":1,"scopus_import":"1","acknowledgement":"We thank J. A. Sauls for useful discussions. For funding of our research project, we acknowledge the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement Nos. 862660/Quantum e-leaps, 899558/aCryComm, 766853/EFINED, and ECSEL programme 101007322/MatQu. This project has also received funding from Business Finland through Quantum Technologies Industrial (QuTI) Project No. 128291 and from Research Council of Finland through Grant Nos. 310909, 350220 and Finnish Quantum Flagship project 359284. This work was performed as part of the Research Council of Finland Centres of Excellence program (Project Nos. 336817, 336819, 352934, and 352935). We also acknowledge funding from an internal strategic innovation project of VTT related to the development of quantum computing technologies. This research was supported by the Scientific Service Units of IST Austria through resources provided by Electron Microscopy Facility. J. Senior acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. Ronzani acknowledges funding from Research Council of Finland (Research Fellowship Project No. 356542).","issue":"7","doi":"10.1063/5.0202851","has_accepted_license":"1","_id":"17235","department":[{"_id":"AnHi"}],"date_created":"2024-07-14T22:01:11Z","author":[{"first_name":"Katja","last_name":"Kohopää","full_name":"Kohopää, Katja"},{"first_name":"Alberto","last_name":"Ronzani","full_name":"Ronzani, Alberto"},{"first_name":"Robab Najafi","full_name":"Jabdaraghi, Robab Najafi","last_name":"Jabdaraghi"},{"first_name":"Arijit","full_name":"Bera, Arijit","last_name":"Bera"},{"full_name":"Ribeiro, Mário","last_name":"Ribeiro","first_name":"Mário"},{"last_name":"Hazra","full_name":"Hazra, Dibyendu","first_name":"Dibyendu"},{"first_name":"Jorden L","orcid":"0000-0002-0672-9295","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L"},{"full_name":"Prunnila, Mika","last_name":"Prunnila","first_name":"Mika"},{"first_name":"Joonas","last_name":"Govenius","full_name":"Govenius, Joonas"},{"full_name":"Lehtinen, Janne S.","last_name":"Lehtinen","first_name":"Janne S."},{"first_name":"Antti","full_name":"Kemppinen, Antti","last_name":"Kemppinen"}],"year":"2024","isi":1,"article_number":"071101","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-07-16T06:30:30Z","language":[{"iso":"eng"}]},{"month":"06","type":"conference","external_id":{"arxiv":["2307.00115"],"isi":["001253331900044"]},"page":"403-414","quality_controlled":"1","OA_place":"publisher","conference":{"location":"Nantes, France","start_date":"2024-06-17","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2024-06-21"},"publication_identifier":{"issn":["1548-6109"],"isbn":["9798400704161"]},"publisher":"Association for Computing Machinery","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"file":[{"file_size":1116166,"access_level":"open_access","date_updated":"2024-07-16T06:38:08Z","relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","date_created":"2024-07-16T06:38:08Z","file_name":"2024_SPAA_Kolmogorov.pdf","checksum":"6ca18ac8508719dbd5d5735f4c991af2","file_id":"17245"}],"citation":{"ama":"Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In: <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2024:403-414. doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>","apa":"Kolmogorov, V. (2024). A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 403–414). Nantes, France: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>","ieee":"V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut,” in <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Nantes, France, 2024, pp. 403–414.","ista":"Kolmogorov V. 2024. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 403–414.","chicago":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 403–14. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>.","mla":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2024, pp. 403–14, doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>.","short":"V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–414."},"arxiv":1,"abstract":[{"text":"Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain \"chaining\" algorithm that combines results of multiple calls to the maxflow algorithm.\r\nWe present an alternative approach that avoids solving the multicommodity flow problem and instead computes \"violating paths\". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors.\r\nWe also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.","lang":"eng"}],"ddc":["510"],"title":"A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut","article_processing_charge":"Yes (via OA deal)","date_published":"2024-06-17T00:00:00Z","day":"17","date_updated":"2026-01-21T09:46:25Z","oa_version":"Published Version","status":"public","publication_status":"published","publication":"Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures","date_created":"2024-07-14T22:01:11Z","department":[{"_id":"VlKo"}],"author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"has_accepted_license":"1","doi":"10.1145/3626183.3659969","_id":"17236","scopus_import":"1","language":[{"iso":"eng"}],"file_date_updated":"2024-07-16T06:38:08Z","OA_type":"hybrid","corr_author":"1","related_material":{"record":[{"id":"21007","relation":"extended_version","status":"public"}]},"year":"2024","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2404.14003","open_access":"1"}],"language":[{"iso":"eng"}],"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-07-14T22:01:12Z","department":[{"_id":"NiBa"}],"author":[{"last_name":"Reynes","full_name":"Reynes, Lauric","first_name":"Lauric"},{"orcid":"0000-0003-0371-9339","first_name":"Louise","full_name":"Fouqueau, Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","last_name":"Fouqueau"},{"full_name":"Aurelle, Didier","last_name":"Aurelle","first_name":"Didier"},{"full_name":"Mauger, Stephane","last_name":"Mauger","first_name":"Stephane"},{"first_name":"Christophe","full_name":"Destombe, Christophe","last_name":"Destombe"},{"full_name":"Valero, Myriam","last_name":"Valero","first_name":"Myriam"}],"doi":"10.1093/jeb/voae048","_id":"17237","scopus_import":"1","issue":"6","acknowledgement":"This work was funded by the EU project MARFOR Biodiversa/004/2015. L.F. was additionally funded by the Region Bretagne (ARED 2017 REEALG) and the NOMIS Foundation. The project leading to this publication has received funding from the EC2CO (CNRS) fund and from the European FEDER Fund under project 1166-39417.\r\nThis work is especially dedicated to the memory of Gernot Glöckner who contributed to the sequencing of Laminaria digitata genome and passed away in very recent time. The authors thank the ABiMS platform of the Roscoff biological station (http://abims.sb-roscoff.fr) for providing the HPC resources that contributed to the search results reported in this document. We also acknowledge the staff of the “Cluster de calcul intensif HPC” Platform of the OSU Institut Pythéas (Aix-Marseille Université, INSU-CNRS) for providing the computing facilities.","abstract":[{"text":"The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.","lang":"eng"}],"arxiv":1,"title":"Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations","date_published":"2024-06-01T00:00:00Z","article_processing_charge":"No","oa_version":"Preprint","day":"01","date_updated":"2025-06-04T07:23:23Z","publication_status":"published","status":"public","publication":"Journal of Evolutionary Biology","page":"677-692","external_id":{"arxiv":["2404.14003"],"pmid":["38629140"]},"month":"06","type":"journal_article","quality_controlled":"1","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"intvolume":"        37","oa":1,"publisher":"Oxford University Press","volume":37,"article_type":"original","citation":{"short":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal of Evolutionary Biology 37 (2024) 677–692.","mla":"Reynes, Lauric, et al. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:<a href=\"https://doi.org/10.1093/jeb/voae048\">10.1093/jeb/voae048</a>.","ista":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. 2024. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. Journal of Evolutionary Biology. 37(6), 677–692.","chicago":"Reynes, Lauric, Louise Fouqueau, Didier Aurelle, Stephane Mauger, Christophe Destombe, and Myriam Valero. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae048\">https://doi.org/10.1093/jeb/voae048</a>.","ieee":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, and M. Valero, “Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations,” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6. Oxford University Press, pp. 677–692, 2024.","apa":"Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., &#38; Valero, M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae048\">https://doi.org/10.1093/jeb/voae048</a>","ama":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. <i>Journal of Evolutionary Biology</i>. 2024;37(6):677-692. doi:<a href=\"https://doi.org/10.1093/jeb/voae048\">10.1093/jeb/voae048</a>"},"pmid":1},{"acknowledgement":"This work was supported by a grant from the ERC, 101055327, “HaplotypeStructure”. I thank Himani Sachdeva, Michal Hledik, Jitka Polechova, and the reviewers for their helpful comments.","issue":"6","scopus_import":"1","_id":"17238","has_accepted_license":"1","doi":"10.1093/jeb/voae052","author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"date_created":"2024-07-14T22:01:12Z","department":[{"_id":"NiBa"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","corr_author":"1","file_date_updated":"2024-07-15T09:45:25Z","language":[{"iso":"eng"}],"file":[{"date_created":"2024-07-15T09:45:25Z","content_type":"application/pdf","creator":"dernst","file_id":"17241","checksum":"94e6b68bddf6cadcec29c7f41647359f","file_name":"2024_JourEvolutionaryBiology_Barton.pdf","file_size":1194263,"access_level":"open_access","date_updated":"2024-07-15T09:45:25Z","success":1,"relation":"main_file"}],"citation":{"apa":"Barton, N. H. (2024). Limits to species’ range: The tension between local and global adaptation. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae052\">https://doi.org/10.1093/jeb/voae052</a>","ama":"Barton NH. Limits to species’ range: The tension between local and global adaptation. <i>Journal of Evolutionary Biology</i>. 2024;37(6):605-615. doi:<a href=\"https://doi.org/10.1093/jeb/voae052\">10.1093/jeb/voae052</a>","short":"N.H. Barton, Journal of Evolutionary Biology 37 (2024) 605–615.","mla":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 605–15, doi:<a href=\"https://doi.org/10.1093/jeb/voae052\">10.1093/jeb/voae052</a>.","ista":"Barton NH. 2024. Limits to species’ range: The tension between local and global adaptation. Journal of Evolutionary Biology. 37(6), 605–615.","chicago":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae052\">https://doi.org/10.1093/jeb/voae052</a>.","ieee":"N. H. Barton, “Limits to species’ range: The tension between local and global adaptation,” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6. Oxford University Press, pp. 605–615, 2024."},"pmid":1,"project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"article_type":"review","oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Oxford University Press","volume":37,"intvolume":"        37","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"quality_controlled":"1","external_id":{"pmid":["38683160"],"isi":["001225323900001"]},"month":"06","type":"journal_article","page":"605-615","status":"public","publication":"Journal of Evolutionary Biology","publication_status":"published","day":"01","date_updated":"2025-09-08T08:08:41Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","date_published":"2024-06-01T00:00:00Z","ddc":["570"],"title":"Limits to species' range: The tension between local and global adaptation","abstract":[{"text":"We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace.","lang":"eng"}]},{"language":[{"iso":"eng"}],"OA_type":"hybrid","file_date_updated":"2025-01-09T12:06:48Z","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","author":[{"first_name":"Clara","last_name":"Garcia-Sacristan","full_name":"Garcia-Sacristan, Clara"},{"first_name":"Victor G.","full_name":"Gisbert, Victor G.","last_name":"Gisbert"},{"full_name":"Klein, Kevin","id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398","last_name":"Klein","first_name":"Kevin"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Ricardo","full_name":"Garcia, Ricardo","last_name":"Garcia"}],"department":[{"_id":"AnSa"}],"date_created":"2024-07-14T22:01:12Z","_id":"17239","has_accepted_license":"1","doi":"10.1021/acsnano.4c03839","acknowledgement":"We are grateful to Nancy Forde (Simon Fraser University) for her motivating comments. Financial support from the Ministerio de Ciencia, Innovación y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged. A.Š. and K.K. acknowledge support from the Royal Society University Research Fellowship and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant No. 585 80296).","issue":"28","scopus_import":"1","ec_funded":1,"abstract":[{"text":"Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes.","lang":"eng"}],"ddc":["540"],"title":"In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures","date_updated":"2025-12-16T09:01:10Z","day":"16","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","date_published":"2024-07-16T00:00:00Z","status":"public","publication_status":"published","publication":"ACS Nano","quality_controlled":"1","external_id":{"isi":["001263155500001"],"pmid":["38958189"]},"month":"07","type":"journal_article","page":"18485-18492","publisher":"American Chemical Society","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":18,"oa":1,"intvolume":"        18","OA_place":"publisher","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"article_type":"original","file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2025-01-09T12:06:48Z","checksum":"b7e9ce718e92f568bcb3810e8e28e458","file_name":"2024_ACSNano_GarciaSacristan.pdf","file_id":"18808","access_level":"open_access","file_size":10036838,"date_updated":"2025-01-09T12:06:48Z","relation":"main_file","success":1}],"pmid":1,"citation":{"ieee":"C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Šarić, and R. Garcia, “In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,” <i>ACS Nano</i>, vol. 18, no. 28. American Chemical Society, pp. 18485–18492, 2024.","chicago":"Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Šarić, and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>.","ista":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. 2024. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 18(28), 18485–18492.","mla":"Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>, vol. 18, no. 28, American Chemical Society, 2024, pp. 18485–92, doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>.","short":"C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano 18 (2024) 18485–18492.","ama":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. 2024;18(28):18485-18492. doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>","apa":"Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., &#38; Garcia, R. (2024). In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>"}},{"citation":{"short":"E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y. Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20 (2024) 1492–1500.","mla":"Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>.","ista":"Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.","chicago":"Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>.","ieee":"E. Vercruysse <i>et al.</i>, “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1492–1500, 2024.","apa":"Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M., Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous epithelial cell clusters. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>","ama":"Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. <i>Nature Physics</i>. 2024;20:1492-1500. doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>"},"article_type":"original","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"volume":20,"publisher":"Springer Nature","oa":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"intvolume":"        20","OA_place":"repository","quality_controlled":"1","page":"1492-1500","type":"journal_article","external_id":{"isi":["001250246200004"]},"month":"09","status":"public","publication_status":"published","publication":"Nature Physics","oa_version":"Preprint","day":"01","date_updated":"2025-09-08T08:28:31Z","date_published":"2024-09-01T00:00:00Z","article_processing_charge":"No","title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","ec_funded":1,"abstract":[{"text":"The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments.","lang":"eng"}],"acknowledgement":"M.L., E.V. and S.G. acknowledge funding from the European Regional Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS; Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23), the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen, ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow (Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively. E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund for Research Training in Industry and Agriculture (FRIA). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS foundation as a NOMIS fellow and by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen Center for Physics, which is supported by the National Science Foundation (Grant No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia (Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade and Business.","scopus_import":"1","_id":"17269","doi":"10.1038/s41567-024-02532-x","author":[{"full_name":"Vercruysse, Eléonore","last_name":"Vercruysse","first_name":"Eléonore"},{"orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner"},{"last_name":"Gómez-González","full_name":"Gómez-González, Manuel","first_name":"Manuel"},{"last_name":"Remson","full_name":"Remson, Alexandre","first_name":"Alexandre"},{"first_name":"Marine","full_name":"Luciano, Marine","last_name":"Luciano"},{"full_name":"Kalukula, Yohalie","last_name":"Kalukula","first_name":"Yohalie"},{"last_name":"Rossetti","full_name":"Rossetti, Leone","first_name":"Leone"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"first_name":"Sylvain","last_name":"Gabriele","full_name":"Gabriele, Sylvain"}],"date_created":"2024-07-16T12:32:17Z","department":[{"_id":"EdHa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/a-railroad-of-cells/","description":"News on ISTA website","relation":"press_release"}]},"year":"2024","corr_author":"1","OA_type":"green","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2022.07.17.500364","open_access":"1"}]},{"article_type":"original","citation":{"apa":"Brigati, G., Dolbeault, J., &#38; Simonov, N. (2024). Stability for the logarithmic Sobolev inequality. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">https://doi.org/10.1016/j.jfa.2024.110562</a>","ama":"Brigati G, Dolbeault J, Simonov N. Stability for the logarithmic Sobolev inequality. <i>Journal of Functional Analysis</i>. 2024;287(8). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">10.1016/j.jfa.2024.110562</a>","mla":"Brigati, Giovanni, et al. “Stability for the Logarithmic Sobolev Inequality.” <i>Journal of Functional Analysis</i>, vol. 287, no. 8, 110562, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">10.1016/j.jfa.2024.110562</a>.","short":"G. Brigati, J. Dolbeault, N. Simonov, Journal of Functional Analysis 287 (2024).","ieee":"G. Brigati, J. Dolbeault, and N. Simonov, “Stability for the logarithmic Sobolev inequality,” <i>Journal of Functional Analysis</i>, vol. 287, no. 8. Elsevier, 2024.","chicago":"Brigati, Giovanni, Jean Dolbeault, and Nikita Simonov. “Stability for the Logarithmic Sobolev Inequality.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">https://doi.org/10.1016/j.jfa.2024.110562</a>.","ista":"Brigati G, Dolbeault J, Simonov N. 2024. Stability for the logarithmic Sobolev inequality. Journal of Functional Analysis. 287(8), 110562."},"quality_controlled":"1","month":"10","type":"journal_article","external_id":{"arxiv":["2303.12926"],"isi":["001271814000001"]},"oa":1,"volume":287,"publisher":"Elsevier","OA_place":"repository","intvolume":"       287","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"date_updated":"2025-09-08T08:25:34Z","day":"15","oa_version":"Preprint","date_published":"2024-10-15T00:00:00Z","article_processing_charge":"No","publication_status":"published","publication":"Journal of Functional Analysis","status":"public","arxiv":1,"abstract":[{"text":"This paper is devoted to stability results for the Gaussian logarithmic Sobolev inequality, with explicit stability constants.\r\n\r\n","lang":"eng"}],"title":"Stability for the logarithmic Sobolev inequality","_id":"17277","doi":"10.1016/j.jfa.2024.110562","acknowledgement":"The authors thank Max Fathi and Pierre Cardaliaguet for fruitful discussions and Emanuel Indrei for stimulating interactions. They also thank an anonymous referee for useful comments and suggestions which have led to an improvement of the manuscript. They also want to express their gratitude to the managing editor, L. Gross, for his encouragements and questions. G.B. has been funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 754362. This work has been (partially) supported by the Project Conviviality ANR-23-CE40-0003 of the French National Research Agency.","issue":"8","scopus_import":"1","author":[{"first_name":"Giovanni","full_name":"Brigati, Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","last_name":"Brigati"},{"last_name":"Dolbeault","full_name":"Dolbeault, Jean","first_name":"Jean"},{"first_name":"Nikita","last_name":"Simonov","full_name":"Simonov, Nikita"}],"date_created":"2024-07-21T22:01:00Z","department":[{"_id":"JaMa"}],"article_number":"110562","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"10.48550/arXiv.2303.12926"}],"OA_type":"green","corr_author":"1"},{"scopus_import":"1","issue":"3","acknowledgement":"B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No. EP/P020259/1).","doi":"10.1063/5.0217232","_id":"17278","date_created":"2024-07-21T22:01:00Z","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"author":[{"first_name":"Xiaoyu","id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","last_name":"Wang","full_name":"Wang, Xiaoyu"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632"}],"related_material":{"link":[{"url":"https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0","relation":"software"}]},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_number":"034111","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.02216"}],"language":[{"iso":"eng"}],"pmid":1,"citation":{"apa":"Wang, X., &#38; Cheng, B. (2024). Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0217232\">https://doi.org/10.1063/5.0217232</a>","ama":"Wang X, Cheng B. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. <i>Journal of Chemical Physics</i>. 2024;161(3). doi:<a href=\"https://doi.org/10.1063/5.0217232\">10.1063/5.0217232</a>","short":"X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).","mla":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal of Chemical Physics</i>, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0217232\">10.1063/5.0217232</a>.","chicago":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0217232\">https://doi.org/10.1063/5.0217232</a>.","ista":"Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 161(3), 034111.","ieee":"X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures,” <i>Journal of Chemical Physics</i>, vol. 161, no. 3. AIP Publishing, 2024."},"article_type":"original","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"intvolume":"       161","volume":161,"oa":1,"publisher":"AIP Publishing","type":"journal_article","month":"07","external_id":{"pmid":["39007379"],"arxiv":["2405.02216"],"isi":["001281819100016"]},"quality_controlled":"1","publication_status":"published","status":"public","publication":"Journal of Chemical Physics","article_processing_charge":"No","date_published":"2024-07-14T00:00:00Z","oa_version":"Preprint","day":"14","date_updated":"2025-09-08T08:26:09Z","title":"Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures","abstract":[{"text":"An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult due to the complexities and convergence problems of Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes, or lack thereof, in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes and reveal that they tend to form when the mixture components have similar boiling points and strong interactions.","lang":"eng"}],"arxiv":1},{"_id":"17279","doi":"10.1016/j.chembiol.2024.06.011","issue":"7","scopus_import":"1","author":[{"orcid":"0000-0001-6406-524X","first_name":"Mario","full_name":"Avellaneda Sarrió, Mario","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","last_name":"Avellaneda Sarrió"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"date_created":"2024-07-21T22:01:00Z","department":[{"_id":"MiSi"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","language":[{"iso":"eng"}],"corr_author":"1","article_type":"review","citation":{"chicago":"Avellaneda Sarrió, Mario, and Michael K Sixt. “Rescuing T Cells from Stiff Tumors.” <i>Cell Chemical Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">https://doi.org/10.1016/j.chembiol.2024.06.011</a>.","ista":"Avellaneda Sarrió M, Sixt MK. 2024. Rescuing T cells from stiff tumors. Cell Chemical Biology. 31(7), 1242–1243.","ieee":"M. Avellaneda Sarrió and M. K. Sixt, “Rescuing T cells from stiff tumors,” <i>Cell Chemical Biology</i>, vol. 31, no. 7. Elsevier, pp. 1242–1243, 2024.","short":"M. Avellaneda Sarrió, M.K. Sixt, Cell Chemical Biology 31 (2024) 1242–1243.","mla":"Avellaneda Sarrió, Mario, and Michael K. Sixt. “Rescuing T Cells from Stiff Tumors.” <i>Cell Chemical Biology</i>, vol. 31, no. 7, Elsevier, 2024, pp. 1242–43, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">10.1016/j.chembiol.2024.06.011</a>.","ama":"Avellaneda Sarrió M, Sixt MK. Rescuing T cells from stiff tumors. <i>Cell Chemical Biology</i>. 2024;31(7):1242-1243. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">10.1016/j.chembiol.2024.06.011</a>","apa":"Avellaneda Sarrió, M., &#38; Sixt, M. K. (2024). Rescuing T cells from stiff tumors. <i>Cell Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">https://doi.org/10.1016/j.chembiol.2024.06.011</a>"},"pmid":1,"quality_controlled":"1","month":"07","external_id":{"pmid":["39029454"],"isi":["001275725000001"]},"type":"journal_article","page":"1242-1243","volume":31,"publisher":"Elsevier","intvolume":"        31","publication_identifier":{"issn":["2451-9456"],"eissn":["2451-9448"]},"date_updated":"2025-09-08T08:27:03Z","day":"18","oa_version":"None","date_published":"2024-07-18T00:00:00Z","article_processing_charge":"No","status":"public","publication_status":"published","publication":"Cell Chemical Biology","abstract":[{"text":"In a recent issue of Cell, Zhang et al.1 demonstrate that mechanical features of a solid tumor can drive T cells into dysfunctionality and identify pathways that revert this “exhausted” state.","lang":"eng"}],"title":"Rescuing T cells from stiff tumors"},{"date_created":"2024-07-21T22:01:01Z","department":[{"_id":"RySh"},{"_id":"PreCl"}],"author":[{"first_name":"Simon","full_name":"Früh, Simon","last_name":"Früh"},{"last_name":"Boudkkazi","full_name":"Boudkkazi, Sami","first_name":"Sami"},{"last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","first_name":"Peter","orcid":"0000-0002-3509-1948"},{"first_name":"Vita","last_name":"Sereikaite","full_name":"Sereikaite, Vita"},{"full_name":"Chen, Li Yuan","last_name":"Chen","first_name":"Li Yuan"},{"first_name":"Diego","full_name":"Fernandez-Fernandez, Diego","last_name":"Fernandez-Fernandez"},{"first_name":"Pascal D.","last_name":"Rem","full_name":"Rem, Pascal D."},{"first_name":"Daniel","full_name":"Ulrich, Daniel","last_name":"Ulrich"},{"first_name":"Jochen","full_name":"Schwenk, Jochen","last_name":"Schwenk"},{"first_name":"Ziyang","full_name":"Chen, Ziyang","last_name":"Chen"},{"first_name":"Elodie Le","last_name":"Monnier","full_name":"Monnier, Elodie Le"},{"last_name":"Fritzius","full_name":"Fritzius, Thorsten","first_name":"Thorsten"},{"full_name":"Innocenti, Sabrina M.","last_name":"Innocenti","first_name":"Sabrina M."},{"first_name":"Valérie","full_name":"Besseyrias, Valérie","last_name":"Besseyrias"},{"first_name":"Luca","last_name":"Trovò","full_name":"Trovò, Luca"},{"first_name":"Michal","full_name":"Stawarski, Michal","last_name":"Stawarski"},{"last_name":"Argilli","full_name":"Argilli, Emanuela","first_name":"Emanuela"},{"first_name":"Elliott H.","full_name":"Sherr, Elliott H.","last_name":"Sherr"},{"full_name":"Van Bon, Bregje","last_name":"Van Bon","first_name":"Bregje"},{"first_name":"Erik Jan","last_name":"Kamsteeg","full_name":"Kamsteeg, Erik Jan"},{"full_name":"Iascone, Maria","last_name":"Iascone","first_name":"Maria"},{"full_name":"Pilotta, Alba","last_name":"Pilotta","first_name":"Alba"},{"first_name":"Maria R.","last_name":"Cutrì","full_name":"Cutrì, Maria R."},{"first_name":"Mahshid S.","last_name":"Azamian","full_name":"Azamian, Mahshid S."},{"full_name":"Hernández-García, Andrés","last_name":"Hernández-García","first_name":"Andrés"},{"last_name":"Lalani","full_name":"Lalani, Seema R.","first_name":"Seema R."},{"full_name":"Rosenfeld, Jill A.","last_name":"Rosenfeld","first_name":"Jill A."},{"first_name":"Xiaonan","last_name":"Zhao","full_name":"Zhao, Xiaonan"},{"first_name":"Tiphanie P.","full_name":"Vogel, Tiphanie P.","last_name":"Vogel"},{"first_name":"Herda","full_name":"Ona, Herda","last_name":"Ona"},{"first_name":"Daryl A.","full_name":"Scott, Daryl A.","last_name":"Scott"},{"first_name":"Peter","last_name":"Scheiffele","full_name":"Scheiffele, Peter"},{"first_name":"Kristian","full_name":"Strømgaard, Kristian","last_name":"Strømgaard"},{"full_name":"Tafti, Mehdi","last_name":"Tafti","first_name":"Mehdi"},{"last_name":"Gassmann","full_name":"Gassmann, Martin","first_name":"Martin"},{"full_name":"Fakler, Bernd","last_name":"Fakler","first_name":"Bernd"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Bettler, Bernhard","last_name":"Bettler","first_name":"Bernhard"}],"scopus_import":"1","acknowledgement":"Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration with Pawel Pelczar at the center for transgenic models at the University of Basel, Switzerland. We thank the imaging core facility (IMCF, University of Basel) and in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM microscope.\r\nThis work was supported by a grant from the Swiss National Science Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1, 16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative Medicines Initiatives from the European Commission joint undertaking under grant agreement No 777394.","issue":"28","doi":"10.1126/sciadv.adk5462","has_accepted_license":"1","DOAJ_listed":"1","_id":"17280","file_date_updated":"2024-07-22T06:29:27Z","OA_type":"gold","language":[{"iso":"eng"}],"year":"2024","isi":1,"article_number":"adk5462","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        10","OA_place":"publisher","publication_identifier":{"eissn":["2375-2548"]},"oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"American Association for the Advancement of Science","volume":10,"type":"journal_article","external_id":{"pmid":["38985877"],"isi":["001280159000022"]},"month":"07","quality_controlled":"1","file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2024-07-22T06:29:27Z","file_name":"2024_ScienceAdv_Früh.pdf","checksum":"9cbc4501fcd4ba1c0811fd244031422b","file_id":"17287","date_updated":"2024-07-22T06:29:27Z","access_level":"open_access","file_size":7241489,"relation":"main_file","success":1}],"citation":{"apa":"Früh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez, D., … Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>","ama":"Früh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. 2024;10(28). doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>","mla":"Früh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>, vol. 10, no. 28, adk5462, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>.","short":"S. Früh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez, P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti, V. Besseyrias, L. Trovò, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J. Kamsteeg, M. Iascone, A. Pilotta, M.R. Cutrì, M.S. Azamian, A. Hernández-García, S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele, K. Strømgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science Advances 10 (2024).","ieee":"S. Früh <i>et al.</i>, “Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release,” <i>Science Advances</i>, vol. 10, no. 28. American Association for the Advancement of Science, 2024.","chicago":"Früh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>.","ista":"Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM, Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ, Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 10(28), adk5462."},"pmid":1,"article_type":"original","ddc":["570"],"title":"Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release","abstract":[{"text":"Adherens junction–associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function AJAP1 variants.","lang":"eng"}],"publication":"Science Advances","status":"public","publication_status":"published","article_processing_charge":"Yes","date_published":"2024-07-12T00:00:00Z","date_updated":"2025-09-08T08:15:54Z","day":"12","oa_version":"Published Version"},{"article_type":"original","citation":{"ama":"Campbell AJ, O’Rourke S, Renfrew DT. The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation. <i>International Mathematics Research Notices</i>. 2024;2024(13):10189-10218. doi:<a href=\"https://doi.org/10.1093/imrn/rnae062\">10.1093/imrn/rnae062</a>","apa":"Campbell, A. J., O’Rourke, S., &#38; Renfrew, D. T. (2024). The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnae062\">https://doi.org/10.1093/imrn/rnae062</a>","ista":"Campbell AJ, O’Rourke S, Renfrew DT. 2024. The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation. International Mathematics Research Notices. 2024(13), 10189–10218.","chicago":"Campbell, Andrew J, Sean O’Rourke, and David T Renfrew. “The Fractional Free Convolution of R-Diagonal Elements and Random Polynomials under Repeated Differentiation.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/imrn/rnae062\">https://doi.org/10.1093/imrn/rnae062</a>.","ieee":"A. J. Campbell, S. O’Rourke, and D. T. Renfrew, “The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation,” <i>International Mathematics Research Notices</i>, vol. 2024, no. 13. Oxford University Press, pp. 10189–10218, 2024.","short":"A.J. Campbell, S. O’Rourke, D.T. Renfrew, International Mathematics Research Notices 2024 (2024) 10189–10218.","mla":"Campbell, Andrew J., et al. “The Fractional Free Convolution of R-Diagonal Elements and Random Polynomials under Repeated Differentiation.” <i>International Mathematics Research Notices</i>, vol. 2024, no. 13, Oxford University Press, 2024, pp. 10189–218, doi:<a href=\"https://doi.org/10.1093/imrn/rnae062\">10.1093/imrn/rnae062</a>."},"file":[{"access_level":"open_access","file_size":1233508,"date_updated":"2024-07-22T06:40:19Z","relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","date_created":"2024-07-22T06:40:19Z","file_name":"2024_IMRN_Campbell.pdf","checksum":"f36a7dbf53f23d5833db711052e69b49","file_id":"17288"}],"quality_controlled":"1","page":"10189-10218","type":"journal_article","month":"07","external_id":{"isi":["001198019500001"]},"publisher":"Oxford University Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":2024,"oa":1,"publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"intvolume":"      2024","oa_version":"Published Version","day":"01","date_updated":"2025-09-08T08:16:32Z","date_published":"2024-07-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","publication":"International Mathematics Research Notices","publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"We extend the free convolution of Brown measures of R-diagonal elements introduced by Kösters and Tikhomirov [ 28] to fractional powers. We then show how this fractional free convolution arises naturally when studying the roots of random polynomials with independent coefficients under repeated differentiation. When the proportion of derivatives to the degree approaches one, we establish central limit theorem-type behavior and discuss stable distributions."}],"title":"The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation","ddc":["510"],"_id":"17281","doi":"10.1093/imrn/rnae062","has_accepted_license":"1","issue":"13","acknowledgement":"This work was supported by the National Science Foundation [Grant No. DMS-2143142 to S.O.]; and the European Research Council [Grant No. 101020331].The third author acknowledges the support of the University of Colorado Boulder, where a portion of this work was completed. The authors thank Martin Auer, Vadim Gorin, Brian Hall, and Noah Williams for comments, corrections, and references. The authors also wish to thank the anonymous referees for useful feedback and corrections.","scopus_import":"1","author":[{"last_name":"Campbell","id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","full_name":"Campbell, Andrew J","first_name":"Andrew J"},{"last_name":"O'Rourke","full_name":"O'Rourke, Sean","first_name":"Sean"},{"id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","last_name":"Renfrew","full_name":"Renfrew, David T","first_name":"David T","orcid":"0000-0003-3493-121X"}],"date_created":"2024-07-21T22:01:01Z","department":[{"_id":"LaEr"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2024","language":[{"iso":"eng"}],"corr_author":"1","file_date_updated":"2024-07-22T06:40:19Z"},{"volume":63,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","oa":1,"intvolume":"        63","publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]},"quality_controlled":"1","month":"07","type":"journal_article","external_id":{"pmid":["38947856"],"arxiv":["2209.11149"],"isi":["001258097800003"]},"file":[{"success":1,"relation":"main_file","date_updated":"2024-07-22T07:05:32Z","access_level":"open_access","file_size":416622,"file_id":"17289","file_name":"2024_CalculusVariations_Brooks.pdf","checksum":"a0cf0e0ba2157aabb287cb597be17dac","date_created":"2024-07-22T07:05:32Z","content_type":"application/pdf","creator":"dernst"}],"pmid":1,"citation":{"ama":"Brooks M, Maas J. Characterisation of gradient flows for a given functional. <i>Calculus of Variations and Partial Differential Equations</i>. 2024;63(6). doi:<a href=\"https://doi.org/10.1007/s00526-024-02755-z\">10.1007/s00526-024-02755-z</a>","apa":"Brooks, M., &#38; Maas, J. (2024). Characterisation of gradient flows for a given functional. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-024-02755-z\">https://doi.org/10.1007/s00526-024-02755-z</a>","ieee":"M. Brooks and J. Maas, “Characterisation of gradient flows for a given functional,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 63, no. 6. Springer Nature, 2024.","ista":"Brooks M, Maas J. 2024. Characterisation of gradient flows for a given functional. Calculus of Variations and Partial Differential Equations. 63(6), 153.","chicago":"Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a given Functional.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00526-024-02755-z\">https://doi.org/10.1007/s00526-024-02755-z</a>.","mla":"Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a given Functional.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 63, no. 6, 153, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00526-024-02755-z\">10.1007/s00526-024-02755-z</a>.","short":"M. Brooks, J. Maas, Calculus of Variations and Partial Differential Equations 63 (2024)."},"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"article_type":"original","ddc":["510"],"title":"Characterisation of gradient flows for a given functional","ec_funded":1,"arxiv":1,"abstract":[{"text":"Let  X  be a vector field and  Y  be a co-vector field on a smooth manifold  M. Does there exist a smooth Riemannian metric  gαβ  on  M  such that  Yβ=gαβXα ? The main result of this note gives necessary and sufficient conditions for this to be true. As an application of this result we show that a finite-dimensional ergodic Lindblad equation admits a gradient flow structure for the von Neumann relative entropy if and only if the condition of BKM-detailed balance holds.","lang":"eng"}],"publication_status":"published","status":"public","publication":"Calculus of Variations and Partial Differential Equations","day":"01","date_updated":"2025-09-08T08:24:51Z","oa_version":"Published Version","date_published":"2024-07-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Morris","orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","full_name":"Brooks, Morris"},{"orcid":"0000-0002-0845-1338","first_name":"Jan","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas"}],"date_created":"2024-07-21T22:01:01Z","department":[{"_id":"JaMa"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).J. M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117), and by the Austrian Science Fund (FWF), Project SFB F65. We thank the anonymous referee for valuable comments on the paper.","issue":"6","scopus_import":"1","_id":"17282","has_accepted_license":"1","doi":"10.1007/s00526-024-02755-z","corr_author":"1","file_date_updated":"2024-07-22T07:05:32Z","language":[{"iso":"eng"}],"isi":1,"article_number":"153","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024"},{"citation":{"ama":"Chatterjee K, Goharshady E, Novotný P, Zikelic D. Equivalence and similarity refutation for probabilistic programs. <i>Proceedings of the ACM on Programming Languages</i>. 2024;8. doi:<a href=\"https://doi.org/10.1145/3656462\">10.1145/3656462</a>","apa":"Chatterjee, K., Goharshady, E., Novotný, P., &#38; Zikelic, D. (2024). Equivalence and similarity refutation for probabilistic programs. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3656462\">https://doi.org/10.1145/3656462</a>","ieee":"K. Chatterjee, E. Goharshady, P. Novotný, and D. Zikelic, “Equivalence and similarity refutation for probabilistic programs,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 8. Association for Computing Machinery, 2024.","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Petr Novotný, and Dorde Zikelic. “Equivalence and Similarity Refutation for Probabilistic Programs.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3656462\">https://doi.org/10.1145/3656462</a>.","ista":"Chatterjee K, Goharshady E, Novotný P, Zikelic D. 2024. Equivalence and similarity refutation for probabilistic programs. Proceedings of the ACM on Programming Languages. 8, 232.","mla":"Chatterjee, Krishnendu, et al. “Equivalence and Similarity Refutation for Probabilistic Programs.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 8, 232, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3656462\">10.1145/3656462</a>.","short":"K. Chatterjee, E. Goharshady, P. Novotný, D. Zikelic, Proceedings of the ACM on Programming Languages 8 (2024)."},"file":[{"file_id":"17290","checksum":"8cbf220f284a4a87d093db5320c5afdd","file_name":"2024_ACMProgLang_Chatterjee.pdf","content_type":"application/pdf","date_created":"2024-07-22T07:17:14Z","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","file_size":355421,"date_updated":"2024-07-22T07:17:14Z"}],"article_type":"original","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"publication_identifier":{"eissn":["2475-1421"]},"OA_place":"publisher","intvolume":"         8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":8,"publisher":"Association for Computing Machinery","oa":1,"type":"journal_article","month":"06","external_id":{"arxiv":["2404.03430"]},"quality_controlled":"1","publication_status":"published","status":"public","publication":"Proceedings of the ACM on Programming Languages","date_published":"2024-06-20T00:00:00Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","date_updated":"2025-04-14T07:52:47Z","day":"20","title":"Equivalence and similarity refutation for probabilistic programs","ddc":["000"],"abstract":[{"text":"We consider the problems of statically refuting equivalence and similarity of output distributions defined by a pair of probabilistic programs. Equivalence and similarity are two fundamental relational properties of probabilistic programs that are essential for their correctness both in implementation and in compilation. In this work, we present a new method for static equivalence and similarity refutation. Our method refutes equivalence and similarity by computing a function over program outputs whose expected value with respect to the output distributions of two programs is different. The function is computed simultaneously with an upper expectation supermartingale and a lower expectation submartingale for the two programs, which we show to together provide a formal certificate for refuting equivalence and similarity. To the best of our knowledge, our method is the first approach to relational program analysis to offer the combination of the following desirable features: (1) it is fully automated, (2) it is applicable to infinite-state probabilistic programs, and (3) it provides formal guarantees on the correctness of its results. We implement a prototype of our method and our experiments demonstrate the effectiveness of our method to refute equivalence and similarity for a number of examples collected from the literature.","lang":"eng"}],"arxiv":1,"ec_funded":1,"scopus_import":"1","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant. Petr Novotný\r\nis supported by the Czech Science Foundation grant no. GA23-06963S.\r\n","has_accepted_license":"1","doi":"10.1145/3656462","_id":"17283","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_created":"2024-07-21T22:01:01Z","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kafshdar Goharshadi, Ehsan","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","last_name":"Kafshdar Goharshadi","orcid":"0000-0002-8595-0587","first_name":"Ehsan"},{"first_name":"Petr","full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","orcid":"0000-0002-4681-1699"}],"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"232","file_date_updated":"2024-07-22T07:17:14Z","corr_author":"1","OA_type":"hybrid","language":[{"iso":"eng"}]}]