[{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2024-06-06T00:00:00Z","day":"06","file":[{"date_updated":"2024-06-25T11:47:26Z","checksum":"6a2ddc8b51aa58f197a8b294750f1f8d","file_size":20886142,"creator":"cfillmor","success":1,"date_created":"2024-06-25T11:47:26Z","relation":"main_file","file_id":"17171","access_level":"open_access","file_name":"LIPIcs.SoCG.2024.11.pdf","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2024.11","language":[{"iso":"eng"}],"external_id":{"arxiv":["2206.10485"]},"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35"},{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"type":"conference","status":"public","_id":"17170","doi":"10.4230/LIPIcs.SoCG.2024.11","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-06-25T11:47:26Z","conference":{"end_date":"2024-06-14","location":"Athens, Greece","start_date":"2024-06-11","name":"SoCG: Symposium on Computational Geometry"},"abstract":[{"text":"In this article we extend and strengthen the seminal work by Niyogi, Smale, and Weinberger on the learning of the homotopy type from a sample of an underlying space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds with positive reach embedded in ℝ^d. We extend their results in the following ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with lower bounded sectional curvature. - In both types of ambient spaces, we study sets of positive reach - a significantly more general setting than C² manifolds - as well as general manifolds of positive reach. - The sample P of a set (or a manifold) 𝒮 of positive reach may be noisy. We work with two one-sided Hausdorff distances - ε and δ - between P and 𝒮. We provide tight bounds in terms of ε and δ, that guarantee that there exists a parameter r such that the union of balls of radius r centred at the sample P deformation-retracts to 𝒮. We exhibit their tightness by an explicit construction. We carefully distinguish the roles of δ and ε. This is not only essential to achieve tight bounds, but also sensible in practical situations, since it allows one to adapt the bound according to sample density and the amount of noise present in the sample separately.","lang":"eng"}],"title":"Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds","page":"11:1-11:19","date_updated":"2025-04-15T07:16:57Z","oa_version":"Published Version","intvolume":"       293","month":"06","article_processing_charge":"No","oa":1,"year":"2024","ddc":["516"],"publication_status":"published","author":[{"last_name":"Attali","full_name":"Attali, Dominique","first_name":"Dominique"},{"last_name":"Kourimska","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091","full_name":"Kourimska, Hana","first_name":"Hana"},{"first_name":"Christopher D","full_name":"Fillmore, Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","last_name":"Fillmore"},{"first_name":"Ishika","full_name":"Ghosh, Ishika","id":"ee449b28-344d-11ef-a6d5-9ca430e9e9ff","last_name":"Ghosh"},{"first_name":"André","full_name":"Lieutier, André","last_name":"Lieutier"},{"last_name":"Stephenson","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220"}],"arxiv":1,"quality_controlled":"1","publication_identifier":{"isbn":["9783959773164"],"eissn":["1868-8969"]},"volume":293,"ec_funded":1,"acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I 02979-N35.\r\nWintraecken, Mathijs: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Côte d'Azur.","publication":"40th International Symposium on Computational Geometry","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"scopus_import":"1","date_created":"2024-06-25T11:45:58Z","alternative_title":["LIPIcs"],"has_accepted_license":"1","citation":{"chicago":"Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh, André Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” In <i>40th International Symposium on Computational Geometry</i>, 293:11:1-11:19. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>.","ieee":"D. Attali <i>et al.</i>, “Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293, p. 11:1-11:19.","apa":"Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson, E. R., &#38; Wintraecken, M. (2024). Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293, p. 11:1-11:19). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>","short":"D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19.","mla":"Attali, Dominique, et al. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>.","ama":"Attali D, Kourimska H, Fillmore CD, et al. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:11:1-11:19. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>","ista":"Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken M. 2024. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 11:1-11:19."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","doi":"10.1016/j.xpro.2024.103157","status":"public","_id":"17187","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"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"}],"type":"journal_article","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2025-12-30T10:54:11Z","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","abstract":[{"lang":"eng","text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1"}],"file_date_updated":"2025-01-09T12:12:40Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["38935508"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2024_STARProtoc_Cheung.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"18809","date_created":"2025-01-09T12:12:40Z","relation":"main_file","creator":"dernst","success":1,"file_size":5186071,"date_updated":"2025-01-09T12:12:40Z","checksum":"d8a8cdba82a394e731aa699ace1ae433"}],"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103157","day":"20","date_published":"2024-09-20T00:00:00Z","article_number":"103157","acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","ec_funded":1,"volume":5,"publication_identifier":{"eissn":["2666-1667"]},"OA_place":"publisher","quality_controlled":"1","OA_type":"gold","citation":{"ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>","ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>."},"corr_author":"1","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_created":"2024-06-30T22:01:04Z","department":[{"_id":"SiHi"}],"scopus_import":"1","publication":"STAR Protocols","oa":1,"year":"2024","article_processing_charge":"Yes","month":"09","APC_amount":"804 EUR","issue":"3","intvolume":"         5","oa_version":"Published Version","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"article_type":"original","publication_status":"published","ddc":["570"]},{"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.artint.2024.104171","isi":1,"file":[{"file_name":"2024_ArtificialIntelligence_Braun.pdf","content_type":"application/pdf","file_id":"18806","access_level":"open_access","success":1,"creator":"dernst","date_created":"2025-01-09T10:45:24Z","relation":"main_file","checksum":"f02a56bc7ea88f41fcc68968e4ceddf3","date_updated":"2025-01-09T10:45:24Z","file_size":772226}],"external_id":{"arxiv":["2203.01084"],"isi":["001260448100001"]},"day":"01","date_published":"2024-09-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-09-08T08:00:42Z","abstract":[{"lang":"eng","text":"In a delegation problem, a principal P with commitment power tries to pick one out of 𝑛 options.\r\nEach option is drawn independently from a known distribution. Instead of inspecting the options\r\nherself, P delegates the information acquisition to a rational and self-interested agent A. After\r\ninspection, A proposes one of the options, and P can accept or reject.\r\nDelegation is a classic setting in economic information design with many prominent applications,\r\nbut the computational problems are only poorly understood. In this paper, we study a natural\r\nonline variant of delegation, in which the agent searches through the options in an online fashion.\r\nFor each option, he has to irrevocably decide if he wants to propose the current option or discard\r\nit, before seeing information on the next option(s). How can we design algorithms for P that\r\napproximate the utility of her best option in hindsight?\r\nWe show that in general P can obtain a Θ(1∕𝑛)-approximation and extend this result to ratios\r\nof Θ(𝑘∕𝑛) in case (1) A has a lookahead of 𝑘 rounds, or (2) A can propose up to 𝑘 different\r\noptions. We provide fine-grained bounds independent of 𝑛 based on three parameters. If the ratio\r\nof maximum and minimum utility for A is bounded by a factor 𝛼, we obtain an Ω(loglog 𝛼∕ log 𝛼)-\r\napproximation algorithm, and we show that this is best possible. Additionally, if P cannot\r\ndistinguish options with the same value for herself, we show that ratios polynomial in 1∕𝛼 cannot\r\nbe avoided. If there are at most 𝛽 different utility values for A, we show a Θ(1∕𝛽)-approximation.\r\nIf the utilities of P and A for each option are related by a factor 𝛾, we obtain an Ω(1∕ log 𝛾)-\r\napproximation, where 𝑂(log log 𝛾∕ log 𝛾) is best possible."}],"file_date_updated":"2025-01-09T10:45:24Z","title":"Delegated online search","doi":"10.1016/j.artint.2024.104171","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Elsevier","status":"public","_id":"17188","type":"journal_article","author":[{"last_name":"Braun","full_name":"Braun, Pirmin","first_name":"Pirmin"},{"id":"0a01c7b2-b823-11ed-9928-cc3f874f9ffd","full_name":"Hahn, Niklas","first_name":"Niklas","last_name":"Hahn"},{"last_name":"Hoefer","full_name":"Hoefer, Martin","first_name":"Martin"},{"first_name":"Conrad","full_name":"Schecker, Conrad","last_name":"Schecker"}],"article_type":"original","publication_status":"published","ddc":["000"],"oa":1,"year":"2024","article_processing_charge":"Yes (in subscription journal)","intvolume":"       334","oa_version":"Published Version","month":"09","has_accepted_license":"1","citation":{"short":"P. Braun, N. Hahn, M. Hoefer, C. Schecker, Artificial Intelligence 334 (2024).","ieee":"P. Braun, N. Hahn, M. Hoefer, and C. Schecker, “Delegated online search,” <i>Artificial Intelligence</i>, vol. 334. Elsevier, 2024.","apa":"Braun, P., Hahn, N., Hoefer, M., &#38; Schecker, C. (2024). Delegated online search. <i>Artificial Intelligence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.artint.2024.104171\">https://doi.org/10.1016/j.artint.2024.104171</a>","chicago":"Braun, Pirmin, Niklas Hahn, Martin Hoefer, and Conrad Schecker. “Delegated Online Search.” <i>Artificial Intelligence</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.artint.2024.104171\">https://doi.org/10.1016/j.artint.2024.104171</a>.","ista":"Braun P, Hahn N, Hoefer M, Schecker C. 2024. Delegated online search. Artificial Intelligence. 334, 104171.","mla":"Braun, Pirmin, et al. “Delegated Online Search.” <i>Artificial Intelligence</i>, vol. 334, 104171, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.artint.2024.104171\">10.1016/j.artint.2024.104171</a>.","ama":"Braun P, Hahn N, Hoefer M, Schecker C. Delegated online search. <i>Artificial Intelligence</i>. 2024;334. doi:<a href=\"https://doi.org/10.1016/j.artint.2024.104171\">10.1016/j.artint.2024.104171</a>"},"corr_author":"1","publication":"Artificial Intelligence","date_created":"2024-06-30T22:01:05Z","scopus_import":"1","department":[{"_id":"MoHe"}],"article_number":"104171","acknowledgement":"Hahn gratefully acknowledges the support of GIF grant I-1419-118.4/2017. Hoefer gratefully acknowledges the support of GIF grant I-1419-118.4/2017, DFG Research Unit ADYN (project number 411362735), and DFG grant Ho 3831/9-1 (project number 514505843).","quality_controlled":"1","arxiv":1,"OA_place":"publisher","OA_type":"hybrid","volume":334,"publication_identifier":{"issn":["0004-3702"]}},{"date_published":"2024-06-07T00:00:00Z","day":"07","isi":1,"fulldoi":"https://doi.org/10.1137/22M1489071","language":[{"iso":"eng"}],"external_id":{"isi":["001292728600001"],"arxiv":["2204.01077"]},"abstract":[{"lang":"eng","text":"For a locally finite set, 𝐴⊆ℝ𝑑\r\n, the 𝑘\r\nth Brillouin zone of 𝑎∈𝐴\r\n is the region of points 𝑥∈ℝ𝑑\r\n for which ‖𝑥−𝑎‖\r\n is the 𝑘\r\nth smallest among the Euclidean distances between 𝑥\r\n and the points in 𝐴\r\n. If 𝐴\r\n is a lattice, the 𝑘\r\nth Brillouin zones of the points in 𝐴\r\n are translates of each other, and together they tile space. Depending on the value of 𝑘\r\n, they express medium- or long-range order in the set. We study fundamental geometric and combinatorial properties of Brillouin zones, focusing on the integer lattice and its perturbations. Our results include the stability of a Brillouin zone under perturbations, a linear upper bound on the number of chambers in a zone for lattices in ℝ2\r\n, and the convergence of the maximum volume of a chamber to zero for the integer lattice."}],"title":"Brillouin zones of integer lattices and their perturbations","date_updated":"2025-09-08T08:06:04Z","page":"1784-1807","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mathematics, Computer Science"}],"type":"journal_article","_id":"17190","status":"public","doi":"10.1137/22M1489071","publisher":"Society for Industrial and Applied Mathematics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","publication_status":"published","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Garber","full_name":"Garber, Alexey","first_name":"Alexey"},{"last_name":"Ghafaris","first_name":"Mohadese","full_name":"Ghafaris, Mohadese"},{"last_name":"Heiss","orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","first_name":"Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Morteza","full_name":"Saghafiant, Morteza","last_name":"Saghafiant"},{"last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","intvolume":"        38","issue":"2","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.01077","open_access":"1"}],"month":"06","article_processing_charge":"No","year":"2024","oa":1,"publication":"SIAM Journal on Discrete Mathematics","department":[{"_id":"HeEd"}],"scopus_import":"1","date_created":"2024-06-30T22:01:05Z","corr_author":"1","citation":{"chicago":"Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafaris, Teresa Heiss, Morteza Saghafiant, and Mathijs Wintraecken. “Brillouin Zones of Integer Lattices and Their Perturbations.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/22M1489071\">https://doi.org/10.1137/22M1489071</a>.","short":"H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, M. Wintraecken, SIAM Journal on Discrete Mathematics 38 (2024) 1784–1807.","apa":"Edelsbrunner, H., Garber, A., Ghafaris, M., Heiss, T., Saghafiant, M., &#38; Wintraecken, M. (2024). Brillouin zones of integer lattices and their perturbations. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/22M1489071\">https://doi.org/10.1137/22M1489071</a>","ieee":"H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, and M. Wintraecken, “Brillouin zones of integer lattices and their perturbations,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 38, no. 2. Society for Industrial and Applied Mathematics, pp. 1784–1807, 2024.","ama":"Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M. Brillouin zones of integer lattices and their perturbations. <i>SIAM Journal on Discrete Mathematics</i>. 2024;38(2):1784-1807. doi:<a href=\"https://doi.org/10.1137/22M1489071\">10.1137/22M1489071</a>","mla":"Edelsbrunner, Herbert, et al. “Brillouin Zones of Integer Lattices and Their Perturbations.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 38, no. 2, Society for Industrial and Applied Mathematics, 2024, pp. 1784–807, doi:<a href=\"https://doi.org/10.1137/22M1489071\">10.1137/22M1489071</a>.","ista":"Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M. 2024. Brillouin zones of integer lattices and their perturbations. SIAM Journal on Discrete Mathematics. 38(2), 1784–1807."},"quality_controlled":"1","arxiv":1,"ec_funded":1,"volume":38,"publication_identifier":{"issn":["0895-4801"]},"acknowledgement":"The second author is partially supported by the Alexander von Humboldt Foundation. The sixth author is supported by the European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement 754411, and by Austrian Science Fund(FWF) grant M-3073. All other authors are supported by European Research Council (ERC) grant 788183, by the Wittgenstein Prize, by Austrian Science Fund (FWF) grant Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF) grant I 02979-N35."},{"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. ","citation":{"chicago":"Sagi, Oliver. “A Gate-Tunable Transmon in Planar Ge.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">https://doi.org/10.15479/AT:ISTA:17196</a>.","ieee":"O. Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and Technology Austria, 2024.","apa":"Sagi, O. (2024). A gate-tunable transmon in planar Ge. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">https://doi.org/10.15479/AT:ISTA:17196</a>","short":"O. Sagi, (2024).","ama":"Sagi O. A gate-tunable transmon in planar Ge. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>","mla":"Sagi, Oliver. <i>A Gate-Tunable Transmon in Planar Ge</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>.","ista":"Sagi O. 2024. A gate-tunable transmon in planar Ge, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>."},"corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"17202"}]},"date_created":"2024-07-04T10:14:34Z","department":[{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"JoFi"}],"oa":1,"year":"2024","article_processing_charge":"No","month":"07","oa_version":"Published Version","author":[{"last_name":"Sagi","full_name":"Sagi, Oliver","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"}],"ddc":["530"],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:17196","status":"public","_id":"17196","type":"research_data","project":[{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"}],"date_updated":"2026-04-16T12:20:39Z","title":"A gate-tunable transmon in planar Ge","abstract":[{"lang":"eng","text":"This .zip File contains the data for the figures presented in the main text and supplementary material of \"A gate tunable transmon qubit in planar Ge\" by O.Sagi et al. The measurements were done using Qcodes. The description of the files and the instructions on opening the data can be found in the Readme. An additional Jupyter Notebook is attached that walks through the data analysis."}],"file_date_updated":"2024-07-04T10:11:40Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"contributor":[{"last_name":"Crippa","contributor_type":"project_member","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","first_name":"Alessandro","orcid":"0000-0002-2968-611X"},{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Janik","first_name":"Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87"},{"id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","first_name":"Levon","contributor_type":"project_member","last_name":"Baghumyan"},{"first_name":"Giorgio","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","last_name":"Fabris","contributor_type":"project_member"},{"id":"84b9700b-15b2-11ec-abd3-831089e67615","first_name":"Lucky","last_name":"Kapoor","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","first_name":"Farid"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","contributor_type":"project_member"},{"first_name":"Stefano","last_name":"Calcaterra","contributor_type":"project_member"},{"first_name":"Daniel","contributor_type":"project_member","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","contributor_type":"project_member"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","contributor_type":"supervisor"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:17196","file":[{"relation":"main_file","date_created":"2024-07-04T10:01:51Z","creator":"osagi","success":1,"file_size":1960182,"date_updated":"2024-07-04T10:01:51Z","checksum":"a9f640a0b72a92171353f3ea14406f0b","file_name":"GeGatemon_DataAnalysis.ipynb","content_type":"application/octet-stream","access_level":"open_access","file_id":"17197"},{"content_type":"application/vnd.openxmlformats-officedocument.presentationml.presentation","file_name":"OlSa_Readme.pptx","access_level":"open_access","file_id":"17198","relation":"main_file","date_created":"2024-07-04T10:01:50Z","creator":"osagi","success":1,"file_size":34194,"checksum":"f0feec931233e8e845ade56165c1588f","date_updated":"2024-07-04T10:01:50Z"},{"date_updated":"2024-07-04T10:11:16Z","checksum":"92bb11e3a508d736d01ff0738a1172c7","file_size":72939292,"creator":"osagi","success":1,"relation":"main_file","date_created":"2024-07-04T10:11:16Z","file_id":"17199","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"Al_Transmon.zip"},{"file_id":"17200","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"Gatemon_RT_5nm_1.zip","checksum":"871e96fe0ecc97581196e883045cd516","date_updated":"2024-07-04T10:11:40Z","file_size":465618029,"creator":"osagi","success":1,"relation":"main_file","date_created":"2024-07-04T10:11:40Z"},{"file_size":281503513,"checksum":"a3e141af90f0104b7269c8a72370848a","date_updated":"2024-07-04T10:11:35Z","date_created":"2024-07-04T10:11:35Z","relation":"main_file","success":1,"creator":"osagi","access_level":"open_access","file_id":"17201","file_name":"Gatemon_RT_5nm_2.zip","content_type":"application/x-zip-compressed"}],"day":"04","date_published":"2024-07-04T00:00:00Z"},{"month":"10","intvolume":"        15","oa_version":"Published Version","APC_amount":"6828 EUR","article_processing_charge":"Yes","year":"2024","oa":1,"ddc":["570"],"publication_status":"published","article_type":"original","author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva"},{"id":"46046B7A-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan K","orcid":"0009-0006-2974-5075","full_name":"Satapathy, Roshan K","last_name":"Satapathy"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","full_name":"Symonova, Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova"},{"last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"volume":15,"publication_identifier":{"eissn":["2041-1723"]},"OA_type":"gold","quality_controlled":"1","OA_place":"publisher","acknowledgement":"We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance with the reconstruction experiments. We would also like to thank Laura Burnett for drawing scientific illustrations used in the figures. We are particularly grateful to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing material support and technical advice. We are grateful to Daria Siekhaus, Eugenia Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory for valuable discussions and comments on the manuscript. Stocks from the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center were used in this study. The Scientific Service Units of ISTA supported the project through resources provided by the Imaging and Optics Facility, MIBA Machine Shop, and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) as part of the SPP 2205 – 429960716 (M.J.).","article_number":"8830","department":[{"_id":"MaJö"}],"scopus_import":"1","date_created":"2024-10-20T22:02:05Z","publication":"Nature Communications","corr_author":"1","citation":{"ista":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. 15, 8830.","mla":"Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>, vol. 15, 8830, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>.","ama":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>","short":"V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications 15 (2024).","ieee":"V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Pokusaeva, V., Satapathy, R. K., Symonova, O., &#38; Jösch, M. A. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>","chicago":"Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>."},"related_material":{"record":[{"id":"18568","relation":"dissertation_contains","status":"public"},{"id":"17488","status":"public","relation":"research_data"}]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"day":"12","date_published":"2024-10-12T00:00:00Z","external_id":{"pmid":["39396050"],"isi":["001336422500001"]},"file":[{"file_size":8276667,"checksum":"2af4d6e7364329107aa94d072d594ce0","date_updated":"2024-10-21T12:11:10Z","relation":"main_file","date_created":"2024-10-21T12:11:10Z","success":1,"creator":"dernst","access_level":"open_access","file_id":"18459","content_type":"application/pdf","file_name":"2024_NatureComm_Pokusaeva.pdf"}],"fulldoi":"https://doi.org/10.1038/s41467-024-53173-w","isi":1,"language":[{"iso":"eng"}],"project":[{"grant_number":"429960716","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","name":"Evolution of Sensorimotor Transformation Across Diptera"}],"type":"journal_article","_id":"18444","status":"public","publisher":"Springer Nature","DOAJ_listed":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/s41467-024-53173-w","title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","file_date_updated":"2024-10-21T12:11:10Z","abstract":[{"text":"Animals rely on compensatory actions to maintain stability and navigate their environment efficiently. These actions depend on global visual motion cues known as optic-flow. While the optomotor response has been the traditional focus for studying optic-flow compensation in insects, its simplicity has been insufficient to determine the role of the intricate optic-flow processing network involved in visual course control. Here, we reveal a series of course control behaviours in Drosophila and link them to specific neural circuits. We show that bilateral electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate are required for a proper course control. This electrical interaction works alongside chemical synapses within the HS-H2 network to control the dynamics and direction of turning behaviours. Our findings reveal how insects use bilateral motion cues for navigation, assigning a new functional significance to the HS-H2 network and suggesting a previously unknown role for gap junctions in non-linear operations.","lang":"eng"}],"pmid":1,"date_updated":"2026-06-10T07:58:34Z"},{"publication_status":"published","article_type":"original","author":[{"last_name":"Zhou","full_name":"Zhou, Yu","first_name":"Yu"},{"first_name":"Ahmed","full_name":"Shaukat, Ahmed","last_name":"Shaukat"},{"last_name":"Seitsonen","full_name":"Seitsonen, Jani","first_name":"Jani"},{"last_name":"Rigoni","first_name":"Carlo","full_name":"Rigoni, Carlo","id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0"},{"last_name":"Timonen","full_name":"Timonen, Jaakko V.I.","first_name":"Jaakko V.I."},{"last_name":"Kostiainen","full_name":"Kostiainen, Mauri A.","first_name":"Mauri A."}],"ddc":["540"],"article_processing_charge":"Yes","oa":1,"year":"2024","month":"12","issue":"45","intvolume":"        11","oa_version":"Published Version","citation":{"ama":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. Protein cage directed assembly of binary nanoparticle superlattices. <i>Advanced Science</i>. 2024;11(45). doi:<a href=\"https://doi.org/10.1002/advs.202408416\">10.1002/advs.202408416</a>","mla":"Zhou, Yu, et al. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” <i>Advanced Science</i>, vol. 11, no. 45, 2408416, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/advs.202408416\">10.1002/advs.202408416</a>.","ista":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. 2024. Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. 11(45), 2408416.","chicago":"Zhou, Yu, Ahmed Shaukat, Jani Seitsonen, Carlo Rigoni, Jaakko V.I. Timonen, and Mauri A. Kostiainen. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” <i>Advanced Science</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/advs.202408416\">https://doi.org/10.1002/advs.202408416</a>.","ieee":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J. V. I. Timonen, and M. A. Kostiainen, “Protein cage directed assembly of binary nanoparticle superlattices,” <i>Advanced Science</i>, vol. 11, no. 45. Wiley, 2024.","apa":"Zhou, Y., Shaukat, A., Seitsonen, J., Rigoni, C., Timonen, J. V. I., &#38; Kostiainen, M. A. (2024). Protein cage directed assembly of binary nanoparticle superlattices. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.202408416\">https://doi.org/10.1002/advs.202408416</a>","short":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen, Advanced Science 11 (2024)."},"has_accepted_license":"1","department":[{"_id":"RaKl"}],"scopus_import":"1","date_created":"2024-10-20T22:02:07Z","publication":"Advanced Science","acknowledgement":"This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 101002258). The authors acknowledge the provision of facilities and technical support by Aalto University Bioeconomy Facilities and OtaNanoNanomicroscopy Center (Aalto-NMC). This work was carried out under the Academy of Finland's Centers of Excellence Programme, Life Inspired Hybrid Materials (LIBER) Center of Excellence (2022–2029), project number 346110 and 346112.","article_number":"2408416","volume":11,"publication_identifier":{"eissn":["2198-3844"]},"OA_type":"gold","quality_controlled":"1","OA_place":"publisher","external_id":{"isi":["001330745600001"],"pmid":["39401426"]},"isi":1,"fulldoi":"https://doi.org/10.1002/advs.202408416","file":[{"file_id":"18834","access_level":"open_access","content_type":"application/pdf","file_name":"2024_AdvancedScience_Zhou.pdf","date_updated":"2025-01-13T09:16:25Z","checksum":"00451eeb2c9eecf1ff41ad243c793a51","file_size":7040083,"creator":"dernst","success":1,"relation":"main_file","date_created":"2025-01-13T09:16:25Z"}],"language":[{"iso":"eng"}],"day":"04","date_published":"2024-12-04T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pmid":1,"date_updated":"2025-09-08T14:20:31Z","title":"Protein cage directed assembly of binary nanoparticle superlattices","file_date_updated":"2025-01-13T09:16:25Z","abstract":[{"lang":"eng","text":"Inorganic nanoparticles can be assembled into superlattices with unique optical and magnetic properties arising from collective behavior. Protein cages can be utilized to guide this assembly by encapsulating nanoparticles and promoting their assembly into ordered structures. However, creating ordered multi-component structures with different protein cage types and sizes remains a challenge. Here, the co-crystallization of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized by opposing surface charges and unequal diameter is shown. Precise tuning of the electrostatic attraction between the cages enabled the preparation of binary crystals with dimensions up to several tens of micrometers. Additionally, binary metal nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles inside the cavities of the protein cages. The resulting structure adopts an AB2FCC configuration that also impacts the dipolar coupling between the particles and hence the optical properties of the crystals, providing key insight for the future preparation of plasmonic and magnetic nanoparticle metamaterials."}],"publisher":"Wiley","DOAJ_listed":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1002/advs.202408416","type":"journal_article","_id":"18451","status":"public"},{"intvolume":"        59","oa_version":"Published Version","issue":"14","month":"12","year":"2024","oa":1,"article_processing_charge":"Yes (in subscription journal)","ddc":["570"],"author":[{"last_name":"Janacek","first_name":"DP","full_name":"Janacek, DP"},{"first_name":"M","full_name":"Kolb, M","last_name":"Kolb"},{"last_name":"Schulz","first_name":"L","full_name":"Schulz, L"},{"last_name":"Mergner","first_name":"J","full_name":"Mergner, J"},{"first_name":"B","full_name":"Kuster, B","last_name":"Kuster"},{"last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"first_name":"K","full_name":"Ten Tusscher, K","last_name":"Ten Tusscher"},{"last_name":"Schwechheimer","full_name":"Schwechheimer, C","first_name":"C"},{"first_name":"UZ","full_name":"Hammes, UZ","last_name":"Hammes"}],"article_type":"original","publication_status":"published","OA_place":"publisher","quality_controlled":"1","OA_type":"hybrid","volume":59,"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"acknowledgement":"This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H. We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished results and valuable discussions.","publication":"Developmental Cell","date_created":"2024-10-23T08:41:27Z","scopus_import":"1","department":[{"_id":"JiFr"}],"has_accepted_license":"1","citation":{"chicago":"Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>.","apa":"Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes, U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>","ieee":"D. Janacek <i>et al.</i>, “Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport,” <i>Developmental Cell</i>, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024.","short":"D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml, K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0.","mla":"Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>.","ama":"Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. 2024;59(14):S1534-5807(24)00569-0. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>","ista":"Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 59(14), S1534-5807(24)00569–0."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"day":"16","date_published":"2024-12-16T00:00:00Z","language":[{"iso":"eng"}],"file":[{"checksum":"34423ee9fb4e30334f3572eddf1da2ae","date_updated":"2025-01-13T09:20:15Z","file_size":3675955,"success":1,"creator":"dernst","date_created":"2025-01-13T09:20:15Z","relation":"main_file","file_id":"18835","access_level":"open_access","file_name":"2024_DevelopmentalCell_Janacek.pdf","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.1016/j.devcel.2024.09.020","isi":1,"external_id":{"isi":["001390774300001"],"pmid":["39413780"]},"status":"public","_id":"18465","type":"journal_article","doi":"10.1016/j.devcel.2024.09.020","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Elsevier","abstract":[{"text":"The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.","lang":"eng"}],"file_date_updated":"2025-01-13T09:20:15Z","title":"Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport","page":"S1534-5807(24)00569-0","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2025-09-08T14:33:17Z","pmid":1},{"acknowledgement":"We are grateful to the anonymous referee for their careful reading and valuable remarks and comments which helped to improve significantly the paper. Open access funding provided by Institute of Science and Technology (IST Austria). V.K. and C.E.K. gratefully acknowledge support from the European Research Council (ERC) through the Advanced Grant “SPERIG” (#885 707).","arxiv":1,"quality_controlled":"1","OA_place":"publisher","OA_type":"hybrid","ec_funded":1,"volume":34,"publication_identifier":{"issn":["1016-443X"],"eissn":["1420-8970"]},"has_accepted_license":"1","citation":{"mla":"Kaloshin, Vadim, et al. “Birkhoff Conjecture for Nearly Centrally Symmetric Domains.” <i>Geometric and Functional Analysis</i>, vol. 34, Springer Nature, 2024, pp. 1973–2007, doi:<a href=\"https://doi.org/10.1007/s00039-024-00695-6\">10.1007/s00039-024-00695-6</a>.","ama":"Kaloshin V, Koudjinan E, Zhang K. Birkhoff conjecture for nearly centrally symmetric domains. <i>Geometric and Functional Analysis</i>. 2024;34:1973-2007. doi:<a href=\"https://doi.org/10.1007/s00039-024-00695-6\">10.1007/s00039-024-00695-6</a>","ista":"Kaloshin V, Koudjinan E, Zhang K. 2024. Birkhoff conjecture for nearly centrally symmetric domains. Geometric and Functional Analysis. 34, 1973–2007.","chicago":"Kaloshin, Vadim, Edmond Koudjinan, and Ke Zhang. “Birkhoff Conjecture for Nearly Centrally Symmetric Domains.” <i>Geometric and Functional Analysis</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00039-024-00695-6\">https://doi.org/10.1007/s00039-024-00695-6</a>.","apa":"Kaloshin, V., Koudjinan, E., &#38; Zhang, K. (2024). Birkhoff conjecture for nearly centrally symmetric domains. <i>Geometric and Functional Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00039-024-00695-6\">https://doi.org/10.1007/s00039-024-00695-6</a>","ieee":"V. Kaloshin, E. Koudjinan, and K. Zhang, “Birkhoff conjecture for nearly centrally symmetric domains,” <i>Geometric and Functional Analysis</i>, vol. 34. Springer Nature, pp. 1973–2007, 2024.","short":"V. Kaloshin, E. Koudjinan, K. Zhang, Geometric and Functional Analysis 34 (2024) 1973–2007."},"corr_author":"1","publication":"Geometric and Functional Analysis","date_created":"2024-10-27T23:01:45Z","department":[{"_id":"VaKa"}],"scopus_import":"1","year":"2024","oa":1,"article_processing_charge":"Yes (via OA deal)","intvolume":"        34","oa_version":"Published Version","month":"12","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin"},{"first_name":"Edmond","orcid":"0000-0003-2640-4049","full_name":"Koudjinan, Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","last_name":"Koudjinan"},{"last_name":"Zhang","first_name":"Ke","full_name":"Zhang, Ke"}],"article_type":"original","publication_status":"published","ddc":["510"],"doi":"10.1007/s00039-024-00695-6","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer Nature","status":"public","_id":"18483","type":"journal_article","project":[{"grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows"}],"date_updated":"2025-09-08T14:27:45Z","page":"1973-2007","abstract":[{"lang":"eng","text":"In this paper we prove a perturbative version of a remarkable Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) result. They prove non perturbative Birkhoff conjecture for centrally-symmetric convex domains, namely, a centrally-symmetric convex domain with integrable billiard is ellipse. We combine techniques from Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) with a local result by Kaloshin–Sorrentino (Ann. Math. 188(1):315–380, 2018) and show that a domain close enough to a centrally symmetric one with integrable billiard is ellipse. To combine these results we derive a slight extension of Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) by proving that a notion of rational integrability is equivalent to the C0-integrability condition used in their paper."}],"file_date_updated":"2025-01-13T09:14:24Z","title":"Birkhoff conjecture for nearly centrally symmetric domains","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1007/s00039-024-00695-6","isi":1,"file":[{"access_level":"open_access","file_id":"18833","content_type":"application/pdf","file_name":"2024_GeometricFunctionalAnalysis_Kaloshin.pdf","file_size":2260980,"checksum":"e7fcd9f78beb40408c7d858ac0625e27","date_updated":"2025-01-13T09:14:24Z","date_created":"2025-01-13T09:14:24Z","relation":"main_file","creator":"dernst","success":1}],"external_id":{"arxiv":["2306.12301"],"isi":["001329804200001"]},"day":"01","date_published":"2024-12-01T00:00:00Z"},{"date_updated":"2025-09-08T14:26:29Z","title":"Tangent space generators of matrix product states and exact floquet quantum scars","abstract":[{"lang":"eng","text":"The advancement of quantum simulators motivates the development of a theoretical framework to assist with efficient state preparation in quantum many-body systems. Generally, preparing a target entangled state via unitary evolution with time-dependent couplings is a challenging task and very little is known about the existence of solutions and their properties. In this work we develop a constructive approach for preparing matrix product states (MPS) via continuous unitary evolution. We provide an explicit construction of the operator that exactly implements the evolution of a given MPS along a specified direction in its tangent space. This operator can be written as a sum of local terms of finite range, yet it is in general non-Hermitian. Relying on the explicit construction of the non-Hermitian generator of the dynamics, we demonstrate the existence of a Hermitian sequence of operators that implements the desired MPS evolution with an error that decreases exponentially with the operator range. The construction is benchmarked on an explicit periodic trajectory in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary generating the dynamics over one period of the trajectory features an approximate MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results show that our construction is not only useful for state preparation and control of many-body systems, but also provides a generic route towards Floquet scars—periodically driven models with quasilocal generators of dynamics that have exact MPS eigenstates in their spectrum."}],"file_date_updated":"2024-10-30T08:59:09Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","DOAJ_listed":"1","publisher":"American Physical Society","doi":"10.1103/prxquantum.5.040311","_id":"18488","status":"public","type":"journal_article","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"external_id":{"isi":["001346198800001"],"arxiv":["2403.12325"]},"language":[{"iso":"eng"}],"file":[{"file_size":1151431,"checksum":"2e057ba021744d0a74602517935326b3","date_updated":"2024-10-30T08:59:09Z","date_created":"2024-10-30T08:59:09Z","relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","file_id":"18489","file_name":"2024_PRXQuantum_Ljubotina.pdf","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.1103/prxquantum.5.040311","isi":1,"date_published":"2024-10-23T00:00:00Z","day":"23","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).","apa":"Ljubotina, M., Petrova, E., Schuch, N., &#38; Serbyn, M. (2024). Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>","ieee":"M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators of matrix product states and exact floquet quantum scars,” <i>PRX Quantum</i>, vol. 5, no. 4. American Physical Society, 2024.","chicago":"Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>.","ista":"Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.","mla":"Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>, vol. 5, no. 4, 040311, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>.","ama":"Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>"},"corr_author":"1","has_accepted_license":"1","date_created":"2024-10-29T16:04:05Z","department":[{"_id":"MaSe"}],"scopus_import":"1","publication":"PRX Quantum","article_number":"040311","acknowledgement":"We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions. This research was funded in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1, 10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This work was performed in part at the Aspen Center for Physics, which is supported by National Science Foundation Grant PHY-2210452. This research was supported in part by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).","publication_identifier":{"eissn":["2691-3399"]},"ec_funded":1,"volume":5,"OA_place":"publisher","quality_controlled":"1","arxiv":1,"OA_type":"gold","author":[{"last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","first_name":"Marko"},{"last_name":"Petrova","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","first_name":"Elena","full_name":"Petrova, Elena"},{"full_name":"Schuch, Norbert","first_name":"Norbert","last_name":"Schuch"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","publication_status":"published","ddc":["530"],"oa":1,"year":"2024","article_processing_charge":"Yes","month":"10","APC_amount":"3711,01 EUR","intvolume":"         5","issue":"4","oa_version":"Published Version"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"external_id":{"isi":["001351918100029"]},"file":[{"date_created":"2024-11-04T08:54:26Z","relation":"main_file","creator":"dernst","success":1,"file_size":911476,"date_updated":"2024-11-04T08:54:26Z","checksum":"143816823b5f43bd3748da8e3e91cef5","content_type":"application/pdf","file_name":"2024_JourLondonMathSoc_Schiavo.pdf","access_level":"open_access","file_id":"18497"}],"fulldoi":"https://doi.org/10.1112/jlms.70003","isi":1,"language":[{"iso":"eng"}],"date_published":"2024-11-01T00:00:00Z","day":"01","publisher":"London Mathematical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1112/jlms.70003","type":"journal_article","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"status":"public","_id":"18490","date_updated":"2025-09-08T14:29:45Z","title":"Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension","file_date_updated":"2024-11-04T08:54:26Z","abstract":[{"lang":"eng","text":"For large classes of even-dimensional Riemannian manifolds (Formula presented.), we construct and analyze conformally invariant random fields. These centered Gaussian fields (Formula presented.), called co-polyharmonic Gaussian fields, are characterized by their covariance kernels k which exhibit a precise logarithmic divergence: (Formula presented.). They share a fundamental quasi-invariance property under conformal transformations. In terms of the co-polyharmonic Gaussian field (Formula presented.), we define the Liouville Quantum Gravity measure, a random measure on (Formula presented.), heuristically given as (Formula presented.) and rigorously obtained as almost sure weak limit of the right-hand side with (Formula presented.) replaced by suitable regular approximations (Formula presented.). In terms on the Liouville Quantum Gravity measure, we define the Liouville Brownian motion on (Formula presented.) and the random GJMS operators. Finally, we present an approach to a conformal field theory in arbitrary even dimension with an ansatz based on Branson's (Formula presented.) -curvature: we give a rigorous meaning to the Polyakov–Liouville measure (Formula presented.) and we derive the corresponding conformal anomaly. The set of admissible manifolds is conformally invariant. It includes all compact 2-dimensional Riemannian manifolds, all compact non-negatively curved Einstein manifolds of even dimension, and large classes of compact hyperbolic manifolds of even dimension. However, not every compact even-dimensional Riemannian manifold is admissible. Our results concerning the logarithmic divergence of the kernel (Formula presented.) rely on new sharp estimates for heat kernels and higher order Green kernels on arbitrary closed manifolds. "}],"article_processing_charge":"Yes (via OA deal)","oa":1,"year":"2024","month":"11","intvolume":"       110","issue":"5","oa_version":"Published Version","article_type":"original","publication_status":"published","author":[{"last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo"},{"last_name":"Herry","first_name":"Ronan","full_name":"Herry, Ronan"},{"last_name":"Kopfer","full_name":"Kopfer, Eva","first_name":"Eva"},{"last_name":"Sturm","first_name":"Karl Theodor","full_name":"Sturm, Karl Theodor"}],"ddc":["510"],"acknowledgement":"The authors are grateful to Masha Gordina for helpful references, and to Nathanaël Berestycki, Baptiste Cerclé, and Ewain Gwynne for valuable comments on the first circulated version of this paper. They also would like to thank Sebastian Andres, Peter Friz, and Yizheng Yuan for pointing out an erroneous formulation in the previous version of Theorem 5.7. Moreover, KTS would liketo express his thanks to Sebastian Andres, Matthias Erbar, Martin Huesmann, and Jan Mass for stimulating discussions on previous attempts to this project. LDS gratefully acknowledges financial support from the European Research Council (grant agreement No 716117, awarded to J. Maas), from the Austrian Science Fund (FWF) project 10.55776/ESP208, and from the Austrian Science Fund (FWF) project 10.55776/F65.RH, EK, and KTS gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through the project “Random Riemannian Geometry” within the SPP 2265 “Random Geomet-ric Systems,” through the Hausdorff Center for Mathematics (project ID 390685813), and through project B03 within the CRC 1060 (project ID 211504053). RH and KTS also gratefully acknowledge financial support from the European Research Council through the ERC AdG “RicciBounds”(grant agreement 694405).Data sharing not applicable to this article as no datasets were generated or analyzed during the current study. Open access funding enabled and organized by Projekt DEAL.","article_number":"e70003","ec_funded":1,"publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"volume":110,"OA_type":"hybrid","quality_controlled":"1","OA_place":"publisher","citation":{"chicago":"Dello Schiavo, Lorenzo, Ronan Herry, Eva Kopfer, and Karl Theodor Sturm. “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” <i>Journal of the London Mathematical Society</i>. London Mathematical Society, 2024. <a href=\"https://doi.org/10.1112/jlms.70003\">https://doi.org/10.1112/jlms.70003</a>.","short":"L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Journal of the London Mathematical Society 110 (2024).","apa":"Dello Schiavo, L., Herry, R., Kopfer, E., &#38; Sturm, K. T. (2024). Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. <i>Journal of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/jlms.70003\">https://doi.org/10.1112/jlms.70003</a>","ieee":"L. Dello Schiavo, R. Herry, E. Kopfer, and K. T. Sturm, “Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension,” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 5. London Mathematical Society, 2024.","ama":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. <i>Journal of the London Mathematical Society</i>. 2024;110(5). doi:<a href=\"https://doi.org/10.1112/jlms.70003\">10.1112/jlms.70003</a>","mla":"Dello Schiavo, Lorenzo, et al. “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 5, e70003, London Mathematical Society, 2024, doi:<a href=\"https://doi.org/10.1112/jlms.70003\">10.1112/jlms.70003</a>.","ista":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. 2024. Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. Journal of the London Mathematical Society. 110(5), e70003."},"has_accepted_license":"1","department":[{"_id":"JaMa"}],"scopus_import":"1","date_created":"2024-11-03T23:01:44Z","publication":"Journal of the London Mathematical Society"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2024-10-01T00:00:00Z","day":"01","fulldoi":"https://doi.org/10.3847/1538-4357/ad778b","isi":1,"file":[{"relation":"main_file","date_created":"2024-11-04T08:42:23Z","success":1,"creator":"dernst","file_size":1042470,"checksum":"1fcac3d11d01d91cf2bb4963b6e10b22","date_updated":"2024-11-04T08:42:23Z","file_name":"2024_AstrophysicalJour_Eilers.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"18496"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001338877100001"]},"project":[{"_id":"bd9b2118-d553-11ed-ba76-db24564edfea","name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224"}],"type":"journal_article","_id":"18494","status":"public","doi":"10.3847/1538-4357/ad778b","publisher":"IOP Publishing","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","DOAJ_listed":"1","file_date_updated":"2024-11-04T08:42:23Z","abstract":[{"lang":"eng","text":"We expect luminous (M 1450 ≲ −26.5) high-redshift quasars to trace the highest-density peaks in the early Universe. Here, we present observations of four z ≳ 6 quasar fields using JWST/NIRCam in the imaging and wide-field slitless spectroscopy mode and report a wide range in the number of detected [O iii]-emitting galaxies in the quasars’ environments, ranging between a density enhancement of δ ≈ 65 within a 2 cMpc radius—one of the largest protoclusters during the Epoch of Reionization discovered to date—to a density contrast consistent with zero, indicating the presence of a UV-luminous quasar in a region comparable to the average density of the Universe. By measuring the two-point cross-correlation function of quasars and their surrounding galaxies, as well as the galaxy autocorrelation function, we infer a correlation length of quasars at 〈z〉 = 6.25 of r 0 QQ = 22.0 − 2.9 + 3.0 cMpc h − 1 , while we obtain a correlation length of the [O iii]-emitting galaxies of r 0 GG = 4.1 ± 0.3 cMpc h − 1 . By comparing the correlation functions to dark-matter-only simulations we estimate the minimum mass of the quasars’ host dark matter halos to be log 10 ( M halo , min / M ⊙ ) = 12.43 − 0.15 + 0.13 (and log 10 ( M halo , min [ OIII ] / M ⊙ ) = 10.56 − 0.03 + 0.05 for the [O iii] emitters), indicating that (a) luminous quasars do not necessarily reside within the most overdense regions in the early Universe, and that (b) the UV-luminous duty cycle of quasar activity at these redshifts is f duty ≪ 1. Such short quasar activity timescales challenge our understanding of early supermassive black hole growth and provide evidence for highly dust-obscured growth phases or episodic, radiatively inefficient accretion rates."}],"title":"EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6","date_updated":"2025-09-08T14:29:05Z","intvolume":"       974","oa_version":"Published Version","issue":"2","month":"10","article_processing_charge":"Yes","oa":1,"year":"2024","ddc":["520"],"article_type":"original","publication_status":"published","author":[{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"last_name":"Mackenzie","full_name":"Mackenzie, Ruari","first_name":"Ruari"},{"last_name":"Pizzati","first_name":"Elia","full_name":"Pizzati, Elia"},{"last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"Joseph F.","full_name":"Hennawi, Joseph F.","last_name":"Hennawi"},{"last_name":"Zhang","first_name":"Haowen","full_name":"Zhang, Haowen"},{"last_name":"Bordoloi","full_name":"Bordoloi, Rongmon","first_name":"Rongmon"},{"full_name":"Kashino, Daichi","first_name":"Daichi","last_name":"Kashino"},{"last_name":"Lilly","first_name":"Simon J.","full_name":"Lilly, Simon J."},{"full_name":"Naidu, Rohan P.","first_name":"Rohan P.","last_name":"Naidu"},{"last_name":"Simcoe","first_name":"Robert A.","full_name":"Simcoe, Robert A."},{"first_name":"Minghao","full_name":"Yue, Minghao","last_name":"Yue"},{"first_name":"Carlos S.","full_name":"Frenk, Carlos S.","last_name":"Frenk"},{"first_name":"John C.","full_name":"Helly, John C.","last_name":"Helly"},{"last_name":"Schaller","first_name":"Matthieu","full_name":"Schaller, Matthieu"},{"last_name":"Schaye","first_name":"Joop","full_name":"Schaye, Joop"}],"OA_type":"gold","quality_controlled":"1","OA_place":"publisher","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"volume":974,"acknowledgement":"The authors would like to thank the anonymous referee for the thoughtful comments, which significantly improved our manuscript, and Jan-Torge Schindler, Jiamu Huang, and Feige Wang for helpful discussions.\r\n\r\nJ.F.H. and E.P. acknowledge support from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation program (grant agreement No. 885301). J.M. acknowledges support from the European Union (ERC, AGENTS, 101076224).\r\n\r\nThis work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The JWST data presented in this article were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The specific observations analyzed are associated with program #1243 and can be accessed via doi:10.17909/m5mp-5v90.\r\n\r\nThis work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Directors Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded DiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure.\r\n\r\nWe thank the Instituto de Astrofisica de Andalucia (IAA-CSIC), Centro de Supercomputacion de Galicia (CESGA), and Spanish Academic and Research Network (RedIRIS) in Spain for hosting Uchuu DR1, DR2, and DR3 in the Skies & Universes site for cosmological simulations. The Uchuu simulations were carried out on the Aterui II supercomputer at the Center for Computational Astrophysics, CfCA, of the National Astronomical Observatory of Japan, and the K computer at the RIKEN Advanced Institute for Computational Science. The Uchuu Data Releases efforts have made use of the skunIAA_RedIRIS and skun6IAA computer facilities managed by the IAA-CSIC in Spain (MICINN EU-Feder grant EQC2018-004366-P).","article_number":"275","publication":"Astrophysical Journal","scopus_import":"1","department":[{"_id":"JoMa"}],"date_created":"2024-11-03T23:01:45Z","has_accepted_license":"1","citation":{"ista":"Eilers AC, Mackenzie R, Pizzati E, Matthee JJ, Hennawi JF, Zhang H, Bordoloi R, Kashino D, Lilly SJ, Naidu RP, Simcoe RA, Yue M, Frenk CS, Helly JC, Schaller M, Schaye J. 2024. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. 974(2), 275.","mla":"Eilers, Anna Christina, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” <i>Astrophysical Journal</i>, vol. 974, no. 2, 275, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778b\">10.3847/1538-4357/ad778b</a>.","ama":"Eilers AC, Mackenzie R, Pizzati E, et al. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. <i>Astrophysical Journal</i>. 2024;974(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778b\">10.3847/1538-4357/ad778b</a>","short":"A.C. Eilers, R. Mackenzie, E. Pizzati, J.J. Matthee, J.F. Hennawi, H. Zhang, R. Bordoloi, D. Kashino, S.J. Lilly, R.P. Naidu, R.A. Simcoe, M. Yue, C.S. Frenk, J.C. Helly, M. Schaller, J. Schaye, Astrophysical Journal 974 (2024).","ieee":"A. C. Eilers <i>et al.</i>, “EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6,” <i>Astrophysical Journal</i>, vol. 974, no. 2. IOP Publishing, 2024.","apa":"Eilers, A. C., Mackenzie, R., Pizzati, E., Matthee, J. J., Hennawi, J. F., Zhang, H., … Schaye, J. (2024). EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad778b\">https://doi.org/10.3847/1538-4357/ad778b</a>","chicago":"Eilers, Anna Christina, Ruari Mackenzie, Elia Pizzati, Jorryt J Matthee, Joseph F. Hennawi, Haowen Zhang, Rongmon Bordoloi, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” <i>Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad778b\">https://doi.org/10.3847/1538-4357/ad778b</a>."}},{"abstract":[{"text":"Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715","lang":"eng"}],"date_created":"2024-11-04T09:33:17Z","title":"Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails","department":[{"_id":"NiBa"}],"has_accepted_license":"1","date_updated":"2026-04-16T12:20:37Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"20991"},{"status":"public","relation":"used_in_publication","id":"18491"}]},"citation":{"ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","mla":"Garcia Castillo, Diego Fernando, et al. <i>Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, (2024).","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>","ieee":"D. F. Garcia Castillo <i>et al.</i>, “Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails.” Zenodo, 2024.","chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>."},"corr_author":"1","OA_place":"repository","_id":"18498","status":"public","type":"research_data_reference","doi":"10.5281/ZENODO.12159343","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","ddc":["570"],"date_published":"2024-06-19T00:00:00Z","day":"19","author":[{"last_name":"Garcia Castillo","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Larsson","first_name":"Jenny","full_name":"Larsson, Jenny"},{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"}],"fulldoi":"https://doi.org/10.5281/ZENODO.12159343","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.12159344","open_access":"1"}],"oa_version":"Published Version","month":"06","oa":1,"year":"2024","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"fulldoi":"https://doi.org/10.1137/1.9781611977912.111","language":[{"iso":"eng"}],"external_id":{"arxiv":["2401.05627"]},"date_published":"2024-01-04T00:00:00Z","day":"04","page":"3089-3139","date_updated":"2025-06-24T12:09:26Z","conference":{"start_date":"2024-01-07","location":"Alexandria, VA,  United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2024-01-10"},"abstract":[{"lang":"eng","text":"In 1996, Karger [Kar96] gave a startling randomized algorithm that finds a minimum-cut in a (weighted) graph in time O(m log3 n) which he termed near-linear time meaning linear (in the size of the input) times a polylogarthmic factor. In this paper, we give the first deterministic algorithm which runs in near-linear time for weighted graphs.\r\nPreviously, the breakthrough results of Kawarabayashi and Thorup [KT19] gave a near-linear time algorithm for simple graphs (which was improved to have running time O(m log2 n log log n) in [HRW20].) The main technique here is a clustering procedure that perfectly preserves minimum cuts. Recently, Li [Li21] gave an m1+o(1) deterministic minimum-cut algorithm for weighted graphs; this form of running time has been termed “almost-linear”. Li uses almost-linear time deterministic expander decompositions which do not perfectly preserve minimum cuts, but he can use these clusterings to, in a sense, “derandomize” the methods of Karger.\r\nIn terms of techniques, we provide a structural theorem that says there exists a sparse clustering that preserves minimum cuts in a weighted graph with o(1) error. In addition, we construct it deterministically in near linear time. This was done exactly for simple graphs in [KT19, HRW20] and with polylogarithmic error for weighted graphs in [Li21]. Extending the techniques in [KT19, HRW20] to weighted graphs presents significant challenges, and moreover, the algorithm can only polylogarithmically approximately preserve minimum cuts. A remaining challenge is to reduce the polylogarithmic-approximate clusterings to 1 + o(1/ log n)-approximate so that they can be applied recursively as in [Li21] over O(log n) many levels. This is an additional challenge that requires building on properties of tree-packings in the presence of a wide range of edge weights to, for example, find sources for local flow computations which identify minimum cuts that cross clusters."}],"title":"Deterministic near-linear time minimum cut in weighted graphs","doi":"10.1137/1.9781611977912.111","publisher":"Society for Industrial and Applied Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms","grant_number":"Z00422"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"}],"status":"public","_id":"18503","publication_status":"published","author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Li, Jason","first_name":"Jason","last_name":"Li"},{"last_name":"Rao","full_name":"Rao, Satish","first_name":"Satish"},{"last_name":"Wang","full_name":"Wang, Di","first_name":"Di"}],"article_processing_charge":"No","year":"2024","oa":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2401.05627"}],"month":"01","corr_author":"1","citation":{"short":"M. Henzinger, J. Li, S. Rao, D. Wang, in:, 35th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 3089–3139.","ieee":"M. Henzinger, J. Li, S. Rao, and D. Wang, “Deterministic near-linear time minimum cut in weighted graphs,” in <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Alexandria, VA,  United States, 2024, pp. 3089–3139.","apa":"Henzinger, M., Li, J., Rao, S., &#38; Wang, D. (2024). Deterministic near-linear time minimum cut in weighted graphs. In <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 3089–3139). Alexandria, VA,  United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977912.111\">https://doi.org/10.1137/1.9781611977912.111</a>","chicago":"Henzinger, Monika, Jason Li, Satish Rao, and Di Wang. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” In <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 3089–3139. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/1.9781611977912.111\">https://doi.org/10.1137/1.9781611977912.111</a>.","ista":"Henzinger M, Li J, Rao S, Wang D. 2024. Deterministic near-linear time minimum cut in weighted graphs. 35th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 3089–3139.","ama":"Henzinger M, Li J, Rao S, Wang D. Deterministic near-linear time minimum cut in weighted graphs. In: <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2024:3089-3139. doi:<a href=\"https://doi.org/10.1137/1.9781611977912.111\">10.1137/1.9781611977912.111</a>","mla":"Henzinger, Monika, et al. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2024, pp. 3089–139, doi:<a href=\"https://doi.org/10.1137/1.9781611977912.111\">10.1137/1.9781611977912.111</a>."},"publication":"35th Annual ACM-SIAM Symposium on Discrete Algorithms","department":[{"_id":"MoHe"}],"scopus_import":"1","date_created":"2024-11-04T10:54:21Z","acknowledgement":"This project has received funding from the European Research Council(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDyn-Struct)” and the Austrian Science Fund (FWF) project Z 422-N, project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","OA_type":"free access","OA_place":"repository","arxiv":1,"quality_controlled":"1","ec_funded":1,"publication_identifier":{"eisbn":["9781611977912"]}},{"file_date_updated":"2024-11-07T10:59:42Z","abstract":[{"text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations.","lang":"eng"}],"title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"219","date_updated":"2026-04-07T12:56:52Z","type":"dissertation","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"status":"public","_id":"18515","doi":"10.15479/at:ista:18515","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"07","date_published":"2024-11-07T00:00:00Z","file":[{"success":1,"creator":"psurendr","relation":"main_file","date_created":"2024-11-07T10:59:29Z","date_updated":"2024-11-07T10:59:29Z","checksum":"c32cf7bc75748d9c551d8eb70178bbec","file_size":37019760,"file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","content_type":"application/pdf","file_id":"18519","access_level":"open_access"},{"access_level":"closed","file_id":"18520","file_name":"PhD Thesis- Parvathy_071124.zip","content_type":"application/zip","file_size":41198857,"checksum":"4417e02d54084d89e75734e18caaa96d","date_updated":"2024-11-07T10:59:42Z","date_created":"2024-11-07T10:59:42Z","relation":"source_file","creator":"psurendr"}],"fulldoi":"https://doi.org/10.15479/at:ista:18515","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2024-11-06T21:25:37Z","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","citation":{"chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria."},"OA_type":"gold","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","ddc":["576"],"publication_status":"published","author":[{"last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","month":"11","degree_awarded":"PhD","article_processing_charge":"No","year":"2024","oa":1},{"doi":"10.1007/978-3-031-74234-7_18","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"type":"conference","_id":"18521","status":"public","page":"282-301","date_updated":"2026-05-20T08:43:20Z","conference":{"location":"Istanbul, Turkey","start_date":"2024-10-15","name":"RV: Conference on Runtime Verification","end_date":"2024-10-17"},"file_date_updated":"2024-11-11T09:42:28Z","abstract":[{"lang":"eng","text":"In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples."}],"title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"fulldoi":"https://doi.org/10.1007/978-3-031-74234-7_18","file":[{"creator":"dernst","success":1,"relation":"main_file","date_created":"2024-11-11T09:42:28Z","date_updated":"2024-11-11T09:42:28Z","checksum":"7b8ca21b8c19ab796fa445b0e54003ca","file_size":1897101,"content_type":"application/pdf","file_name":"2024_LNCS_Bonakdarpour.pdf","file_id":"18539","access_level":"open_access"}],"isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["001420093700018"],"arxiv":["2408.05033"]},"day":"12","date_published":"2024-10-12T00:00:00Z","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. This work is sponsored in part by the United States NSF CCF-2118356 award. This research was partially funded by A-IQ Ready (Chips JU, grant agreement No. 101096658).","OA_type":"hybrid","arxiv":1,"OA_place":"publisher","quality_controlled":"1","volume":15191,"ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031742330"]},"alternative_title":["LNCS"],"has_accepted_license":"1","corr_author":"1","citation":{"ista":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. 2024. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. 24th International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 15191, 282–301.","ama":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In: <i>24th International Conference on Runtime Verification</i>. Vol 15191. Springer Nature; 2024:282-301. doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>","mla":"Bonakdarpour, Borzoo, et al. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” <i>24th International Conference on Runtime Verification</i>, vol. 15191, Springer Nature, 2024, pp. 282–301, doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>.","short":"B. Bonakdarpour, A. Momtaz, D. Nickovic, N.E. Sarac, in:, 24th International Conference on Runtime Verification, Springer Nature, 2024, pp. 282–301.","ieee":"B. Bonakdarpour, A. Momtaz, D. Nickovic, and N. E. Sarac, “Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy,” in <i>24th International Conference on Runtime Verification</i>, Istanbul, Turkey, 2024, vol. 15191, pp. 282–301.","apa":"Bonakdarpour, B., Momtaz, A., Nickovic, D., &#38; Sarac, N. E. (2024). Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In <i>24th International Conference on Runtime Verification</i> (Vol. 15191, pp. 282–301). Istanbul, Turkey: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>","chicago":"Bonakdarpour, Borzoo, Anik Momtaz, Dejan Nickovic, and Naci E Sarac. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” In <i>24th International Conference on Runtime Verification</i>, 15191:282–301. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>."},"publication":"24th International Conference on Runtime Verification","scopus_import":"1","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"date_created":"2024-11-10T23:01:58Z","article_processing_charge":"Yes (in subscription journal)","year":"2024","oa":1,"oa_version":"Published Version","intvolume":"     15191","APC_amount":"2748 EUR","month":"10","publication_status":"published","author":[{"first_name":"Borzoo","full_name":"Bonakdarpour, Borzoo","last_name":"Bonakdarpour"},{"last_name":"Momtaz","full_name":"Momtaz, Anik","first_name":"Anik"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"},{"first_name":"Naci E","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"ddc":["000"]},{"citation":{"short":"Y. Weyer, S.I. Schwabl, X. Tang, A. Purwar, K. Siegmann, A. Ruepp, T. Dunzendorfer-Matt, M.A. Widerin, V. Niedrist, N.J.M. Mutsters, M.G. Tettamanti, S. Weys, B. Sarg, L. Kremser, K.R. Liedl, O. Schmidt, D. Teis, Nature Communications 15 (2024).","apa":"Weyer, Y., Schwabl, S. I., Tang, X., Purwar, A., Siegmann, K., Ruepp, A., … Teis, D. (2024). The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53676-6\">https://doi.org/10.1038/s41467-024-53676-6</a>","ieee":"Y. Weyer <i>et al.</i>, “The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Weyer, Yannick, Sinead I. Schwabl, Xuechen Tang, Astha Purwar, Konstantin Siegmann, Angela Ruepp, Theresia Dunzendorfer-Matt, et al. “The Dsc Ubiquitin Ligase Complex Identifies Transmembrane Degrons to Degrade Orphaned Proteins at the Golgi.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53676-6\">https://doi.org/10.1038/s41467-024-53676-6</a>.","ista":"Weyer Y, Schwabl SI, Tang X, Purwar A, Siegmann K, Ruepp A, Dunzendorfer-Matt T, Widerin MA, Niedrist V, Mutsters NJM, Tettamanti MG, Weys S, Sarg B, Kremser L, Liedl KR, Schmidt O, Teis D. 2024. The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. Nature Communications. 15, 9257.","mla":"Weyer, Yannick, et al. “The Dsc Ubiquitin Ligase Complex Identifies Transmembrane Degrons to Degrade Orphaned Proteins at the Golgi.” <i>Nature Communications</i>, vol. 15, 9257, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53676-6\">10.1038/s41467-024-53676-6</a>.","ama":"Weyer Y, Schwabl SI, Tang X, et al. The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53676-6\">10.1038/s41467-024-53676-6</a>"},"has_accepted_license":"1","scopus_import":"1","date_created":"2024-11-10T23:01:58Z","publication":"Nature Communications","acknowledgement":"We thank Snezhana Oliferenko, Hesso Farhan, Chris Dunworth, and Lukas A Huber for critically reading the manuscript, Ming Li, Peter Espenshade, Sebastien Leon, and Scott Emr for reagents, Bob Kaufmann for help in characterizing the Dsc2 L1 loop mutant. This research was funded in part by the Austrian Science Fund (FWF) (10.55776/P32161, 10.55776/P34907, 10.55776/DOC82 to DT, and 10.55776/P36187 to OS), by a Lipotype lipidomics excellence award (LEA 2019) to OS, by a Luxembourg National Research Fund (FNR): Grant #13571826 to YW, and by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 847681 (to KRL). For open access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission.","article_number":"9257","volume":15,"publication_identifier":{"eissn":["2041-1723"]},"OA_type":"gold","OA_place":"publisher","quality_controlled":"1","publication_status":"published","article_type":"original","author":[{"last_name":"Weyer","full_name":"Weyer, Yannick","first_name":"Yannick"},{"last_name":"Schwabl","first_name":"Sinead I.","full_name":"Schwabl, Sinead I."},{"first_name":"Xuechen","full_name":"Tang, Xuechen","last_name":"Tang"},{"last_name":"Purwar","full_name":"Purwar, Astha","first_name":"Astha"},{"last_name":"Siegmann","first_name":"Konstantin","full_name":"Siegmann, Konstantin"},{"full_name":"Ruepp, Angela","first_name":"Angela","last_name":"Ruepp"},{"first_name":"Theresia","full_name":"Dunzendorfer-Matt, Theresia","last_name":"Dunzendorfer-Matt"},{"full_name":"Widerin, Michael A.","first_name":"Michael A.","last_name":"Widerin"},{"last_name":"Niedrist","full_name":"Niedrist, Veronika","first_name":"Veronika"},{"last_name":"Mutsters","first_name":"Noa J.M.","full_name":"Mutsters, Noa J.M."},{"last_name":"Tettamanti","full_name":"Tettamanti, Maria G.","first_name":"Maria G."},{"id":"caffa136-9669-11ed-9092-ceac12ac9c05","first_name":"Sabine","full_name":"Weys, Sabine","last_name":"Weys"},{"last_name":"Sarg","full_name":"Sarg, Bettina","first_name":"Bettina"},{"first_name":"Leopold","full_name":"Kremser, Leopold","last_name":"Kremser"},{"full_name":"Liedl, Klaus R.","first_name":"Klaus R.","last_name":"Liedl"},{"full_name":"Schmidt, Oliver","first_name":"Oliver","last_name":"Schmidt"},{"last_name":"Teis","full_name":"Teis, David","first_name":"David"}],"ddc":["570"],"article_processing_charge":"Yes","oa":1,"year":"2024","month":"12","intvolume":"        15","oa_version":"Published Version","pmid":1,"date_updated":"2026-03-05T11:20:12Z","title":"The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi","file_date_updated":"2025-01-22T14:36:33Z","abstract":[{"lang":"eng","text":"The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex uses its rhomboid pseudo-protease subunit, Dsc2, to assess the hydrophobic length of α-helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex likely interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation. Some Dsc substrates will be extracted by Cdc48 for endosome and Golgi associated proteasomal degradation (EGAD), while others will undergo ESCRT dependent vacuolar degradation. Some substrates are degraded by both, EGAD- or ESCRT pathways. The accumulation of Dsc substrates entails a specific increase in glycerophospholipids with shorter and asymmetric fatty acyl chains. Hence, the Dsc complex mediates the selective degradation of orphaned proteins at the sorting center of cells, which prevents their spreading across other organelles and thereby preserves cellular membrane protein and lipid composition."}],"publisher":"Springer Nature","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41467-024-53676-6","type":"journal_article","status":"public","_id":"18522","external_id":{"isi":["001345548100007"],"pmid":["39461958"]},"fulldoi":"https://doi.org/10.1038/s41467-024-53676-6","isi":1,"file":[{"file_name":"2024_NatureComm_Weyer.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"18870","date_created":"2025-01-22T14:36:33Z","relation":"main_file","creator":"dernst","success":1,"file_size":5634494,"date_updated":"2025-01-22T14:36:33Z","checksum":"32c986fc3babec999c03a5c043310f40"}],"language":[{"iso":"eng"}],"date_published":"2024-12-01T00:00:00Z","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"doi":"10.1093/mnras/stae2307","publisher":"Oxford University Press","DOAJ_listed":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","status":"public","_id":"18523","date_updated":"2025-09-08T14:40:22Z","page":"3155-3175","file_date_updated":"2024-11-12T07:17:26Z","abstract":[{"text":"Recent observations from the EIGER JWST program have measured for the first time the quasar–galaxy cross-correlation function at z ≈ 6. The autocorrelation function of faint z ≈ 6 quasars was also recently estimated. These measurements provide key insights into the properties of quasars and galaxies at high redshift and their relation with the host dark matter haloes. In this work, we interpret these data building upon an empirical quasar population model that has been applied successfully to quasar clustering and demographic measurements at z ≈ 2–4. We use a new, large-volume N-body simulation with more than a trillion particles, FLAMINGO-10k, to model quasars and galaxies simultaneously. We successfully reproduce observations of z ≈ 6 quasars and galaxies (i.e. their clustering properties and luminosity functions), and infer key quantities such as their luminosity–halo mass relation, the mass function of their host haloes, and their duty cycle/occupation fraction. Our key findings\r\nare (i) quasars reside on average in ≈ 1012.5 M haloes (corresponding to ≈ 5σ fluctuations in the initial conditions of the linear density field), but the distribution of host halo masses is quite broad; (ii) the duty cycle of (UV-bright) quasar activity is relatively low (≈ 1 per cent); (iii) galaxies (that are bright in [O III]) live in much smaller haloes (≈ 1010.9 M) and have a larger duty cycle (occupation fraction) of ≈ 13 per cent. Finally, we focus on the inferred properties of quasars and present a homogeneous analysis of their evolution with redshift. The picture that emerges reveals a strong evolution of the host halo mass and duty cycle of quasars at z ≈ 2–6, and calls for new investigations of the role of quasar activity across cosmic time.","lang":"eng"}],"title":"A unified model for the clustering of quasars and galaxies at z ≈ 6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file":[{"checksum":"9ea6285dd1d04d7a9e7b40a4c9e11edb","date_updated":"2024-11-12T07:17:26Z","file_size":2954312,"success":1,"creator":"dernst","relation":"main_file","date_created":"2024-11-12T07:17:26Z","file_id":"18542","access_level":"open_access","file_name":"2024_MonthlyNRoyalAstronSoc_Pizzati.pdf","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.1093/mnras/stae2307","isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["001335663900008"]},"day":"01","date_published":"2024-11-01T00:00:00Z","acknowledgement":"We are grateful to Junya Arita and the SHELLQs team for sharing their data on the quasar autocorrelation function and to Jan-Torge Schindler for discussion on the QLF. We acknowledge helpful conversations with the ENIGMA group at UC Santa Barbara and Leiden University. EP is grateful to Rob McGibbon and Victor Forouhar Moreno for help with the simulation outputs, and to Timo Kist, Jiamu Huang, and Vikram Khaire for comments on an early version of the manuscript. JFH and EP acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 885301). This work is partly supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 860744 (BiD4BESt). FW acknowledges support from NSF grant AST-2308258. This work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Director’s Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded\r\nDiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University, and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure.","OA_type":"gold","OA_place":"publisher","quality_controlled":"1","volume":534,"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"has_accepted_license":"1","citation":{"ama":"Pizzati E, Hennawi JF, Schaye J, et al. A unified model for the clustering of quasars and galaxies at z ≈ 6. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;534(4):3155-3175. doi:<a href=\"https://doi.org/10.1093/mnras/stae2307\">10.1093/mnras/stae2307</a>","mla":"Pizzati, Elia, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 4, Oxford University Press, 2024, pp. 3155–75, doi:<a href=\"https://doi.org/10.1093/mnras/stae2307\">10.1093/mnras/stae2307</a>.","ista":"Pizzati E, Hennawi JF, Schaye J, Schaller M, Eilers AC, Wang F, Frenk CS, Elbers W, Helly JC, Mackenzie R, Matthee JJ, Bordoloi R, Kashino D, Naidu RP, Yue M. 2024. A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. 534(4), 3155–3175.","chicago":"Pizzati, Elia, Joseph F. Hennawi, Joop Schaye, Matthieu Schaller, Anna Christina Eilers, Feige Wang, Carlos S. Frenk, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stae2307\">https://doi.org/10.1093/mnras/stae2307</a>.","apa":"Pizzati, E., Hennawi, J. F., Schaye, J., Schaller, M., Eilers, A. C., Wang, F., … Yue, M. (2024). A unified model for the clustering of quasars and galaxies at z ≈ 6. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stae2307\">https://doi.org/10.1093/mnras/stae2307</a>","ieee":"E. Pizzati <i>et al.</i>, “A unified model for the clustering of quasars and galaxies at z ≈ 6,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 4. Oxford University Press, pp. 3155–3175, 2024.","short":"E. Pizzati, J.F. Hennawi, J. Schaye, M. Schaller, A.C. Eilers, F. Wang, C.S. Frenk, W. Elbers, J.C. Helly, R. Mackenzie, J.J. Matthee, R. Bordoloi, D. Kashino, R.P. Naidu, M. Yue, Monthly Notices of the Royal Astronomical Society 534 (2024) 3155–3175."},"publication":"Monthly Notices of the Royal Astronomical Society","department":[{"_id":"JoMa"}],"scopus_import":"1","date_created":"2024-11-10T23:01:58Z","article_processing_charge":"Yes","oa":1,"year":"2024","intvolume":"       534","oa_version":"Published Version","issue":"4","month":"11","article_type":"original","publication_status":"published","author":[{"full_name":"Pizzati, Elia","first_name":"Elia","last_name":"Pizzati"},{"last_name":"Hennawi","first_name":"Joseph F.","full_name":"Hennawi, Joseph F."},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"first_name":"Matthieu","full_name":"Schaller, Matthieu","last_name":"Schaller"},{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"last_name":"Wang","full_name":"Wang, Feige","first_name":"Feige"},{"full_name":"Frenk, Carlos S.","first_name":"Carlos S.","last_name":"Frenk"},{"last_name":"Elbers","first_name":"Willem","full_name":"Elbers, Willem"},{"first_name":"John C.","full_name":"Helly, John C.","last_name":"Helly"},{"full_name":"Mackenzie, Ruari","first_name":"Ruari","last_name":"Mackenzie"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee"},{"first_name":"Rongmon","full_name":"Bordoloi, Rongmon","last_name":"Bordoloi"},{"full_name":"Kashino, Daichi","first_name":"Daichi","last_name":"Kashino"},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"last_name":"Yue","first_name":"Minghao","full_name":"Yue, Minghao"}],"ddc":["520"]},{"status":"public","_id":"18545","type":"journal_article","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","doi":"10.1038/s41467-024-53418-8","title":"Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles","abstract":[{"lang":"eng","text":"Clinical implementation of therapeutic genome editing relies on efficient in vivo delivery and the safety of CRISPR-Cas tools. Previously, we identified PsCas9 as a Type II-B family enzyme capable of editing mouse liver genome upon adenoviral delivery without detectable off-targets and reduced chromosomal translocations. Yet, its efficacy remains insufficient with non-viral delivery, a common challenge for many Cas9 orthologues. Here, we sought to redesign PsCas9 for in vivo editing using lipid nanoparticles. We solve the PsCas9 ribonucleoprotein structure with cryo-EM and characterize it biochemically, providing a basis for its rational engineering. Screening over numerous guide RNA and protein variants lead us to develop engineered PsCas9 (ePsCas9) with up to 20-fold increased activity across various targets and preserved safety advantages. We apply the same design principles to boost the activity of FnCas9, an enzyme phylogenetically relevant to PsCas9. Remarkably, a single administration of mRNA encoding ePsCas9 and its guide formulated with lipid nanoparticles results in high levels of editing in the Pcsk9 gene in mouse liver, a clinically relevant target for hypercholesterolemia treatment. Collectively, our findings introduce ePsCas9 as a highly efficient, and precise tool for therapeutic genome editing, in addition to the engineering strategy applicable to other Cas9 orthologues."}],"file_date_updated":"2024-11-12T10:18:32Z","date_updated":"2024-11-13T08:19:50Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"07","date_published":"2024-11-07T00:00:00Z","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41467-024-53418-8","file":[{"checksum":"dcfadc806f4144d065eb8e2032554782","date_updated":"2024-11-12T10:18:32Z","file_size":2967001,"creator":"jbravo","success":1,"relation":"main_file","date_created":"2024-11-12T10:18:32Z","file_id":"18546","access_level":"open_access","file_name":"s41467-024-53418-8.pdf","content_type":"application/pdf"}],"volume":15,"publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","OA_place":"publisher","OA_type":"gold","article_number":"9173","date_created":"2024-11-12T10:18:04Z","scopus_import":"1","publication":"Nature Communications","citation":{"short":"D. Degtev, J.P.K. Bravo, A. Emmanouilidi, A. Zdravković, O.K. Choong, J. Liz Touza, N. Selfjord, I. Weisheit, M. Francescatto, P. Akcakaya, M. Porritt, M. Maresca, D. Taylor, G. Sienski, Nature Communications 15 (2024).","apa":"Degtev, D., Bravo, J. P. K., Emmanouilidi, A., Zdravković, A., Choong, O. K., Liz Touza, J., … Sienski, G. (2024). Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53418-8\">https://doi.org/10.1038/s41467-024-53418-8</a>","ieee":"D. Degtev <i>et al.</i>, “Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Degtev, Dmitrii, Jack Peter Kelly Bravo, Aikaterini Emmanouilidi, Aleksandar Zdravković, Oi Kuan Choong, Julia Liz Touza, Niklas Selfjord, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53418-8\">https://doi.org/10.1038/s41467-024-53418-8</a>.","ista":"Degtev D, Bravo JPK, Emmanouilidi A, Zdravković A, Choong OK, Liz Touza J, Selfjord N, Weisheit I, Francescatto M, Akcakaya P, Porritt M, Maresca M, Taylor D, Sienski G. 2024. Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. Nature Communications. 15, 9173.","ama":"Degtev D, Bravo JPK, Emmanouilidi A, et al. Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53418-8\">10.1038/s41467-024-53418-8</a>","mla":"Degtev, Dmitrii, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.” <i>Nature Communications</i>, vol. 15, 9173, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53418-8\">10.1038/s41467-024-53418-8</a>."},"has_accepted_license":"1","extern":"1","month":"11","oa_version":"Published Version","intvolume":"        15","year":"2024","oa":1,"article_processing_charge":"Yes","ddc":["572"],"author":[{"first_name":"Dmitrii","full_name":"Degtev, Dmitrii","last_name":"Degtev"},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","first_name":"Jack Peter Kelly","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo"},{"last_name":"Emmanouilidi","full_name":"Emmanouilidi, Aikaterini","first_name":"Aikaterini"},{"full_name":"Zdravković, Aleksandar","first_name":"Aleksandar","last_name":"Zdravković"},{"full_name":"Choong, Oi Kuan","first_name":"Oi Kuan","last_name":"Choong"},{"last_name":"Liz Touza","first_name":"Julia","full_name":"Liz Touza, Julia"},{"full_name":"Selfjord, Niklas","first_name":"Niklas","last_name":"Selfjord"},{"last_name":"Weisheit","first_name":"Isabel","full_name":"Weisheit, Isabel"},{"full_name":"Francescatto, Margherita","first_name":"Margherita","last_name":"Francescatto"},{"last_name":"Akcakaya","full_name":"Akcakaya, Pinar","first_name":"Pinar"},{"last_name":"Porritt","full_name":"Porritt, Michelle","first_name":"Michelle"},{"last_name":"Maresca","first_name":"Marcello","full_name":"Maresca, Marcello"},{"first_name":"David","full_name":"Taylor, David","last_name":"Taylor"},{"first_name":"Grzegorz","full_name":"Sienski, Grzegorz","last_name":"Sienski"}],"publication_status":"published","article_type":"original"},{"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","article_number":"282","OA_type":"hybrid","arxiv":1,"OA_place":"publisher","quality_controlled":"1","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"volume":405,"related_material":{"record":[{"id":"20575","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","corr_author":"1","citation":{"chicago":"Erdös, László, and Volodymyr Riabov. “Eigenstate Thermalization Hypothesis for Wigner-Type Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00220-024-05143-y\">https://doi.org/10.1007/s00220-024-05143-y</a>.","apa":"Erdös, L., &#38; Riabov, V. (2024). Eigenstate Thermalization Hypothesis for Wigner-type matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-024-05143-y\">https://doi.org/10.1007/s00220-024-05143-y</a>","ieee":"L. Erdös and V. Riabov, “Eigenstate Thermalization Hypothesis for Wigner-type matrices,” <i>Communications in Mathematical Physics</i>, vol. 405, no. 12. Springer Nature, 2024.","short":"L. Erdös, V. Riabov, Communications in Mathematical Physics 405 (2024).","mla":"Erdös, László, and Volodymyr Riabov. “Eigenstate Thermalization Hypothesis for Wigner-Type Matrices.” <i>Communications in Mathematical Physics</i>, vol. 405, no. 12, 282, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00220-024-05143-y\">10.1007/s00220-024-05143-y</a>.","ama":"Erdös L, Riabov V. Eigenstate Thermalization Hypothesis for Wigner-type matrices. <i>Communications in Mathematical Physics</i>. 2024;405(12). doi:<a href=\"https://doi.org/10.1007/s00220-024-05143-y\">10.1007/s00220-024-05143-y</a>","ista":"Erdös L, Riabov V. 2024. Eigenstate Thermalization Hypothesis for Wigner-type matrices. Communications in Mathematical Physics. 405(12), 282."},"publication":"Communications in Mathematical Physics","scopus_import":"1","department":[{"_id":"LaEr"}],"date_created":"2024-11-17T23:01:46Z","article_processing_charge":"Yes (via OA deal)","oa":1,"year":"2024","issue":"12","intvolume":"       405","oa_version":"Published Version","month":"12","article_type":"original","publication_status":"published","author":[{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","first_name":"Volodymyr","full_name":"Riabov, Volodymyr","last_name":"Riabov"}],"ddc":["510"],"doi":"10.1007/s00220-024-05143-y","publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","_id":"18554","status":"public","date_updated":"2026-04-07T12:32:19Z","pmid":1,"file_date_updated":"2024-11-18T08:15:07Z","abstract":[{"lang":"eng","text":"We prove the Eigenstate Thermalization Hypothesis for general Wigner-type matrices in the bulk of the self-consistent spectrum, with optimal control on the fluctuations for obs ervables of arbitrary rank. As the main technical ingredient, we prove rank-uniform optimal local laws for one and two resolvents of a Wigner-type matrix with regular observables. Our results hold under very general conditions on the variance profile, even allowing many vanishing entries, demonstrating that Eigenstate Thermalization occurs robustly across a diverse class of random matrix ensembles, for which the underlying quantum system has a non-trivial spatial structure."}],"title":"Eigenstate Thermalization Hypothesis for Wigner-type matrices","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","file_name":"2024_CommMathPhysics_Erdoes.pdf","file_id":"18562","access_level":"open_access","creator":"dernst","success":1,"relation":"main_file","date_created":"2024-11-18T08:15:07Z","checksum":"c9ae0ea195bd39b8b3a630d492fb00dc","date_updated":"2024-11-18T08:15:07Z","file_size":1426046}],"fulldoi":"https://doi.org/10.1007/s00220-024-05143-y","isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["001348943900004"],"pmid":["39526190"],"arxiv":["2403.10359"]},"date_published":"2024-12-01T00:00:00Z","day":"01"}]