[{"date_updated":"2026-08-12T09:15:49Z","abstract":[{"lang":"eng","text":"Phase-field models such as the Allen–Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen–Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow. In the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: as long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen–Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε \r\n1/2\r\n ). Our approach is based on the gradient-flow structure of the Allen–Cahn equation and its limiting motion: building on the recent concept of “gradient-flow calibrations” for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen–Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen–Cahn operator or additional convergence hypotheses for the energy at positive times."}],"month":"01","external_id":{"isi":["001293853900003"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","article_type":"original","intvolume":"        41","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"status":"public","id":"14597","relation":"earlier_version"}]},"oa_version":"Published Version","quality_controlled":"1","author":[{"first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marveggio, Alice","first_name":"Alice","last_name":"Marveggio","id":"25647992-AA84-11E9-9D75-8427E6697425"}],"has_accepted_license":"1","isi":1,"_id":"17481","publication":"Annales de l'Institut Henri Poincaré C","ddc":["510"],"publication_identifier":{"eissn":["1873-1430"],"issn":["0294-1449"]},"date_published":"2024-01-24T00:00:00Z","department":[{"_id":"JuFi"}],"doi":"10.4171/AIHPC/109","acknowledgement":"The authors thank Sebastian Hensel for useful and helpful commentson the first draft of this work.\r\nThis project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement no. 948819.","language":[{"iso":"eng"}],"article_processing_charge":"Yes","file":[{"checksum":"b5ad02d9abd5b4701269cd1ad0a1cc8f","file_id":"17923","content_type":"application/pdf","creator":"dernst","date_created":"2024-09-09T07:46:42Z","access_level":"open_access","date_updated":"2024-09-09T07:46:42Z","relation":"main_file","file_size":1348896,"success":1,"file_name":"2024_AnnInstHPoincare_Fischer.pdf"}],"project":[{"name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819"}],"publication_status":"published","publisher":"EMS Press","year":"2024","page":"1117-1178","corr_author":"1","file_date_updated":"2024-09-09T07:46:42Z","title":"Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow","type":"journal_article","issue":"5","citation":{"ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow,” <i>Annales de l’Institut Henri Poincaré C</i>, vol. 41, no. 5. EMS Press, pp. 1117–1178, 2024.","apa":"Fischer, J. L., &#38; Marveggio, A. (2024). Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press. <a href=\"https://doi.org/10.4171/AIHPC/109\">https://doi.org/10.4171/AIHPC/109</a>","ista":"Fischer JL, Marveggio A. 2024. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincaré C. 41(5), 1117–1178.","short":"J.L. Fischer, A. Marveggio, Annales de l’Institut Henri Poincaré C 41 (2024) 1117–1178.","ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. <i>Annales de l’Institut Henri Poincaré C</i>. 2024;41(5):1117-1178. doi:<a href=\"https://doi.org/10.4171/AIHPC/109\">10.4171/AIHPC/109</a>","mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” <i>Annales de l’Institut Henri Poincaré C</i>, vol. 41, no. 5, EMS Press, 2024, pp. 1117–78, doi:<a href=\"https://doi.org/10.4171/AIHPC/109\">10.4171/AIHPC/109</a>.","chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press, 2024. <a href=\"https://doi.org/10.4171/AIHPC/109\">https://doi.org/10.4171/AIHPC/109</a>."},"volume":41,"date_created":"2024-09-01T22:01:09Z","scopus_import":"1","ec_funded":1,"day":"24"},{"_id":"15048","isi":1,"has_accepted_license":"1","author":[{"first_name":"Alexandra","last_name":"Schauer","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["570"],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication":"Development","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","language":[{"iso":"eng"}],"doi":"10.1242/dev.202316","date_published":"2024-02-01T00:00:00Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"file":[{"checksum":"6961ea10012bf0d266681f9628bb8f13","content_type":"application/pdf","file_id":"15050","date_created":"2024-03-04T07:24:43Z","access_level":"open_access","creator":"dernst","file_size":14839986,"relation":"main_file","date_updated":"2024-03-04T07:24:43Z","success":1,"file_name":"2024_Development_Schauer.pdf"}],"project":[{"grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"article_processing_charge":"Yes (via OA deal)","month":"02","date_updated":"2026-08-12T10:00:14Z","abstract":[{"text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.","lang":"eng"}],"external_id":{"pmid":["38372390"],"isi":["001170580200001"]},"related_material":{"record":[{"relation":"research_data","id":"14926","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"       151","pmid":1,"article_type":"original","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","oa_version":"Published Version","citation":{"ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. Company of Biologists, pp. 1–18, 2024.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>"},"date_created":"2024-03-03T23:00:50Z","volume":151,"scopus_import":"1","ec_funded":1,"day":"01","publisher":"Company of Biologists","publication_status":"published","corr_author":"1","page":"1-18","year":"2024","type":"journal_article","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","file_date_updated":"2024-03-04T07:24:43Z","issue":"4"},{"year":"2024","publisher":"Company of Biologists","publication_status":"published","issue":"15","type":"journal_article","title":"Compensation of gene dosage on the mammalian X","file_date_updated":"2024-08-28T10:32:16Z","date_created":"2024-08-25T22:01:07Z","volume":151,"article_number":"dev202891","citation":{"ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” <i>Development</i>, vol. 151, no. 15. Company of Biologists, 2024.","short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. <i>Development</i>. 2024;151(15). doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>","ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891.","apa":"Cecalev, D., Vicoso, B., &#38; Galupa, R. (2024). Compensation of gene dosage on the mammalian X. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>","chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>.","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>, vol. 151, no. 15, dev202891, Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>."},"day":"14","scopus_import":"1","external_id":{"pmid":["39140247"],"isi":["001292608800003"]},"month":"08","abstract":[{"text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.","lang":"eng"}],"date_updated":"2026-08-12T10:01:13Z","quality_controlled":"1","oa_version":"Published Version","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"intvolume":"       151","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","ddc":["599"],"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"publication":"Development","_id":"17458","isi":1,"has_accepted_license":"1","author":[{"full_name":"Cecalev, Daniela","last_name":"Cecalev","first_name":"Daniela"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"},{"first_name":"Rafael","last_name":"Galupa","full_name":"Galupa, Rafael"}],"file":[{"file_name":"2024_Development_Cecalev.pdf","success":1,"relation":"main_file","date_updated":"2024-08-28T10:32:16Z","file_size":2085135,"creator":"cchlebak","access_level":"open_access","date_created":"2024-08-28T10:32:16Z","content_type":"application/pdf","checksum":"5e428bda0440d3f957c694b315a8f2a9","file_id":"17464"}],"article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release.","doi":"10.1242/dev.202891","date_published":"2024-08-14T00:00:00Z","department":[{"_id":"BeVi"}]},{"doi":"10.15479/AT:ISTA:14926","date_published":"2024-02-02T00:00:00Z","department":[{"_id":"Bio"}],"file":[{"file_name":"README.md","success":1,"file_size":736,"relation":"main_file","date_updated":"2024-02-02T14:40:31Z","file_id":"14927","content_type":"application/octet-stream","checksum":"df7f358ae19a176cf710c0a802ce31b1","date_created":"2024-02-02T14:40:31Z","access_level":"open_access","creator":"rhauschild"},{"file_size":3543,"date_updated":"2024-02-02T14:40:31Z","relation":"main_file","checksum":"10194cc11619eccd8f4b24472e465b7f","file_id":"14928","content_type":"application/x-zip-compressed","access_level":"open_access","date_created":"2024-02-02T14:40:31Z","creator":"rhauschild","file_name":"Supplementary_file_1.zip","success":1}],"day":"02","_id":"14926","citation":{"ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>","short":"R. Hauschild, (2024).","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>","mla":"Hauschild, Robert. <i>Matlab Script for Analysis of Clone Dispersal</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>.","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of Science and Technology Austria, 2024."},"has_accepted_license":"1","author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"}],"date_created":"2024-02-02T14:42:26Z","ddc":["570"],"related_material":{"record":[{"relation":"used_in_publication","id":"15048","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"software","tmp":{"name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT"},"title":"Matlab script for analysis of clone dispersal","status":"public","file_date_updated":"2024-02-02T14:40:31Z","month":"02","publisher":"Institute of Science and Technology Austria","date_updated":"2026-08-12T10:00:13Z","corr_author":"1","year":"2024"},{"date_created":"2026-07-02T10:38:53Z","ddc":["500"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.25625/4FLFH8"}],"_id":"22234","citation":{"apa":"Browning, T. D., &#38; Sutherland, A. (2024). Data and code for: Integral points on cubic surfaces: heuristics and numerics. Göttingen Research Online Data. <a href=\"https://doi.org/10.25625/4FLFH8\">https://doi.org/10.25625/4FLFH8</a>","ista":"Browning TD, Sutherland A. 2024. Data and code for: Integral points on cubic surfaces: heuristics and numerics, Göttingen Research Online Data, <a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>.","ama":"Browning TD, Sutherland A. Data and code for: Integral points on cubic surfaces: heuristics and numerics. 2024. doi:<a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>","short":"T.D. Browning, A. Sutherland, (2024).","mla":"Browning, Timothy D., and Andrew Sutherland. <i>Data and Code for: Integral Points on Cubic Surfaces: Heuristics and Numerics</i>. Göttingen Research Online Data, 2024, doi:<a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>.","chicago":"Browning, Timothy D, and Andrew Sutherland. “Data and Code for: Integral Points on Cubic Surfaces: Heuristics and Numerics.” Göttingen Research Online Data, 2024. <a href=\"https://doi.org/10.25625/4FLFH8\">https://doi.org/10.25625/4FLFH8</a>.","ieee":"T. D. Browning and A. Sutherland, “Data and code for: Integral points on cubic surfaces: heuristics and numerics.” Göttingen Research Online Data, 2024."},"OA_type":"green","has_accepted_license":"1","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D"},{"full_name":"Sutherland, Andrew","last_name":"Sutherland","first_name":"Andrew"}],"day":"22","OA_place":"repository","article_processing_charge":"No","contributor":[{"id":"560601DA-8D36-11E9-A136-7AC1E5697425","last_name":"Wilsch","first_name":"Florian Alexander","orcid":"0000-0001-7302-8256"}],"doi":"10.25625/4FLFH8","date_published":"2024-07-22T00:00:00Z","department":[{"_id":"TiBr"}],"corr_author":"1","year":"2024","month":"07","publisher":"Göttingen Research Online Data","date_updated":"2026-08-12T12:15:33Z","abstract":[{"lang":"eng","text":"Lists of nontrivial integral points on some (families of) cubic surfaces. (2024-07-18)"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"20249","status":"public","relation":"used_in_publication"}]},"oa":1,"type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","title":"Data and code for: Integral points on cubic surfaces: heuristics and numerics"},{"OA_place":"publisher","article_processing_charge":"Yes","file":[{"checksum":"1e6d1230e0387f72752e3268f5330c9e","content_type":"application/pdf","file_id":"18815","date_created":"2025-01-09T13:42:42Z","access_level":"open_access","creator":"dernst","file_size":855818,"relation":"main_file","date_updated":"2025-01-09T13:42:42Z","success":1,"file_name":"2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf"}],"project":[{"_id":"05970B30-7A3F-11EA-A408-12923DDC885E","name":"LGI1 antibody-induced pathophysiology in synapses","grant_number":"I04638"}],"department":[{"_id":"RySh"}],"date_published":"2024-09-01T00:00:00Z","doi":"10.1212/NXI.0000000000200284","acknowledgement":"The authors thank Claudia Sommer for expert technical assistance, the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. ","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2332-7812"]},"DOAJ_listed":"1","ddc":["570"],"publication":"Neurology, Neuroimmunology & Neuroinflammation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"author":[{"first_name":"Andreas","last_name":"Ritzau-Jost","full_name":"Ritzau-Jost, Andreas"},{"first_name":"Felix","last_name":"Gsell","full_name":"Gsell, Felix"},{"full_name":"Sell, Josefine","last_name":"Sell","first_name":"Josefine"},{"last_name":"Sachs","first_name":"Stefan","full_name":"Sachs, Stefan"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kirmann, Toni","first_name":"Toni","last_name":"Kirmann"},{"first_name":"Sebastian","last_name":"Maaß","full_name":"Maaß, Sebastian"},{"first_name":"Sarosh R.","last_name":"Irani","full_name":"Irani, Sarosh R."},{"full_name":"Werner, Christian","first_name":"Christian","last_name":"Werner"},{"full_name":"Geis, Christian","first_name":"Christian","last_name":"Geis"},{"last_name":"Sauer","first_name":"Markus","full_name":"Sauer, Markus"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hallermann","first_name":"Stefan","full_name":"Hallermann, Stefan"}],"has_accepted_license":"1","isi":1,"_id":"17457","oa_version":"Published Version","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","article_type":"original","pmid":1,"intvolume":"        11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2023.10.04.560631"}]},"oa":1,"external_id":{"isi":["001291908600001"],"pmid":["39141878"]},"abstract":[{"lang":"eng","text":"Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1) cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate\r\nautoantibody-induced synaptic strengthening."}],"date_updated":"2026-08-12T14:17:59Z","month":"09","day":"01","scopus_import":"1","volume":11,"date_created":"2024-08-25T22:01:07Z","citation":{"ista":"Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology &#38; Neuroinflammation. 11(5), e200284.","apa":"Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C., Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>","short":"A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber, T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S. Hallermann, Neurology, Neuroimmunology &#38; Neuroinflammation 11 (2024) e200284.","ama":"Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. 2024;11(5):e200284. doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>","mla":"Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>.","chicago":"Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer, 2024. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>.","ieee":"A. Ritzau-Jost <i>et al.</i>, “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024."},"OA_type":"gold","issue":"5","title":"LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening","file_date_updated":"2025-01-09T13:42:42Z","type":"journal_article","page":"e200284","year":"2024","publication_status":"published","publisher":"Wolters Kluwer"},{"external_id":{"arxiv":["2403.06833"]},"abstract":[{"lang":"eng","text":"Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n"}],"date_updated":"2026-08-13T07:26:54Z","month":"03","oa_version":"Preprint","arxiv":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"related_material":{"link":[{"url":" https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed","relation":"software"}]},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv","ddc":["000"],"acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"full_name":"Zverev, Egor","last_name":"Zverev","first_name":"Egor","id":"05162b19-1340-11ed-8f02-fa94e0e8c3bc"},{"last_name":"Abdelnabi","first_name":"Sahar","full_name":"Abdelnabi, Sahar"},{"first_name":"Soroush","last_name":"Tabesh","orcid":"0009-0003-4119-6281","full_name":"Tabesh, Soroush","id":"06000900-6068-11ef-8d61-c2472ef2e752"},{"first_name":"Mario","last_name":"Fritz","full_name":"Fritz, Mario"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","_id":"19063","article_processing_charge":"No","OA_place":"repository","file":[{"success":1,"file_name":"2403.06833v3.pdf","file_id":"19064","content_type":"application/pdf","checksum":"35eb43968684b87be59144603ef10af0","date_created":"2025-02-20T10:11:45Z","access_level":"open_access","creator":"ezverev","file_size":530972,"relation":"main_file","date_updated":"2025-02-20T10:11:45Z"}],"date_published":"2024-03-01T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"doi":"10.48550/arXiv.2403.06833","acknowledgement":"The authors would like to sincerely thank Juan Rocamonde for valuable feedback to our manuscript. We acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We thank Dan Alistarh for providing us with computational resources. This work was partially funded by the German Federal Ministry of Education and Research (BMBF) under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and Safe AI funded by the European Union under grant agreement No. 101070617. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or European Commission. Neither the European Union nor the European Commission can be held responsible for them.","language":[{"iso":"eng"}],"year":"2024","corr_author":"1","publication_status":"submitted","file_date_updated":"2025-02-20T10:11:45Z","title":"Can LLMs separate instructions from data? And what do we even mean by that?","type":"preprint","date_created":"2025-02-20T10:13:42Z","OA_type":"green","article_number":"2403.06833","citation":{"ista":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv, 2403.06833.","apa":"Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., &#38; Lampert, C. (n.d.). Can LLMs separate instructions from data? And what do we even mean by that? <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.06833\">https://doi.org/10.48550/arXiv.2403.06833</a>","ama":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>","short":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.).","mla":"Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” <i>ArXiv</i>, 2403.06833, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>.","chicago":"Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.06833\">https://doi.org/10.48550/arXiv.2403.06833</a>.","ieee":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate instructions from data? And what do we even mean by that?,” <i>arXiv</i>. ."},"day":"01"},{"acknowledgement":"We thank Dominique Madern (IBS Grenoble) for providing the plasmid for MalDH and feedback on the article, Alicia Vallet for excellent support at the Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of Max Perutz Labs for the mass spectrometry analysis using the instruments of the Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu (Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University Dortmund) for sharing a paper draft describing a similar study. This work was supported by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis (Lyon) and the reviewers for constructive input.\r\nThis research has been supported by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien Arnaud was funded by GRAL.","language":[{"iso":"eng"}],"date_published":"2024-04-19T00:00:00Z","department":[{"_id":"PaSc"}],"doi":"10.5194/mr-5-33-2024","OA_place":"publisher","article_processing_charge":"Yes","project":[{"grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"file":[{"file_name":"2024_MagneticResonance_Napoli.pdf","success":1,"relation":"main_file","date_updated":"2024-05-22T07:01:15Z","file_size":6657865,"checksum":"80ea50114e428461ca9530d3bd5d89e4","content_type":"application/pdf","file_id":"15413","date_created":"2024-05-22T07:01:15Z","creator":"dernst","access_level":"open_access"}],"_id":"15401","author":[{"last_name":"Napoli","first_name":"Federico","full_name":"Napoli, Federico","orcid":"0000-0002-9043-136X","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b"},{"full_name":"Guan, Jia-Ying","first_name":"Jia-Ying","last_name":"Guan"},{"full_name":"Arnaud, Charles-Adrien","last_name":"Arnaud","first_name":"Charles-Adrien"},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"first_name":"Hugo","last_name":"Fraga","full_name":"Fraga, Hugo"},{"full_name":"Breyton, Cécile","first_name":"Cécile","last_name":"Breyton"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"has_accepted_license":"1","ddc":["530"],"publication":"Magnetic Resonance","publication_identifier":{"issn":["2699-0016"]},"acknowledged_ssus":[{"_id":"NMR"}],"pmid":1,"intvolume":"         5","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_type":"original","oa_version":"Published Version","quality_controlled":"1","month":"04","date_updated":"2025-07-17T08:12:23Z","abstract":[{"text":"Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has become a main technique in NMR-based structural biology. In standard deuteration protocols that rely on D2O-based culture media, non-exchangeable amide sites remain deuterated, making these sites unobservable. Here we demonstrate that proteins produced with a H2O-based culture medium doped with deuterated cell lysate allow scientists to overcome this “reprotonation bottleneck” while retaining a high level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence lifetimes of several proteins prepared with this labeling pattern over a range of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling approach are comparable to those of perdeuterated proteins and better than those of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range, many previously unobserved amides become visible. We report how to prepare the deuterated cell lysate for our approach from fractions of perdeuterated cultures which are usually discarded, and we show that such media can be used identically to commercial media. The residual protonation of Hα sites allows for well-resolved Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments.","lang":"eng"}],"external_id":{"pmid":["40384771"]},"scopus_import":"1","day":"19","citation":{"ama":"Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. 2024;5(1):33-49. doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>","short":"F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda, Magnetic Resonance 5 (2024) 33–49.","apa":"Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C., &#38; Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>","ista":"Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. 5(1), 33–49.","chicago":"Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>. Copernicus Publications, 2024. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>.","mla":"Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>, vol. 5, no. 1, Copernicus Publications, 2024, pp. 33–49, doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>.","ieee":"F. Napoli <i>et al.</i>, “Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications, pp. 33–49, 2024."},"OA_type":"gold","volume":5,"date_created":"2024-05-16T15:02:43Z","APC_amount":"1530 EUR","file_date_updated":"2024-05-22T07:01:15Z","title":"Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck","type":"journal_article","issue":"1","publisher":"Copernicus Publications","publication_status":"published","year":"2024","page":"33-49","corr_author":"1"},{"doi":"10.15479/at:ista:15094","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"date_published":"2024-03-08T00:00:00Z","language":[{"iso":"eng"}],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342","call_identifier":"FWF"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Persistent Homology, Algorithms and Stochastic Geometry","grant_number":"I4887"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"file":[{"checksum":"1e468bfa42a7dcf04d89f4dadc621c87","content_type":"application/pdf","file_id":"15112","access_level":"open_access","creator":"scultrer","date_created":"2024-03-14T08:55:07Z","relation":"main_file","date_updated":"2024-03-14T08:55:07Z","file_size":4106872,"success":1,"file_name":"Thesis Sebastiano.pdf"},{"file_name":"Thesis (1).zip","relation":"source_file","date_updated":"2024-03-14T14:14:35Z","file_size":4746234,"content_type":"application/zip","checksum":"bcbd213490f5a7e68855a092bbce93f1","file_id":"15113","date_created":"2024-03-14T08:56:24Z","access_level":"closed","creator":"scultrer"}],"OA_place":"publisher","article_processing_charge":"No","has_accepted_license":"1","author":[{"first_name":"Sebastiano","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"}],"_id":"15094","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"ddc":["514","500","516"],"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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"15091"},{"status":"public","id":"15090","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"15093"},{"id":"13182","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11658"},{"id":"11660","status":"public","relation":"part_of_dissertation"}]},"oa":1,"oa_version":"Published Version","date_updated":"2026-08-13T09:41:57Z","abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"month":"03","degree_awarded":"PhD","ec_funded":1,"day":"08","citation":{"ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","apa":"Cultrera di Montesano, S. (2024). <i>Persistence and Morse theory for discrete geometric structures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>.","mla":"Cultrera di Montesano, Sebastiano. <i>Persistence and Morse Theory for Discrete Geometric Structures</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024."},"date_created":"2024-03-08T15:28:10Z","type":"dissertation","file_date_updated":"2024-03-14T14:14:35Z","title":"Persistence and Morse theory for discrete geometric structures","supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","corr_author":"1","page":"108","year":"2024"},{"publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"publication":"Journal of Applied and Computational Topology","ddc":["000"],"_id":"13182","author":[{"first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cultrera Di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera Di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza","first_name":"Morteza","last_name":"Saghafian"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183"},{"name":"Persistent Homology, Algorithms and Stochastic Geometry","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"},{"grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"file":[{"checksum":"d493df5088c222b88d9ca46b623ad0ee","file_id":"18783","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2025-01-09T07:39:41Z","file_size":476896,"relation":"main_file","date_updated":"2025-01-09T07:39:41Z","success":1,"file_name":"2024_JourApplCompTopo_Biswas.pdf"}],"language":[{"iso":"eng"}],"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35. The authors of this paper thank anonymous reviewers for their constructive criticism and Monika Henzinger for detailed comments on an earlier version of this paper.","department":[{"_id":"HeEd"}],"date_published":"2024-10-01T00:00:00Z","doi":"10.1007/s41468-023-00126-9","external_id":{"pmid":["39678706"]},"month":"10","abstract":[{"lang":"eng","text":"We characterize critical points of 1-dimensional maps paired in persistent homology\r\ngeometrically and this way get elementary proofs of theorems about the symmetry\r\nof persistence diagrams and the variation of such maps. In particular, we identify\r\nbranching points and endpoints of networks as the sole source of asymmetry and\r\nrelate the cycle basis in persistent homology with a version of the stable marriage\r\nproblem. Our analysis provides the foundations of fast algorithms for maintaining a\r\ncollection of sorted lists together with its persistence diagram."}],"date_updated":"2026-08-13T09:41:57Z","oa_version":"Published Version","quality_controlled":"1","pmid":1,"intvolume":"         8","oa":1,"related_material":{"record":[{"id":"15094","status":"public","relation":"dissertation_contains"},{"relation":"earlier_version","id":"11660","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_type":"original","volume":8,"date_created":"2023-07-02T22:00:44Z","OA_type":"hybrid","citation":{"apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2024). Geometric characterization of the persistence of 1D maps. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-023-00126-9\">https://doi.org/10.1007/s41468-023-00126-9</a>","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2024. Geometric characterization of the persistence of 1D maps. Journal of Applied and Computational Topology. 8, 1101–1119.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Geometric characterization of the persistence of 1D maps. <i>Journal of Applied and Computational Topology</i>. 2024;8:1101-1119. doi:<a href=\"https://doi.org/10.1007/s41468-023-00126-9\">10.1007/s41468-023-00126-9</a>","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Journal of Applied and Computational Topology 8 (2024) 1101–1119.","mla":"Biswas, Ranita, et al. “Geometric Characterization of the Persistence of 1D Maps.” <i>Journal of Applied and Computational Topology</i>, vol. 8, Springer Nature, 2024, pp. 1101–19, doi:<a href=\"https://doi.org/10.1007/s41468-023-00126-9\">10.1007/s41468-023-00126-9</a>.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Geometric Characterization of the Persistence of 1D Maps.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s41468-023-00126-9\">https://doi.org/10.1007/s41468-023-00126-9</a>.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Geometric characterization of the persistence of 1D maps,” <i>Journal of Applied and Computational Topology</i>, vol. 8. Springer Nature, pp. 1101–1119, 2024."},"day":"01","ec_funded":1,"scopus_import":"1","year":"2024","page":"1101-1119","corr_author":"1","publisher":"Springer Nature","publication_status":"published","title":"Geometric characterization of the persistence of 1D maps","file_date_updated":"2025-01-09T07:39:41Z","type":"journal_article"},{"page":"130-148.e17","year":"2024","publisher":"Elsevier","publication_status":"published","issue":"1","file_date_updated":"2024-01-22T13:41:41Z","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"volume":187,"date_created":"2024-01-17T12:45:40Z","citation":{"ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>."},"day":"04","ec_funded":1,"scopus_import":"1","external_id":{"pmid":["38128538"],"isi":["001152705700001"]},"month":"01","abstract":[{"text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.","lang":"eng"}],"date_updated":"2026-08-14T09:33:45Z","oa_version":"Published Version","quality_controlled":"1","pmid":1,"intvolume":"       187","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19395"}]},"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"status":"public","article_type":"original","publication":"Cell","ddc":["580"],"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"isi":1,"_id":"14826","author":[{"full_name":"Kuhn, Andre","first_name":"Andre","last_name":"Kuhn"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"full_name":"Mutte, Sumanth","last_name":"Mutte","first_name":"Sumanth"},{"full_name":"Dubey, Shiv Mani","first_name":"Shiv Mani","last_name":"Dubey"},{"last_name":"Carrillo Carrasco","first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet"},{"first_name":"Sjef","last_name":"Boeren","full_name":"Boeren, Sjef"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","first_name":"Aline","last_name":"Monzer"},{"last_name":"Koehorst","first_name":"Jasper","full_name":"Koehorst, Jasper"},{"full_name":"Kohchi, Takayuki","first_name":"Takayuki","last_name":"Kohchi"},{"full_name":"Nishihama, Ryuichi","first_name":"Ryuichi","last_name":"Nishihama"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"full_name":"Sprakel, Joris","last_name":"Sprakel","first_name":"Joris"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file":[{"success":1,"file_name":"2024_Cell_Kuhn.pdf","access_level":"open_access","creator":"dernst","date_created":"2024-01-22T13:41:41Z","content_type":"application/pdf","file_id":"14874","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","relation":"main_file","date_updated":"2024-01-22T13:41:41Z","file_size":13194060}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988"}],"acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"date_published":"2024-01-04T00:00:00Z","doi":"10.1016/j.cell.2023.11.021"},{"external_id":{"isi":["001545628900014"]},"abstract":[{"text":"In this work we prove lower bounds on the (communication) cost of maintaining a shared key among a dynamic group of users. Being “dynamic” means one can add and remove users from the group. This captures important protocols like multicast encryption (ME) and continuous group-key agreement (CGKA), which is the primitive underlying many group messaging applications. We prove our bounds in a combinatorial setting where the state of the protocol progresses in rounds. The state of the protocol in each round is captured by a set system, with each of its elements specifying a set of users who share a secret key. We show this combinatorial model implies bounds in symbolic models for ME and CGKA that capture, as building blocks, PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable public-key encryption in the setting of CGKA. The models are related to the ones used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality – that the cost (number of uploaded ciphertexts) for replacing a set of d users in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of Ω(log(n)) for d=1. ","lang":"eng"}],"date_updated":"2026-08-21T10:53:16Z","month":"12","quality_controlled":"1","oa_version":"Preprint","status":"public","related_material":{"record":[{"id":"22664","status":"public","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"     15364","publication":"22nd International Conference on Theory of Cryptography","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031780103"],"eissn":["1611-3349"]},"author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","first_name":"Michael","full_name":"Anastos, Michael"},{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt","last_name":"Auerbach","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt"},{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","first_name":"Mirza Ahad","full_name":"Baig, Mirza Ahad"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","last_name":"Cueto Noval","first_name":"Miguel","full_name":"Cueto Noval, Miguel","orcid":"0000-0002-2505-4246"},{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"full_name":"Pascual Perez, Guillermo","orcid":"0000-0001-8630-415X","last_name":"Pascual Perez","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"_id":"18702","isi":1,"alternative_title":["LNCS"],"OA_place":"repository","article_processing_charge":"No","doi":"10.1007/978-3-031-78011-0_14","date_published":"2024-12-02T00:00:00Z","department":[{"_id":"MaKw"},{"_id":"KrPi"}],"language":[{"iso":"eng"}],"corr_author":"1","year":"2024","page":"413-443","publication_status":"published","publisher":"Springer Nature","type":"conference","title":"The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2024/1097"}],"date_created":"2024-12-22T23:01:47Z","volume":15364,"citation":{"ieee":"M. Anastos <i>et al.</i>, “The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging,” in <i>22nd International Conference on Theory of Cryptography</i>, Milan, Italy, 2024, vol. 15364, pp. 413–443.","short":"M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography, Springer Nature, 2024, pp. 413–443.","ama":"Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In: <i>22nd International Conference on Theory of Cryptography</i>. Vol 15364. Springer Nature; 2024:413-443. doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>","ista":"Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G, Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. 22nd International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.","apa":"Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual Perez, G., &#38; Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In <i>22nd International Conference on Theory of Cryptography</i> (Vol. 15364, pp. 413–443). Milan, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>","chicago":"Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” In <i>22nd International Conference on Theory of Cryptography</i>, 15364:413–43. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>.","mla":"Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” <i>22nd International Conference on Theory of Cryptography</i>, vol. 15364, Springer Nature, 2024, pp. 413–43, doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>."},"OA_type":"green","conference":{"start_date":"2024-12-02","location":"Milan, Italy","name":"TCC: Theory of Cryptography","end_date":"2024-12-06"},"day":"02","scopus_import":"1"},{"department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"date_published":"2024-07-28T00:00:00Z","doi":"10.1063/5.0215151","language":[{"iso":"eng"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank the contributions of the whole Waitukaitis Group for useful discussions and feedback.","article_processing_charge":"No","file":[{"checksum":"6141d05cd68d540a7446dce9490975db","file_id":"17386","content_type":"application/pdf","date_created":"2024-08-05T08:19:58Z","creator":"dernst","access_level":"open_access","file_size":2537502,"date_updated":"2024-08-05T08:19:58Z","relation":"main_file","success":1,"file_name":"2024_JourApplPhysics_Lenton.pdf"}],"project":[{"call_identifier":"H2020","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}],"author":[{"full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","first_name":"Isaac C","last_name":"Lenton","id":"a550210f-223c-11ec-8182-e2d45e817efb"},{"last_name":"Pertl","first_name":"Felix","orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af"},{"id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","first_name":"Lubuna B","last_name":"Shafeek","orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B"},{"first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","isi":1,"_id":"17373","ddc":["530"],"publication":"Journal of Applied Physics","publication_identifier":{"eissn":["1089-7550"],"issn":["0021-8979"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"article_type":"original","intvolume":"       136","related_material":{"record":[{"id":"22684","status":"public","relation":"dissertation_contains"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results.","lang":"eng"}],"date_updated":"2026-08-27T11:42:44Z","month":"07","external_id":{"isi":["001281681100003"]},"ec_funded":1,"scopus_import":"1","day":"28","article_number":"045305","citation":{"short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024).","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. 2024;136(4). doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.","apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>.","mla":"Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>.","ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” <i>Journal of Applied Physics</i>, vol. 136, no. 4. AIP Publishing, 2024."},"volume":136,"date_created":"2024-08-04T22:01:21Z","title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging","file_date_updated":"2024-08-05T08:19:58Z","type":"journal_article","issue":"4","publication_status":"published","publisher":"AIP Publishing","year":"2024","corr_author":"1"},{"volume":2831,"date_created":"2024-08-13T12:16:41Z","series_title":"MIMB","citation":{"ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299."},"day":"13","scopus_import":"1","page":"283-299","year":"2024","corr_author":"1","publisher":"Springer Nature","publication_status":"published","edition":"1","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","type":"book_chapter","publication":"Neuronal Morphogenesis","publication_identifier":{"issn":["1064-3745"],"eisbn":["9781071639696"],"isbn":["9781071639689"],"eissn":["1940-6029"]},"acknowledged_ssus":[{"_id":"Bio"}],"alternative_title":["Methods in Molecular Biology"],"_id":"17425","author":[{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","orcid":"0000-0001-6618-6889","full_name":"Miranda, Osvaldo","last_name":"Miranda","first_name":"Osvaldo"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","language":[{"iso":"eng"}],"date_published":"2024-08-13T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"doi":"10.1007/978-1-0716-3969-6_19","external_id":{"pmid":["39134857"]},"month":"08","place":"New York, NY","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology."}],"date_updated":"2026-08-29T22:30:06Z","oa_version":"None","editor":[{"first_name":"Kazuhito","last_name":"Toyooka","full_name":"Toyooka, Kazuhito"}],"quality_controlled":"1","intvolume":"      2831","pmid":1,"related_material":{"record":[{"id":"20212","status":"public","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"day":"29","date_created":"2024-08-28T15:14:25Z","citation":{"ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>."},"supervisor":[{"last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian"}],"file_date_updated":"2024-10-05T22:30:05Z","title":"High-dimensional limits in artificial neural networks","type":"dissertation","page":"232","year":"2024","corr_author":"1","publication_status":"published","publisher":"Institute of Science and Technology Austria","OA_place":"repository","article_processing_charge":"No","file":[{"file_name":"thesis_a2b.pdf","embargo":"2024-10-04","file_size":4468610,"date_updated":"2024-10-05T22:30:05Z","relation":"main_file","checksum":"da6dd3166078934577f6af93d27000e2","content_type":"application/pdf","file_id":"17482","access_level":"open_access","creator":"ashevche","date_created":"2024-09-02T09:23:32Z"},{"date_updated":"2024-10-05T22:30:05Z","relation":"source_file","file_size":15930999,"access_level":"closed","creator":"ashevche","date_created":"2024-09-02T09:23:46Z","content_type":"application/zip","file_id":"17483","checksum":"76a39ef252239560923cdda4ce0a31a4","embargo_to":"open_access","file_name":"Thesis Alex - ISTA.zip"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"date_published":"2024-08-29T00:00:00Z","doi":"10.15479/at:ista:17465","language":[{"iso":"eng"}],"ddc":["519"],"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"last_name":"Shevchenko","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"_id":"17465","oa_version":"Published Version","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"11420","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14459"},{"status":"public","id":"9198","relation":"part_of_dissertation"},{"id":"17469","status":"public","relation":"part_of_dissertation"}]},"oa":1,"abstract":[{"lang":"eng","text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n"}],"date_updated":"2026-06-18T17:55:53Z","month":"08","degree_awarded":"PhD"},{"publisher":"ML Research Press","publication_status":"published","year":"2024","page":"24964-25015","corr_author":"1","title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth","type":"conference","citation":{"apa":"Kögler, K., Shevchenko, A., Hassani, H., &#38; Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.","ista":"Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.","short":"K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015.","ama":"Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:24964-25015.","mla":"Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 24964–5015.","chicago":"Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:24964–15. ML Research Press, 2024.","ieee":"K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 24964–25015."},"volume":235,"date_created":"2024-08-29T11:47:57Z","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v235/kogler24a.html"}],"scopus_import":"1","day":"01","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21","location":"Vienna, Austria","end_date":"2024-07-27"},"month":"07","date_updated":"2026-08-29T22:30:17Z","abstract":[{"lang":"eng","text":"Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST."}],"external_id":{"arxiv":["2402.05013"]},"intvolume":"       235","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"17465","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","arxiv":1,"oa_version":"Published Version","quality_controlled":"1","alternative_title":["PMLR"],"_id":"17469","author":[{"id":"94ec913c-dc85-11ea-9058-e5051ab2428b","full_name":"Kögler, Kevin","first_name":"Kevin","last_name":"Kögler"},{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"publication":"Proceedings of the 41st International Conference on Machine Learning","ddc":["000"],"language":[{"iso":"eng"}],"acknowledgement":"Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","department":[{"_id":"DaAl"},{"_id":"MaMo"}],"date_published":"2024-07-01T00:00:00Z","article_processing_charge":"No","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}]},{"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"date_published":"2024-09-10T00:00:00Z","doi":"10.15479/at:ista:17881","language":[{"iso":"eng"}],"OA_place":"publisher","article_processing_charge":"No","project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"file":[{"file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","embargo":"2025-03-13","relation":"main_file","date_updated":"2025-03-13T23:30:04Z","file_size":10297052,"access_level":"open_access","date_created":"2024-09-12T10:46:04Z","creator":"smukhopa","content_type":"application/pdf","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","file_id":"18059"},{"file_size":29178634,"relation":"source_file","date_updated":"2025-03-13T23:30:04Z","date_created":"2024-09-12T10:50:58Z","creator":"smukhopa","access_level":"closed","embargo_to":"open_access","file_id":"18060","content_type":"application/zip","checksum":"e352667482701dd18a9a0e7418aef465","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip"}],"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham","first_name":"Soham","last_name":"Mukhopadhyay"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"_id":"17881","ddc":["539"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14032"},{"relation":"part_of_dissertation","id":"18057","status":"public"}]},"oa_version":"Published Version","date_updated":"2026-06-03T07:16:04Z","abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"degree_awarded":"PhD","month":"09","day":"10","citation":{"mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024."},"date_created":"2024-09-08T10:23:25Z","file_date_updated":"2025-03-13T23:30:04Z","title":"Thermal effects in one dimensional Josephson chains","type":"dissertation","supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","page":"82","year":"2024","corr_author":"1"},{"type":"preprint","title":"Dual relaxation oscillations in a Josephson junction array","corr_author":"1","year":"2024","publication_status":"draft","day":"14","ec_funded":1,"date_created":"2024-09-11T09:25:22Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2408.07829","open_access":"1"}],"citation":{"ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” <i>arXiv</i>. .","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.).","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>","apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>.","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, 2408.07829, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>."},"article_number":"2408.07829","arxiv":1,"oa_version":"Preprint","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"20324","status":"public","relation":"later_version"},{"status":"public","id":"17881","relation":"dissertation_contains"}]},"status":"public","external_id":{"arxiv":["2408.07829"]},"month":"08","abstract":[{"lang":"eng","text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations."}],"date_updated":"2026-08-29T22:30:18Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"OA_place":"repository","article_processing_charge":"No","language":[{"iso":"eng"}],"acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","doi":"10.48550/arXiv.2408.07829","date_published":"2024-08-14T00:00:00Z","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication":"arXiv","_id":"18057","author":[{"orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham","first_name":"Soham","last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"},{"last_name":"Lancheros Naranjo","first_name":"Diego A","full_name":"Lancheros Naranjo, Diego A","id":"6c55e976-15b2-11ec-abd3-d790e8937fde"},{"full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295","first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"}]},{"abstract":[{"lang":"eng","text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group."}],"date_updated":"2026-08-29T22:30:30Z","month":"08","external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","related_material":{"link":[{"relation":"software","url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project"}],"record":[{"id":"17362","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"19386","status":"public"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"intvolume":"        20","pmid":1,"quality_controlled":"1","oa_version":"Published Version","has_accepted_license":"1","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"_id":"17890","isi":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"publication":"PLoS Genetics","DOAJ_listed":"1","ddc":["570"],"doi":"10.1371/journal.pgen.1011376","date_published":"2024-08-30T00:00:00Z","department":[{"_id":"BeVi"}],"acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","language":[{"iso":"eng"}],"file":[{"date_updated":"2024-09-11T07:54:12Z","relation":"main_file","file_size":8962687,"file_id":"18056","checksum":"f5d96b9af57126fc1063e951440477d6","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_created":"2024-09-11T07:54:12Z","file_name":"2024_PloSGenetics_Elkrewi.pdf","success":1}],"project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"OA_place":"publisher","article_processing_charge":"Yes","publication_status":"published","publisher":"Public Library of Science","corr_author":"1","year":"2024","type":"journal_article","title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","file_date_updated":"2024-09-11T07:54:12Z","issue":"8","article_number":"e1011376","citation":{"ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>."},"OA_type":"gold","date_created":"2024-09-08T22:01:11Z","APC_amount":"3145,39 EUR","volume":20,"scopus_import":"1","day":"30"},{"doi":"10.15479/at:ista:17119","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"date_published":"2024-06-20T00:00:00Z","language":[{"iso":"eng"}],"project":[{"grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"file":[{"file_name":"thesis.zip","embargo_to":"open_access","file_id":"17121","checksum":"fab59146e3b3dc2e5d214576984a2a63","content_type":"application/zip","date_created":"2024-06-07T16:09:17Z","creator":"rkelemen","access_level":"closed","date_updated":"2025-01-10T23:30:10Z","relation":"source_file","file_size":180557931},{"file_name":"thesis_to_archive.pdf","embargo":"2025-01-10","date_updated":"2025-01-10T23:30:10Z","relation":"main_file","file_size":19405484,"date_created":"2024-07-10T08:00:20Z","creator":"rkelemen","access_level":"open_access","checksum":"91cc4c25a792239e8a7688e8aec7c62a","file_id":"17213","content_type":"application/pdf"}],"article_processing_charge":"No","OA_place":"publisher","has_accepted_license":"1","author":[{"orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K","first_name":"Réka K","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"}],"_id":"17119","alternative_title":["ISTA Thesis"],"ddc":["576"],"publication_identifier":{"isbn":["978-3-99078-039-8"],"issn":["2663-337X"]},"status":"public","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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"id":"542","status":"public","relation":"part_of_dissertation"},{"id":"10767","status":"public","relation":"part_of_dissertation"}]},"oa":1,"oa_version":"Published Version","date_updated":"2026-04-07T13:21:37Z","abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"degree_awarded":"PhD","month":"06","ec_funded":1,"day":"20","citation":{"ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria."},"date_created":"2024-06-07T16:14:13Z","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"type":"dissertation","file_date_updated":"2025-01-10T23:30:10Z","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","corr_author":"1","year":"2024","page":"105"}]