[{"date_published":"2023-07-27T00:00:00Z","article_processing_charge":"No","title":"Closure properties of general grammars - formally verified","date_updated":"2023-09-25T11:04:29Z","month":"07","_id":"13120","date_created":"2023-06-05T07:29:05Z","external_id":{"arxiv":["2302.06420"]},"file_date_updated":"2023-08-07T11:55:43Z","publication":"14th International Conference on Interactive Theorem Proving","article_number":"15","acknowledgement":"Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"       268","volume":268,"alternative_title":["LIPIcs"],"related_material":{"link":[{"relation":"software","url":"https://github.com/madvorak/grammars/tree/publish"}]},"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"last_name":"Dvorak","full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin"},{"full_name":"Blanchette, Jasmin","last_name":"Blanchette","first_name":"Jasmin"}],"conference":{"name":"ITP: International Conference on Interactive Theorem Proving","end_date":"2023-08-04","location":"Bialystok, Poland","start_date":"2023-07-31"},"year":"2023","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publication_identifier":{"isbn":["9783959772846"],"eissn":["1868-8969"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","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":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"27","doi":"10.4230/LIPIcs.ITP.2023.15","arxiv":1,"oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction."}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","ddc":["000"],"file":[{"success":1,"access_level":"open_access","file_name":"2023_LIPIcS_Dvorak.pdf","content_type":"application/pdf","date_updated":"2023-08-07T11:55:43Z","file_size":715976,"checksum":"773a0197f05b67feaa6cb1e17ec3642d","relation":"main_file","creator":"dernst","date_created":"2023-08-07T11:55:43Z","file_id":"13982"}],"citation":{"ieee":"M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in <i>14th International Conference on Interactive Theorem Proving</i>, Bialystok, Poland, 2023, vol. 268.","apa":"Dvorak, M., &#38; Blanchette, J. (2023). Closure properties of general grammars - formally verified. In <i>14th International Conference on Interactive Theorem Proving</i> (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">https://doi.org/10.4230/LIPIcs.ITP.2023.15</a>","short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ista":"Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.","mla":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” <i>14th International Conference on Interactive Theorem Proving</i>, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">10.4230/LIPIcs.ITP.2023.15</a>.","chicago":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In <i>14th International Conference on Interactive Theorem Proving</i>, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">https://doi.org/10.4230/LIPIcs.ITP.2023.15</a>.","ama":"Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: <i>14th International Conference on Interactive Theorem Proving</i>. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">10.4230/LIPIcs.ITP.2023.15</a>"},"type":"conference"},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"13106","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7789418","open_access":"1"}],"abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"status":"public","citation":{"chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>.","ama":"Sahu R. Entangling microwaves with light. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>","mla":"Sahu, Rishabh. <i>Entangling Microwaves with Light</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>","short":"R. Sahu, (2023).","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023."},"type":"research_data_reference","year":"2023","article_processing_charge":"No","date_published":"2023-03-31T00:00:00Z","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"}],"department":[{"_id":"JoFi"}],"date_updated":"2025-07-15T09:17:40Z","title":"Entangling microwaves with light","month":"03","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","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":"Zenodo","_id":"13122","day":"31","date_created":"2023-06-06T06:46:16Z","doi":"10.5281/ZENODO.7789417","oa_version":"Published Version"},{"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7858567"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"13117"}]},"abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>","chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>.","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","mla":"Redchenko, Elena, et al. <i>Tunable Directional Photon Scattering from a Pair of Superconducting Qubits</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023."},"type":"research_data_reference","ddc":["530"],"month":"04","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JoFi"}],"date_updated":"2024-09-10T12:23:51Z","title":"Tunable directional photon scattering from a pair of superconducting qubits","year":"2023","article_processing_charge":"No","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander","first_name":"Alexander"},{"last_name":"Sett","full_name":"Sett, Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"first_name":"Alexander","full_name":"Poddubny, Alexander","last_name":"Poddubny"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"date_published":"2023-04-28T00:00:00Z","oa_version":"Published Version","doi":"10.5281/ZENODO.7858567","day":"28","date_created":"2023-06-06T07:36:50Z","publisher":"Zenodo","_id":"13124"},{"file_date_updated":"2023-06-13T07:28:36Z","publication":"Physical Review A","date_created":"2023-06-07T06:57:32Z","external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]},"_id":"13125","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"month":"06","date_updated":"2023-12-13T14:47:25Z","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","ec_funded":1,"date_published":"2023-06-02T00:00:00Z","article_processing_charge":"No","scopus_import":"1","volume":107,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14622"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"6","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","intvolume":"       107","oa":1,"article_number":"062404","oa_version":"Published Version","arxiv":1,"doi":"10.1103/physreva.107.062404","day":"02","publisher":"American Physical Society","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"department":[{"_id":"MaSe"}],"isi":1,"author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","last_name":"Sack"},{"first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A"},{"full_name":"Kueng, Richard","last_name":"Kueng","first_name":"Richard"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"year":"2023","type":"journal_article","citation":{"apa":"Sack, S., Medina Ramos, R. A., Kueng, R., &#38; Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>.","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>."},"file":[{"date_created":"2023-06-13T07:28:36Z","creator":"dernst","file_id":"13131","file_name":"2023_PhysRevA_Sack.pdf","access_level":"open_access","success":1,"relation":"main_file","checksum":"0d71423888eeccaa60d8f41197f26306","file_size":2524611,"date_updated":"2023-06-13T07:28:36Z","content_type":"application/pdf"}],"article_type":"original","ddc":["530"],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"quality_controlled":"1"},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14257"}],"link":[{"url":"https://pub.ista.ac.at/group_danzl/data/CATS/","description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. ","relation":"research_data"}]},"oa":1,"acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"orcid":"0000-0002-2340-7431","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"last_name":"Stefanickova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson","orcid":"0000-0002-8698-3823"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","last_name":"Cenameri"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"last_name":"Amberg","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","last_name":"Venturino","orcid":"0000-0003-2356-9403"},{"last_name":"Roessler","first_name":"Karl"},{"first_name":"Thomas","last_name":"Czech"},{"first_name":"Romana","last_name":"Höftberger"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"file_date_updated":"2023-08-04T13:19:47Z","date_created":"2023-06-07T07:15:12Z","_id":"13126","project":[{"call_identifier":"FWF","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"month":"08","title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","date_updated":"2024-02-21T12:18:19Z","ec_funded":1,"article_processing_charge":"No","date_published":"2023-08-04T00:00:00Z","type":"research_data","citation":{"short":"J.G. Danzl, (2023).","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>.","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","mla":"Danzl, Johann G. <i>Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.”</i> Institute of Science and Technology Austria, 2023, doi:<a 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Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:13126","day":"04","publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"year":"2023","author":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}]},{"type":"journal_article","citation":{"short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., &#38; Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>.","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>, vol. 14, 3232, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>.","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232."},"file":[{"access_level":"open_access","success":1,"file_name":"2023_NatureComm_CasillasPerez.pdf","file_size":2358167,"content_type":"application/pdf","date_updated":"2023-06-13T08:05:46Z","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","relation":"main_file","creator":"dernst","date_created":"2023-06-13T08:05:46Z","file_id":"13132"}],"article_type":"original","ddc":["570"],"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","pmid":1,"abstract":[{"text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","doi":"10.1038/s41467-023-38947-y","day":"03","publisher":"Springer Nature","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"SyCr"},{"_id":"GaTk"}],"isi":1,"author":[{"first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"last_name":"Bod'Ová","orcid":"0000-0002-7214-0171","full_name":"Bod'Ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"year":"2023","scopus_import":"1","volume":14,"related_material":{"record":[{"id":"12945","status":"public","relation":"research_data"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","intvolume":"        14","oa":1,"article_number":"3232","file_date_updated":"2023-06-13T08:05:46Z","publication":"Nature Communications","date_created":"2023-06-11T22:00:40Z","external_id":{"pmid":["37270641"],"isi":["001002562700005"]},"project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"_id":"13127","month":"06","date_updated":"2023-08-07T13:09:09Z","title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","ec_funded":1,"date_published":"2023-06-03T00:00:00Z","article_processing_charge":"Yes"},{"citation":{"short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","apa":"Mohammadi, A., Pham, T., &#38; Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. Cambridge University Press. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>","ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023.","ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. 2023;66(4):1280-1295. doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>","chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>.","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.","mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>."},"type":"journal_article","article_type":"original","publication_status":"published","abstract":[{"text":"Given  A⊆GL2(Fq), we prove that there exist disjoint subsets  B,C⊆A such that  A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|), where\r\nM(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}.\r\n We also study some related questions on moderate expanders over matrix rings, namely, for  A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever  |A||B||C|≫q10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings,  ForumMath., 31, 951–970).\r\n","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","doi":"10.4153/S000843952300036X","arxiv":1,"oa_version":"Preprint","publisher":"Cambridge University Press","day":"01","publication_identifier":{"issn":["0008-4395"],"eissn":["1496-4287"]},"department":[{"_id":"GradSch"}],"isi":1,"author":[{"first_name":"Ali","full_name":"Mohammadi, Ali","last_name":"Mohammadi"},{"last_name":"Pham","full_name":"Pham, Thang","first_name":"Thang"},{"id":"1917d194-076e-11ed-97cd-837255f88785","first_name":"Yiting","last_name":"Wang","full_name":"Wang, Yiting","orcid":"0000-0002-2856-767X"}],"year":"2023","scopus_import":"1","volume":66,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.07328","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","oa":1,"intvolume":"        66","publication":"Canadian Mathematical Bulletin","page":"1280-1295","_id":"13128","date_created":"2023-06-11T22:00:40Z","external_id":{"arxiv":["2106.07328"],"isi":["001011963000001"]},"title":"An energy decomposition theorem for matrices and related questions","date_updated":"2024-01-29T11:00:46Z","month":"12","date_published":"2023-12-01T00:00:00Z","article_processing_charge":"No"},{"_id":"13129","date_created":"2023-06-11T22:00:40Z","external_id":{"isi":["000999623100001"]},"publication":"Foundations of Computational Mathematics","date_published":"2023-05-30T00:00:00Z","article_processing_charge":"Yes (via OA deal)","title":"Bias in the representative volume element method: Periodize the ensemble instead of its realizations","date_updated":"2023-08-02T06:12:39Z","month":"05","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s10208-023-09613-y","open_access":"1"}],"publisher":"Springer Nature","day":"30","doi":"10.1007/s10208-023-09613-y","oa_version":"Published Version","isi":1,"author":[{"first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas","last_name":"Clozeau"},{"first_name":"Marc","last_name":"Josien","full_name":"Josien, Marc"},{"first_name":"Felix","full_name":"Otto, Felix","last_name":"Otto"},{"first_name":"Qiang","full_name":"Xu, Qiang","last_name":"Xu"}],"year":"2023","department":[{"_id":"JuFi"}],"publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["510"],"article_type":"original","type":"journal_article","citation":{"chicago":"Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” <i>Foundations of Computational Mathematics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10208-023-09613-y\">https://doi.org/10.1007/s10208-023-09613-y</a>.","ama":"Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. <i>Foundations of Computational Mathematics</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s10208-023-09613-y\">10.1007/s10208-023-09613-y</a>","ista":"Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics.","mla":"Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” <i>Foundations of Computational Mathematics</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s10208-023-09613-y\">10.1007/s10208-023-09613-y</a>.","apa":"Clozeau, N., Josien, M., Otto, F., &#38; Xu, Q. (2023). Bias in the representative volume element method: Periodize the ensemble instead of its realizations. <i>Foundations of Computational Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10208-023-09613-y\">https://doi.org/10.1007/s10208-023-09613-y</a>","short":"N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023).","ieee":"N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume element method: Periodize the ensemble instead of its realizations,” <i>Foundations of Computational Mathematics</i>. Springer Nature, 2023."},"quality_controlled":"1","publication_status":"epub_ahead","abstract":[{"lang":"eng","text":"We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function."}],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1"},{"scopus_import":"1","volume":142,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The first author has been partially supported by the Ministry of Science, Technological Development and Innovation of the Republic of Serbia through the project no. 451-03-47/2023-01/200156. The fourth author is funded by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","issue":"10","intvolume":"       142","article_number":"109693","publication":"Pattern Recognition","date_created":"2023-06-18T22:00:45Z","external_id":{"isi":["001013526000001"]},"_id":"13134","project":[{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Discretization in Geometry and Dynamics"}],"month":"10","title":"Discrete analytical objects in the body-centered cubic grid","date_updated":"2023-10-10T07:37:16Z","date_published":"2023-10-01T00:00:00Z","article_processing_charge":"No","citation":{"ieee":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, and E. Andres, “Discrete analytical objects in the body-centered cubic grid,” <i>Pattern Recognition</i>, vol. 142, no. 10. Elsevier, 2023.","apa":"Čomić, L., Largeteau-Skapin, G., Zrour, R., Biswas, R., &#38; Andres, E. (2023). Discrete analytical objects in the body-centered cubic grid. <i>Pattern Recognition</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">https://doi.org/10.1016/j.patcog.2023.109693</a>","short":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, E. Andres, Pattern Recognition 142 (2023).","mla":"Čomić, Lidija, et al. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” <i>Pattern Recognition</i>, vol. 142, no. 10, 109693, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">10.1016/j.patcog.2023.109693</a>.","ista":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. 2023. Discrete analytical objects in the body-centered cubic grid. Pattern Recognition. 142(10), 109693.","ama":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. Discrete analytical objects in the body-centered cubic grid. <i>Pattern Recognition</i>. 2023;142(10). doi:<a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">10.1016/j.patcog.2023.109693</a>","chicago":"Čomić, Lidija, Gaëlle Largeteau-Skapin, Rita Zrour, Ranita Biswas, and Eric Andres. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” <i>Pattern Recognition</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">https://doi.org/10.1016/j.patcog.2023.109693</a>."},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"We propose a characterization of discrete analytical spheres, planes and lines in the body-centered cubic (BCC) grid, both in the Cartesian and in the recently proposed alternative compact coordinate system, in which each integer triplet addresses some voxel in the grid. We define spheres and planes through double Diophantine inequalities and investigate their relevant topological features, such as functionality or the interrelation between the thickness of the objects and their connectivity and separation properties. We define lines as the intersection of planes. The number of the planes (up to six) is equal to the number of the pairs of faces of a BCC voxel that are parallel to the line.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","oa_version":"None","doi":"10.1016/j.patcog.2023.109693","day":"01","publisher":"Elsevier","publication_identifier":{"issn":["0031-3203"]},"department":[{"_id":"HeEd"}],"author":[{"last_name":"Čomić","full_name":"Čomić, Lidija","first_name":"Lidija"},{"first_name":"Gaëlle","last_name":"Largeteau-Skapin","full_name":"Largeteau-Skapin, Gaëlle"},{"first_name":"Rita","last_name":"Zrour","full_name":"Zrour, Rita"},{"last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"last_name":"Andres","full_name":"Andres, Eric","first_name":"Eric"}],"isi":1,"year":"2023"},{"file":[{"content_type":"application/pdf","date_updated":"2024-01-29T11:03:09Z","file_size":834638,"checksum":"246b703b091dfe047bfc79abf0891a63","relation":"main_file","success":1,"access_level":"open_access","file_name":"2023_JourDifferentialEquations_Agresti.pdf","file_id":"14895","creator":"dernst","date_created":"2024-01-29T11:03:09Z"}],"type":"journal_article","citation":{"ama":"Agresti A, Veraar M. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. <i>Journal of Differential Equations</i>. 2023;368(9):247-300. doi:<a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">10.1016/j.jde.2023.05.038</a>","chicago":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” <i>Journal of Differential Equations</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">https://doi.org/10.1016/j.jde.2023.05.038</a>.","ista":"Agresti A, Veraar M. 2023. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. 368(9), 247–300.","mla":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” <i>Journal of Differential Equations</i>, vol. 368, no. 9, Elsevier, 2023, pp. 247–300, doi:<a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">10.1016/j.jde.2023.05.038</a>.","apa":"Agresti, A., &#38; Veraar, M. (2023). Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">https://doi.org/10.1016/j.jde.2023.05.038</a>","short":"A. Agresti, M. Veraar, Journal of Differential Equations 368 (2023) 247–300.","ieee":"A. Agresti and M. Veraar, “Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity,” <i>Journal of Differential Equations</i>, vol. 368, no. 9. Elsevier, pp. 247–300, 2023."},"ddc":["510"],"article_type":"original","abstract":[{"lang":"eng","text":"In this paper we consider a class of stochastic reaction-diffusion equations. We provide local well-posedness, regularity, blow-up criteria and positivity of solutions. The key novelties of this work are related to the use transport noise, critical spaces and the proof of higher order regularity of solutions – even in case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity estimates and sharp blow-up criteria. We view the results of this paper as a general toolbox for establishing global well-posedness for a large class of reaction-diffusion systems of practical interest, of which many are completely open. In our follow-up work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra equations and the Brusselator model."}],"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","quality_controlled":"1","doi":"10.1016/j.jde.2023.05.038","oa_version":"Published Version","publisher":"Elsevier","day":"25","publication_identifier":{"issn":["0022-0396"],"eissn":["1090-2732"]},"department":[{"_id":"JuFi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"isi":1,"year":"2023","scopus_import":"1","volume":368,"acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 948819) Image 1. The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","issue":"9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"       368","file_date_updated":"2024-01-29T11:03:09Z","publication":"Journal of Differential Equations","page":"247-300","_id":"13135","project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"date_created":"2023-06-18T22:00:45Z","external_id":{"isi":["001019018700001"]},"title":"Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity","date_updated":"2024-01-29T11:04:41Z","month":"09","date_published":"2023-09-25T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","ec_funded":1},{"oa_version":"Published Version","doi":"10.1016/j.coisb.2023.100459","day":"01","publisher":"Elsevier","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"AnKi"}],"publication_identifier":{"eissn":["2452-3100"]},"author":[{"first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","full_name":"Minchington, Thomas"},{"last_name":"Rus","orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"year":"2023","type":"journal_article","citation":{"apa":"Minchington, T., Rus, S., &#38; Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” <i>Current Opinion in Systems Biology</i>, vol. 35. Elsevier, 2023.","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. 2023;35. doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>.","mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>, vol. 35, 100459, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>.","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459."},"file":[{"access_level":"open_access","success":1,"file_name":"2023_CurrOpSystBioloy_Minchington.pdf","file_size":598842,"date_updated":"2024-01-29T11:06:45Z","content_type":"application/pdf","relation":"main_file","checksum":"8a75c4e29fd9b62e3c50663c2265b173","creator":"dernst","date_created":"2024-01-29T11:06:45Z","file_id":"14896"}],"article_type":"original","ddc":["570"],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2024-01-29T11:06:45Z","publication":"Current Opinion in Systems Biology","date_created":"2023-06-18T22:00:46Z","project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"name":"Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F07802"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"_id":"13136","month":"09","date_updated":"2024-01-29T11:07:47Z","title":"Control of tissue dimensions in the developing neural tube and somites","date_published":"2023-09-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":35,"acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        35","article_number":"100459"},{"citation":{"apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., &#38; Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">https://doi.org/10.1103/PhysRevB.107.184312</a>","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023).","ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” <i>Physical Review B</i>, vol. 107, no. 18. American Physical Society, 2023.","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. <i>Physical Review B</i>. 2023;107(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">10.1103/PhysRevB.107.184312</a>","chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">https://doi.org/10.1103/PhysRevB.107.184312</a>.","ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” <i>Physical Review B</i>, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">10.1103/PhysRevB.107.184312</a>."},"type":"journal_article","article_type":"original","abstract":[{"text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain.","lang":"eng"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1103/PhysRevB.107.184312","oa_version":"Preprint","arxiv":1,"publisher":"American Physical Society","day":"01","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"department":[{"_id":"GradSch"}],"year":"2023","author":[{"last_name":"Orlov","full_name":"Orlov, Pavel","first_name":"Pavel"},{"full_name":"Tiutiakina, Anastasiia","last_name":"Tiutiakina","first_name":"Anastasiia"},{"last_name":"Sharipov","full_name":"Sharipov, Rustem","first_name":"Rustem"},{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","first_name":"Elena","last_name":"Petrova","full_name":"Petrova, Elena"},{"first_name":"Vladimir","full_name":"Gritsev, Vladimir","last_name":"Gritsev"},{"last_name":"Kurlov","full_name":"Kurlov, Denis V.","first_name":"Denis V."}],"isi":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.00729"}],"volume":107,"article_number":"184312","oa":1,"intvolume":"       107","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","issue":"18","publication":"Physical Review B","_id":"13138","external_id":{"isi":["001003686900004"],"arxiv":["2303.00729"]},"date_created":"2023-06-18T22:00:46Z","date_updated":"2023-08-02T06:16:02Z","title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","month":"05","article_processing_charge":"No","date_published":"2023-05-01T00:00:00Z"},{"day":"22","publisher":"Springer Nature","oa_version":"Published Version","arxiv":1,"doi":"10.1007/978-3-031-30823-9_25","conference":{"start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"year":"2023","author":[{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031308222"]},"department":[{"_id":"KrCh"}],"ddc":["000"],"type":"conference","citation":{"chicago":"Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.” In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, 13993:489–507. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">https://doi.org/10.1007/978-3-031-30823-9_25</a>.","ama":"Meggendorfer T. Correct approximation of stationary distributions. In: <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 13993. Springer Nature; 2023:489-507. doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">10.1007/978-3-031-30823-9_25</a>","mla":"Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.” <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 13993, Springer Nature, 2023, pp. 489–507, doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">10.1007/978-3-031-30823-9_25</a>.","ista":"Meggendorfer T. 2023. Correct approximation of stationary distributions. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 489–507.","short":"T. Meggendorfer, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 489–507.","apa":"Meggendorfer, T. (2023). Correct approximation of stationary distributions. In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 13993, pp. 489–507). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">https://doi.org/10.1007/978-3-031-30823-9_25</a>","ieee":"T. Meggendorfer, “Correct approximation of stationary distributions,” in <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, Paris, France, 2023, vol. 13993, pp. 489–507."},"file":[{"access_level":"open_access","success":1,"file_name":"2023_LNCS_Meggendorfer.pdf","file_size":521951,"date_updated":"2023-06-19T07:18:40Z","content_type":"application/pdf","relation":"main_file","checksum":"59f707a3949c03793251b0d04c62542a","date_created":"2023-06-19T07:18:40Z","creator":"dernst","file_id":"13148"}],"quality_controlled":"1","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"A classical problem for Markov chains is determining their stationary (or steady-state) distribution. This problem has an equally classical solution based on eigenvectors and linear equation systems. However, this approach does not scale to large instances, and iterative solutions are desirable. It turns out that a naive approach, as used by current model checkers, may yield completely wrong results. We present a new approach, which utilizes recent advances in partial exploration and mean payoff computation to obtain a correct, converging approximation."}],"external_id":{"arxiv":["2301.08137"]},"date_created":"2023-06-18T22:00:46Z","_id":"13139","page":"489-507","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","file_date_updated":"2023-06-19T07:18:40Z","article_processing_charge":"No","date_published":"2023-04-22T00:00:00Z","month":"04","date_updated":"2024-02-27T07:19:33Z","title":"Correct approximation of stationary distributions","scopus_import":"1","intvolume":"     13993","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"research_data","status":"public","id":"14990"}]},"volume":13993,"alternative_title":["LNCS"]},{"file_date_updated":"2023-06-19T08:43:21Z","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","page":"211-228","_id":"13141","date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:49:46Z","title":"Computing adequately permissive assumptions for synthesis","month":"04","date_published":"2023-04-20T00:00:00Z","article_processing_charge":"No","scopus_import":"1","alternative_title":["LNCS"],"volume":13994,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     13994","oa":1,"doi":"10.1007/978-3-031-30820-8_15","oa_version":"Published Version","publisher":"Springer Nature","day":"20","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031308192"]},"department":[{"_id":"ToHe"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Anand","full_name":"Anand, Ashwani","first_name":"Ashwani"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik"},{"first_name":"Satya Prakash","full_name":"Nayak, Satya Prakash","last_name":"Nayak"},{"first_name":"Anne Kathrin","last_name":"Schmuck","full_name":"Schmuck, Anne Kathrin"}],"year":"2023","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Paris, France","start_date":"2023-04-22","end_date":"2023-04-27"},"file":[{"success":1,"access_level":"open_access","file_name":"2023_LNCS_Anand.pdf","content_type":"application/pdf","date_updated":"2023-06-19T08:43:21Z","file_size":521425,"relation":"main_file","checksum":"60dcafc1b4f6f070be43bad3fe877974","creator":"dernst","date_created":"2023-06-19T08:43:21Z","file_id":"13151"}],"type":"conference","citation":{"chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, 13994:211–28. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">https://doi.org/10.1007/978-3-031-30820-8_15</a>.","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 13994. Springer Nature; 2023:211-228. doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">10.1007/978-3-031-30820-8_15</a>","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228.","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">10.1007/978-3-031-30820-8_15</a>.","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","apa":"Anand, A., Mallik, K., Nayak, S. P., &#38; Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">https://doi.org/10.1007/978-3-031-30820-8_15</a>","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, Paris, France, 2023, vol. 13994, pp. 211–228."},"ddc":["000"],"publication_status":"published","abstract":[{"lang":"eng","text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive."}],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","quality_controlled":"1"},{"type":"conference","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, Paris, France, 2023, vol. 13993, pp. 3–25.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., &#38; Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In <i>Tools and Algorithms for the Construction and Analysis of Systems </i> (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">https://doi.org/10.1007/978-3-031-30823-9_1</a>","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, vol. 13993, Springer Nature, 2023, pp. 3–25, doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">10.1007/978-3-031-30823-9_1</a>.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, 13993:3–25. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">https://doi.org/10.1007/978-3-031-30823-9_1</a>.","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: <i>Tools and Algorithms for the Construction and Analysis of Systems </i>. Vol 13993. Springer Nature; 2023:3-25. doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">10.1007/978-3-031-30823-9_1</a>"},"file":[{"date_created":"2023-06-19T08:29:30Z","creator":"dernst","file_id":"13150","access_level":"open_access","success":1,"file_name":"2023_LNCS_Chatterjee.pdf","file_size":528455,"content_type":"application/pdf","date_updated":"2023-06-19T08:29:30Z","checksum":"3d8a8bb24d211bc83360dfc2fd744307","relation":"main_file"}],"ddc":["000"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions.","lang":"eng"}],"quality_controlled":"1","oa_version":"Published Version","doi":"10.1007/978-3-031-30823-9_1","day":"22","publisher":"Springer Nature","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308222"]},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic"}],"year":"2023","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27"},"scopus_import":"1","alternative_title":["LNCS"],"volume":13993,"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     13993","oa":1,"page":"3-25","file_date_updated":"2023-06-19T08:29:30Z","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","date_created":"2023-06-18T22:00:47Z","_id":"13142","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"04","date_updated":"2025-07-14T09:09:52Z","title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","ec_funded":1,"date_published":"2023-04-22T00:00:00Z","article_processing_charge":"No"},{"volume":13940,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/238"}],"acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     13940","oa":1,"scopus_import":"1","title":"Certifying giant nonprimes","date_updated":"2023-06-19T08:03:37Z","month":"05","date_published":"2023-05-02T00:00:00Z","article_processing_charge":"No","publication":"Public-Key Cryptography - PKC 2023","page":"530-553","_id":"13143","date_created":"2023-06-18T22:00:47Z","publication_status":"published","abstract":[{"text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","type":"conference","citation":{"mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” <i>Public-Key Cryptography - PKC 2023</i>, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:<a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">10.1007/978-3-031-31368-4_19</a>.","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In <i>Public-Key Cryptography - PKC 2023</i>, 13940:530–53. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">https://doi.org/10.1007/978-3-031-31368-4_19</a>.","ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: <i>Public-Key Cryptography - PKC 2023</i>. Vol 13940. Springer Nature; 2023:530-553. doi:<a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">10.1007/978-3-031-31368-4_19</a>","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in <i>Public-Key Cryptography - PKC 2023</i>, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., &#38; Pietrzak, K. Z. (2023). Certifying giant nonprimes. In <i>Public-Key Cryptography - PKC 2023</i> (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">https://doi.org/10.1007/978-3-031-31368-4_19</a>","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553."},"department":[{"_id":"KrPi"}],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031313677"]},"author":[{"id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","first_name":"Charlotte","last_name":"Hoffmann","full_name":"Hoffmann, Charlotte"},{"last_name":"Hubáček","full_name":"Hubáček, Pavel","first_name":"Pavel"},{"first_name":"Chethan","full_name":"Kamath, Chethan","last_name":"Kamath"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"conference":{"name":"PKC: Public-Key Cryptography","start_date":"2023-05-07","location":"Atlanta, GA, United States","end_date":"2023-05-10"},"year":"2023","doi":"10.1007/978-3-031-31368-4_19","oa_version":"Submitted Version","publisher":"Springer Nature","day":"02"},{"isi":1,"author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo"},{"first_name":"Eugene","full_name":"Lytvynov, Eugene","last_name":"Lytvynov"}],"year":"2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["1083-589X"]},"department":[{"_id":"JaMa"}],"day":"05","publisher":"Institute of Mathematical Statistics","oa_version":"Published Version","doi":"10.1214/23-ECP528","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"text":"We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes.","lang":"eng"}],"publication_status":"published","article_type":"original","ddc":["510"],"type":"journal_article","citation":{"short":"L. Dello Schiavo, E. Lytvynov, Electronic Communications in Probability 28 (2023) 1–12.","apa":"Dello Schiavo, L., &#38; Lytvynov, E. (2023). A Mecke-type characterization of the Dirichlet–Ferguson measure. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-ECP528\">https://doi.org/10.1214/23-ECP528</a>","ieee":"L. Dello Schiavo and E. Lytvynov, “A Mecke-type characterization of the Dirichlet–Ferguson measure,” <i>Electronic Communications in Probability</i>, vol. 28. Institute of Mathematical Statistics, pp. 1–12, 2023.","ama":"Dello Schiavo L, Lytvynov E. A Mecke-type characterization of the Dirichlet–Ferguson measure. <i>Electronic Communications in Probability</i>. 2023;28:1-12. doi:<a href=\"https://doi.org/10.1214/23-ECP528\">10.1214/23-ECP528</a>","chicago":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-ECP528\">https://doi.org/10.1214/23-ECP528</a>.","ista":"Dello Schiavo L, Lytvynov E. 2023. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 28, 1–12.","mla":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” <i>Electronic Communications in Probability</i>, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–12, doi:<a href=\"https://doi.org/10.1214/23-ECP528\">10.1214/23-ECP528</a>."},"file":[{"success":1,"access_level":"open_access","file_name":"2023_ElectronCommProbability_Schiavo.pdf","content_type":"application/pdf","date_updated":"2023-06-19T09:37:40Z","file_size":271434,"checksum":"4a543fe4b3f9e747cc52167c17bfb524","relation":"main_file","date_created":"2023-06-19T09:37:40Z","creator":"dernst","file_id":"13152"}],"date_published":"2023-05-05T00:00:00Z","article_processing_charge":"No","month":"05","date_updated":"2023-12-13T11:24:57Z","title":"A Mecke-type characterization of the Dirichlet–Ferguson measure","date_created":"2023-06-18T22:00:48Z","external_id":{"isi":["001042025400001"]},"project":[{"grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces"}],"_id":"13145","page":"1-12","file_date_updated":"2023-06-19T09:37:40Z","publication":"Electronic Communications in Probability","acknowledgement":"Research supported by the Sfb 1060 The Mathematics of Emergent Effects (University of Bonn). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through project ESPRIT 208.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        28","oa":1,"volume":28,"scopus_import":"1"},{"oa_version":"Submitted Version","day":"01","publisher":"EuroCC","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"author":[{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","full_name":"Elefante, Stefano"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"}],"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia","start_date":"2023-06-13","end_date":"2023-06-15"},"year":"2023","citation":{"ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>. EuroCC; :59-59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, 59–59. EuroCC, n.d.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, EuroCC, pp. 59–59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","apa":"Schlögl, A., Elefante, S., &#38; Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i> (pp. 59–59). Maribor, Slovenia: EuroCC.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, Maribor, Slovenia, pp. 59–59."},"type":"conference_abstract","file":[{"file_id":"13249","creator":"dernst","date_created":"2023-07-18T09:18:55Z","content_type":"application/pdf","date_updated":"2023-07-18T09:18:55Z","file_size":316959,"checksum":"ec8e4295d54171032cdd1b01423eb4a6","relation":"main_file","success":1,"access_level":"open_access","file_name":"2023_ASHPC_Schloegl.pdf"}],"ddc":["000"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"inpress","quality_controlled":"1","page":"59-59","file_date_updated":"2023-07-18T09:18:55Z","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","date_created":"2023-06-23T11:01:23Z","_id":"13161","month":"07","title":"Running Windows-applications on a Linux HPC cluster using WINE","date_updated":"2023-07-18T09:30:54Z","date_published":"2023-07-01T00:00:00Z","article_processing_charge":"No","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"accepted","ddc":["000"],"type":"conference_abstract","citation":{"chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, 42–42. EuroCC, n.d.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>. EuroCC; :42-42.","mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, EuroCC, pp. 42–42.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., &#38; Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i> (pp. 42–42). Maribor, Slovenia: EuroCC.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, Maribor, Slovenia, pp. 42–42."},"file":[{"file_id":"13250","creator":"dernst","date_created":"2023-07-18T09:28:30Z","relation":"main_file","checksum":"0ab6173cd5c5634ed773cd37ff012681","file_size":380354,"content_type":"application/pdf","date_updated":"2023-07-18T09:28:30Z","file_name":"2023_ASHPC_Elefante.pdf","access_level":"open_access","success":1}],"date_published":"2023-07-01T00:00:00Z","author":[{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","full_name":"Elefante, Stefano","last_name":"Elefante"},{"full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan"},{"first_name":"Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Alexander, Michael F","last_name":"Alexander"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"}],"year":"2023","article_processing_charge":"No","conference":{"start_date":"2023-06-12","location":"Maribor, Slovenia","end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"07","title":"Cryo-EM software packages: A sys-admins point of view","date_updated":"2023-07-18T09:32:16Z","department":[{"_id":"ScienComp"}],"date_created":"2023-06-23T11:03:18Z","day":"01","_id":"13162","publisher":"EuroCC","oa_version":"Submitted Version","page":"42-42","file_date_updated":"2023-07-18T09:28:30Z","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"text":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","citation":{"ama":"Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>","chicago":"Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>.","mla":"Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>, vol. 14, 3506, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>.","ista":"Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506.","apa":"Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>","short":"K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).","ieee":"K. R. B. Gert <i>et al.</i>, “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"type":"journal_article","file":[{"date_created":"2023-06-26T10:26:04Z","creator":"dernst","file_id":"13172","file_name":"2023_NatureComm_Gert.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"d6165f41c7f1c2c04b04256ec9f003fb","date_updated":"2023-06-26T10:26:04Z","content_type":"application/pdf","file_size":1555006}],"article_type":"original","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"FyKo"}],"isi":1,"author":[{"last_name":"Gert","full_name":"Gert, Krista R.B.","first_name":"Krista R.B."},{"first_name":"Karin","full_name":"Panser, Karin","last_name":"Panser"},{"first_name":"Joachim","full_name":"Surm, Joachim","last_name":"Surm"},{"first_name":"Benjamin S.","last_name":"Steinmetz","full_name":"Steinmetz, Benjamin S."},{"full_name":"Schleiffer, Alexander","last_name":"Schleiffer","first_name":"Alexander"},{"first_name":"Luca","full_name":"Jovine, Luca","last_name":"Jovine"},{"first_name":"Yehu","last_name":"Moran","full_name":"Moran, Yehu"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","full_name":"Pauli, Andrea","last_name":"Pauli"}],"year":"2023","oa_version":"Published Version","doi":"10.1038/s41467-023-39317-4","day":"14","publisher":"Springer Nature","volume":14,"acknowledgement":"We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        14","article_number":"3506","scopus_import":"1","month":"06","date_updated":"2023-12-13T11:26:34Z","title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","date_published":"2023-06-14T00:00:00Z","article_processing_charge":"No","file_date_updated":"2023-06-26T10:26:04Z","publication":"Nature Communications","date_created":"2023-06-25T22:00:45Z","external_id":{"isi":["001048208600023"]},"_id":"13164"}]