[{"volume":293,"oa_version":"Published Version","page":"11:1-11:19","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"title":"Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds","publication_status":"published","file_date_updated":"2024-06-25T11:47:26Z","quality_controlled":"1","oa":1,"ddc":["516"],"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       293","has_accepted_license":"1","author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"full_name":"Kourimska, Hana","first_name":"Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091","last_name":"Kourimska"},{"id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","last_name":"Fillmore","full_name":"Fillmore, Christopher D","first_name":"Christopher D"},{"last_name":"Ghosh","id":"ee449b28-344d-11ef-a6d5-9ca430e9e9ff","first_name":"Ishika","full_name":"Ghosh, Ishika"},{"last_name":"Lieutier","full_name":"Lieutier, André","first_name":"André"},{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","first_name":"Elizabeth R"},{"orcid":"0000-0002-7472-2220","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","full_name":"Wintraecken, Mathijs"}],"year":"2024","month":"06","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publication_identifier":{"isbn":["9783959773164"],"eissn":["1868-8969"]},"type":"conference","day":"06","publication":"40th International Symposium on Computational Geometry","alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"success":1,"access_level":"open_access","checksum":"6a2ddc8b51aa58f197a8b294750f1f8d","date_created":"2024-06-25T11:47:26Z","file_id":"17171","content_type":"application/pdf","date_updated":"2024-06-25T11:47:26Z","file_size":20886142,"creator":"cfillmor","relation":"main_file","file_name":"LIPIcs.SoCG.2024.11.pdf"}],"date_published":"2024-06-06T00:00:00Z","project":[{"grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"},{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"doi":"10.4230/LIPIcs.SoCG.2024.11","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.","ec_funded":1,"external_id":{"arxiv":["2206.10485"]},"date_created":"2024-06-25T11:45:58Z","_id":"17170","citation":{"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>.","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.","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.","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.","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>.","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>","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>"},"article_processing_charge":"No","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"}],"scopus_import":"1","date_updated":"2025-04-15T07:16:57Z","conference":{"location":"Athens, Greece","start_date":"2024-06-11","name":"SoCG: Symposium on Computational Geometry","end_date":"2024-06-14"}},{"abstract":[{"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","lang":"eng"}],"date_updated":"2025-12-30T10:54:11Z","scopus_import":"1","article_type":"original","external_id":{"pmid":["38935508"]},"ec_funded":1,"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).","date_created":"2024-06-30T22:01:04Z","doi":"10.1016/j.xpro.2024.103157","article_processing_charge":"Yes","_id":"17187","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>.","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.","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>","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>.","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (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>"},"day":"20","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_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"}],"article_number":"103157","date_published":"2024-09-20T00:00:00Z","publication":"STAR Protocols","file":[{"date_created":"2025-01-09T12:12:40Z","file_id":"18809","content_type":"application/pdf","success":1,"access_level":"open_access","checksum":"d8a8cdba82a394e731aa699ace1ae433","file_name":"2024_STARProtoc_Cheung.pdf","date_updated":"2025-01-09T12:12:40Z","file_size":5186071,"relation":"main_file","creator":"dernst"}],"publisher":"Elsevier","year":"2024","month":"09","department":[{"_id":"SiHi"}],"publication_identifier":{"eissn":["2666-1667"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"type":"journal_article","OA_type":"gold","has_accepted_license":"1","intvolume":"         5","issue":"3","APC_amount":"804 EUR","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen","first_name":"Carmen"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"pmid":1,"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"OA_place":"publisher","status":"public","ddc":["570"],"publication_status":"published","file_date_updated":"2025-01-09T12:12:40Z","quality_controlled":"1","oa_version":"Published Version","volume":5,"corr_author":"1","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2024","month":"09","department":[{"_id":"MoHe"}],"publication_identifier":{"issn":["0004-3702"]},"type":"journal_article","OA_type":"hybrid","day":"01","article_number":"104171","date_published":"2024-09-01T00:00:00Z","publication":"Artificial Intelligence","file":[{"file_name":"2024_ArtificialIntelligence_Braun.pdf","file_size":772226,"date_updated":"2025-01-09T10:45:24Z","creator":"dernst","relation":"main_file","date_created":"2025-01-09T10:45:24Z","file_id":"18806","content_type":"application/pdf","success":1,"access_level":"open_access","checksum":"f02a56bc7ea88f41fcc68968e4ceddf3"}],"publisher":"Elsevier","article_type":"original","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).","external_id":{"isi":["001260448100001"],"arxiv":["2203.01084"]},"date_created":"2024-06-30T22:01:05Z","doi":"10.1016/j.artint.2024.104171","article_processing_charge":"Yes (in subscription journal)","_id":"17188","citation":{"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>","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>.","short":"P. Braun, N. Hahn, M. Hoefer, C. Schecker, Artificial Intelligence 334 (2024).","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>.","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>","ieee":"P. Braun, N. Hahn, M. Hoefer, and C. Schecker, “Delegated online search,” <i>Artificial Intelligence</i>, vol. 334. Elsevier, 2024."},"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."}],"date_updated":"2025-09-08T08:00:42Z","scopus_import":"1","oa_version":"Published Version","volume":334,"arxiv":1,"corr_author":"1","title":"Delegated online search","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","file_date_updated":"2025-01-09T10:45:24Z","quality_controlled":"1","oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","isi":1,"ddc":["000"],"status":"public","has_accepted_license":"1","intvolume":"       334","author":[{"first_name":"Pirmin","full_name":"Braun, Pirmin","last_name":"Braun"},{"full_name":"Hahn, Niklas","first_name":"Niklas","id":"0a01c7b2-b823-11ed-9928-cc3f874f9ffd","last_name":"Hahn"},{"last_name":"Hoefer","first_name":"Martin","full_name":"Hoefer, Martin"},{"last_name":"Schecker","full_name":"Schecker, Conrad","first_name":"Conrad"}]},{"publication":"Nature Astronomy","publisher":"Springer Nature","date_published":"2024-09-01T00:00:00Z","project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"day":"01","publication_identifier":{"eissn":["2397-3366"]},"OA_type":"closed access","type":"journal_article","year":"2024","month":"09","department":[{"_id":"LiBu"}],"scopus_import":"1","date_updated":"2025-09-08T08:04:56Z","abstract":[{"lang":"eng","text":"Supergranules, which are solar flow features with a lateral scale of 30,000–40,000 km and a lifetime of ~24 h, form a prominent component of the Sun’s convective spectrum. However, their internal flows, which can be probed only by helioseismology, are not well understood. We analyse dopplergrams recorded by the Solar Dynamics Observatory satellite to identify and characterize ~23,000 supergranules. We find that the vertical flows peak at a depth of ~10,000 km, and remain invariant over the full range of lateral supergranular scales, contrary to numerical predictions. We also infer that, within the local seismic resolution (≳5,000 km), downflows are ~40% weaker than upflows, indicating an apparent mass-flux imbalance. This may imply that the descending flows also comprise plumes, which maintain the mass balance but are simply too small to be detected by seismic waves. These results challenge the widely used mixing-length description of solar convection."}],"_id":"17189","citation":{"chicago":"Hanson, Chris S., Srijan B Das, Prasad Mani, Shravan Hanasoge, and Katepalli R. Sreenivasan. “Supergranular-Scale Solar Convection Not Explained by Mixing-Length Theory.” <i>Nature Astronomy</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41550-024-02304-w\">https://doi.org/10.1038/s41550-024-02304-w</a>.","short":"C.S. Hanson, S.B. Das, P. Mani, S. Hanasoge, K.R. Sreenivasan, Nature Astronomy 8 (2024) 1088–1101.","ieee":"C. S. Hanson, S. B. Das, P. Mani, S. Hanasoge, and K. R. Sreenivasan, “Supergranular-scale solar convection not explained by mixing-length theory,” <i>Nature Astronomy</i>, vol. 8. Springer Nature, pp. 1088–1101, 2024.","ama":"Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. Supergranular-scale solar convection not explained by mixing-length theory. <i>Nature Astronomy</i>. 2024;8:1088-1101. doi:<a href=\"https://doi.org/10.1038/s41550-024-02304-w\">10.1038/s41550-024-02304-w</a>","mla":"Hanson, Chris S., et al. “Supergranular-Scale Solar Convection Not Explained by Mixing-Length Theory.” <i>Nature Astronomy</i>, vol. 8, Springer Nature, 2024, pp. 1088–101, doi:<a href=\"https://doi.org/10.1038/s41550-024-02304-w\">10.1038/s41550-024-02304-w</a>.","ista":"Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. 2024. Supergranular-scale solar convection not explained by mixing-length theory. Nature Astronomy. 8, 1088–1101.","apa":"Hanson, C. S., Das, S. B., Mani, P., Hanasoge, S., &#38; Sreenivasan, K. R. (2024). Supergranular-scale solar convection not explained by mixing-length theory. <i>Nature Astronomy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41550-024-02304-w\">https://doi.org/10.1038/s41550-024-02304-w</a>"},"article_processing_charge":"No","doi":"10.1038/s41550-024-02304-w","article_type":"original","ec_funded":1,"external_id":{"isi":["001254181700001"]},"acknowledgement":"We thank F. J. Simons for the codes for computing Slepian functions,\r\nM. Rempel and R. Cameron for their insights into solar convection, J.\r\nW. Lord for the numerical simulations and J. Naranjo for his help with\r\nthe NYUAD NetDRMS system. This research was carried out with the\r\nHigh Performance Computing resources at NYUAD. The datasets were\r\nprepared in the data centre at the Center for Space Science of NYUAD.\r\nThis research is based upon work supported by Tamkeen under the\r\nNYUAD Research Institute (Grant Nos G1502 and CASS to C.S.H,\r\nS.H. and K.R.S.). S.H. acknowledges funding from the Department\r\nof Atomic Energy, India. K.R.S. and S.H. acknowledge support from\r\nthe Ofice of Sponsored Research of King Abdullah University of\r\nScience and Technology (Award No. OSR-CRG2020-4342). S.B.D.\r\nacknowledges funding from the Elisabeth H. and F. A. Dahlen Award\r\n2022 by the Department of Geosciences, Princeton University. S.B.D.\r\nalso acknowledges funding from the European Union’s Horizon 2020\r\nresearch and innovation programme under a Marie Skłodowska-Curie\r\ngrant (Grant Agreement No. 101034413). Some data products were\r\nprocessed and downloaded from the German Data Center for SDO,\r\nwhich is funded by the German Aerospace Center (DLR Grant No.\r\n500L1701).","date_created":"2024-06-30T22:01:05Z","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"page":"1088-1101","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Supergranular-scale solar convection not explained by mixing-length theory","volume":8,"oa_version":"None","author":[{"last_name":"Hanson","full_name":"Hanson, Chris S.","first_name":"Chris S."},{"id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","orcid":"0000-0003-0896-7972","last_name":"Das","full_name":"Das, Srijan B","first_name":"Srijan B"},{"full_name":"Mani, Prasad","first_name":"Prasad","last_name":"Mani"},{"last_name":"Hanasoge","full_name":"Hanasoge, Shravan","first_name":"Shravan"},{"first_name":"Katepalli R.","full_name":"Sreenivasan, Katepalli R.","last_name":"Sreenivasan"}],"intvolume":"         8","status":"public","isi":1},{"_id":"17190","citation":{"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>","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.","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>.","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>.","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>","short":"H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, M. Wintraecken, SIAM Journal on Discrete Mathematics 38 (2024) 1784–1807."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.01077","open_access":"1"}],"article_processing_charge":"No","doi":"10.1137/22M1489071","article_type":"original","ec_funded":1,"external_id":{"isi":["001292728600001"],"arxiv":["2204.01077"]},"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.","date_created":"2024-06-30T22:01:05Z","scopus_import":"1","date_updated":"2025-09-08T08:06:04Z","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."}],"publication_identifier":{"issn":["0895-4801"]},"type":"journal_article","year":"2024","month":"06","department":[{"_id":"HeEd"}],"publication":"SIAM Journal on Discrete Mathematics","publisher":"Society for Industrial and Applied Mathematics","date_published":"2024-06-07T00:00:00Z","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses","grant_number":"M03073"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342"}],"day":"07","status":"public","isi":1,"oa":1,"author":[{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Garber","first_name":"Alexey","full_name":"Garber, Alexey"},{"first_name":"Mohadese","full_name":"Ghafaris, Mohadese","last_name":"Ghafaris"},{"first_name":"Teresa","full_name":"Heiss, Teresa","last_name":"Heiss","orcid":"0000-0002-1780-2689","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saghafiant","full_name":"Saghafiant, Morteza","first_name":"Morteza"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","first_name":"Mathijs"}],"intvolume":"        38","issue":"2","language":[{"iso":"eng"}],"page":"1784-1807","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"title":"Brillouin zones of integer lattices and their perturbations","corr_author":"1","volume":38,"oa_version":"Preprint","quality_controlled":"1","publication_status":"published"},{"publication_status":"published","quality_controlled":"1","oa_version":"None","volume":25,"title":"Nuclear squeezing wakes up dendritic cells","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"page":"1131–1132 ","intvolume":"        25","author":[{"id":"d993a7b2-292f-11ed-aaac-fb045a912e31","orcid":"0000-0002-2253-8771","last_name":"Lembo","full_name":"Lembo, Sergio","first_name":"Sergio"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"}],"pmid":1,"isi":1,"status":"public","day":"21","date_published":"2024-06-21T00:00:00Z","publisher":"Springer Nature","publication":"Nature Immunology","department":[{"_id":"MiSi"}],"month":"06","year":"2024","type":"journal_article","publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"abstract":[{"text":"Dendritic cells migrate to and from lymph nodes in response to chemokine gradients.Data now show that steady-state migration of these cells can be triggered by a mechanosensitive pathway.","lang":"eng"}],"date_updated":"2025-09-08T08:06:56Z","scopus_import":"1","date_created":"2024-06-30T22:01:05Z","external_id":{"pmid":["38907047"],"isi":["001251509300001"]},"article_type":"letter_note","doi":"10.1038/s41590-024-01881-2","article_processing_charge":"No","citation":{"chicago":"Lembo, Sergio, and Michael K Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” <i>Nature Immunology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41590-024-01881-2\">https://doi.org/10.1038/s41590-024-01881-2</a>.","short":"S. Lembo, M.K. Sixt, Nature Immunology 25 (2024) 1131–1132.","ama":"Lembo S, Sixt MK. Nuclear squeezing wakes up dendritic cells. <i>Nature Immunology</i>. 2024;25:1131–1132. doi:<a href=\"https://doi.org/10.1038/s41590-024-01881-2\">10.1038/s41590-024-01881-2</a>","ieee":"S. Lembo and M. K. Sixt, “Nuclear squeezing wakes up dendritic cells,” <i>Nature Immunology</i>, vol. 25. Springer Nature, pp. 1131–1132, 2024.","ista":"Lembo S, Sixt MK. 2024. Nuclear squeezing wakes up dendritic cells. Nature Immunology. 25, 1131–1132.","mla":"Lembo, Sergio, and Michael K. Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” <i>Nature Immunology</i>, vol. 25, Springer Nature, 2024, pp. 1131–1132, doi:<a href=\"https://doi.org/10.1038/s41590-024-01881-2\">10.1038/s41590-024-01881-2</a>.","apa":"Lembo, S., &#38; Sixt, M. K. (2024). Nuclear squeezing wakes up dendritic cells. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-024-01881-2\">https://doi.org/10.1038/s41590-024-01881-2</a>"},"_id":"17191"},{"year":"2024","department":[{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"JoFi"}],"month":"07","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"type":"research_data","day":"04","project":[{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"_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_published":"2024-07-04T00:00:00Z","publisher":"Institute of Science and Technology Austria","file":[{"checksum":"a9f640a0b72a92171353f3ea14406f0b","access_level":"open_access","success":1,"content_type":"application/octet-stream","file_id":"17197","date_created":"2024-07-04T10:01:51Z","creator":"osagi","relation":"main_file","date_updated":"2024-07-04T10:01:51Z","file_size":1960182,"file_name":"GeGatemon_DataAnalysis.ipynb"},{"access_level":"open_access","checksum":"f0feec931233e8e845ade56165c1588f","success":1,"content_type":"application/vnd.openxmlformats-officedocument.presentationml.presentation","date_created":"2024-07-04T10:01:50Z","file_id":"17198","creator":"osagi","relation":"main_file","date_updated":"2024-07-04T10:01:50Z","file_size":34194,"file_name":"OlSa_Readme.pptx"},{"file_name":"Al_Transmon.zip","creator":"osagi","relation":"main_file","date_updated":"2024-07-04T10:11:16Z","file_size":72939292,"content_type":"application/x-zip-compressed","file_id":"17199","date_created":"2024-07-04T10:11:16Z","checksum":"92bb11e3a508d736d01ff0738a1172c7","access_level":"open_access","success":1},{"checksum":"871e96fe0ecc97581196e883045cd516","access_level":"open_access","success":1,"content_type":"application/x-zip-compressed","file_id":"17200","date_created":"2024-07-04T10:11:40Z","relation":"main_file","creator":"osagi","date_updated":"2024-07-04T10:11:40Z","file_size":465618029,"file_name":"Gatemon_RT_5nm_1.zip"},{"file_id":"17201","date_created":"2024-07-04T10:11:35Z","content_type":"application/x-zip-compressed","success":1,"checksum":"a3e141af90f0104b7269c8a72370848a","access_level":"open_access","file_name":"Gatemon_RT_5nm_2.zip","file_size":281503513,"date_updated":"2024-07-04T10:11:35Z","creator":"osagi","relation":"main_file"}],"date_created":"2024-07-04T10:14:34Z","acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. ","doi":"10.15479/AT:ISTA:17196","article_processing_charge":"No","_id":"17196","citation":{"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>.","short":"O. Sagi, (2024).","ieee":"O. Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and Technology Austria, 2024.","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>.","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>","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>"},"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."}],"date_updated":"2026-04-16T12:20:39Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17202"}]},"oa_version":"Published Version","title":"A gate-tunable transmon in planar Ge","corr_author":"1","contributor":[{"contributor_type":"project_member","first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","orcid":"0000-0002-2968-611X","last_name":"Crippa"},{"first_name":"Marco","contributor_type":"project_member","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini"},{"contributor_type":"project_member","first_name":"Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik"},{"last_name":"Baghumyan","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","first_name":"Levon","contributor_type":"project_member"},{"id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","last_name":"Fabris","contributor_type":"project_member","first_name":"Giorgio"},{"contributor_type":"project_member","first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor"},{"last_name":"Hassani","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Farid"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Johannes M"},{"last_name":"Calcaterra","contributor_type":"project_member","first_name":"Stefano"},{"first_name":"Daniel","contributor_type":"project_member","last_name":"Chrastina"},{"first_name":"Giovanni","contributor_type":"project_member","last_name":"Isella"},{"contributor_type":"supervisor","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","file_date_updated":"2024-07-04T10:11:40Z","oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530"],"status":"public","has_accepted_license":"1","author":[{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","full_name":"Sagi, Oliver","first_name":"Oliver"}]},{"abstract":[{"lang":"eng","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."}],"date_updated":"2026-06-10T07:58:34Z","scopus_import":"1","related_material":{"record":[{"id":"18568","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"17488"}]},"date_created":"2024-10-20T22:02:05Z","external_id":{"isi":["001336422500001"],"pmid":["39396050"]},"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_type":"original","doi":"10.1038/s41467-024-53173-w","article_processing_charge":"Yes","citation":{"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>.","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.","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.","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>.","short":"V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications 15 (2024).","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>","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>"},"_id":"18444","day":"12","date_published":"2024-10-12T00:00:00Z","project":[{"grant_number":"429960716","name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A"}],"article_number":"8830","file":[{"file_name":"2024_NatureComm_Pokusaeva.pdf","file_size":8276667,"date_updated":"2024-10-21T12:11:10Z","relation":"main_file","creator":"dernst","date_created":"2024-10-21T12:11:10Z","file_id":"18459","content_type":"application/pdf","success":1,"access_level":"open_access","checksum":"2af4d6e7364329107aa94d072d594ce0"}],"publisher":"Springer Nature","publication":"Nature Communications","month":"10","department":[{"_id":"MaJö"}],"year":"2024","type":"journal_article","OA_type":"gold","publication_identifier":{"eissn":["2041-1723"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"has_accepted_license":"1","intvolume":"        15","author":[{"full_name":"Pokusaeva, Victoria","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","orcid":"0000-0001-7660-444X"},{"full_name":"Satapathy, Roshan K","first_name":"Roshan K","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","last_name":"Satapathy","orcid":"0009-0006-2974-5075"},{"full_name":"Symonova, Olga","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947","last_name":"Symonova"},{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330"}],"APC_amount":"6828 EUR","oa":1,"pmid":1,"isi":1,"OA_place":"publisher","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","ddc":["570"],"file_date_updated":"2024-10-21T12:11:10Z","publication_status":"published","quality_controlled":"1","oa_version":"Published Version","DOAJ_listed":"1","volume":15,"corr_author":"1","title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}]},{"date_published":"2024-10-05T00:00:00Z","article_number":"8631","file":[{"file_name":"2024_NatureComm_Zupancic.pdf","date_updated":"2024-10-21T12:15:38Z","file_size":7215329,"creator":"dernst","relation":"main_file","date_created":"2024-10-21T12:15:38Z","file_id":"18460","content_type":"application/pdf","success":1,"access_level":"open_access","checksum":"03d6dd1b84efa24e9e9ede748d08764d"}],"publisher":"Springer Nature","publication":"Nature Communications","day":"05","OA_type":"gold","type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"RySh"}],"month":"10","year":"2024","date_updated":"2025-09-08T14:25:06Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus."}],"article_processing_charge":"Yes (via OA deal)","citation":{"short":"M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier, P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer, F. Clotman, T. Harkany, Nature Communications 15 (2024).","ieee":"M. Zupančič <i>et al.</i>, “Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>","chicago":"Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder, Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>.","ista":"Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F, Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.","mla":"Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>, vol. 15, 8631, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>.","apa":"Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier, L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>"},"_id":"18445","external_id":{"pmid":["39366958"],"isi":["001409493300014"]},"date_created":"2024-10-20T22:02:05Z","acknowledgement":"The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility, Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher (Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their technical assistance. C. elegans strains were provided by the National Bioresource Project for the nematode, Japan, and the CGC, with the latter being funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council (2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden, FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.), the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21, to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L). E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska Institute.","article_type":"original","doi":"10.1038/s41467-024-52762-z","quality_controlled":"1","file_date_updated":"2024-10-21T12:15:38Z","publication_status":"published","title":"Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa_version":"Published Version","PlanS_conform":"1","DOAJ_listed":"1","volume":15,"author":[{"first_name":"Maja","full_name":"Zupančič, Maja","last_name":"Zupančič"},{"first_name":"Erik","full_name":"Keimpema, Erik","last_name":"Keimpema"},{"full_name":"Tretiakov, Evgenii O.","first_name":"Evgenii O.","last_name":"Tretiakov"},{"first_name":"Stephanie J.","full_name":"Eder, Stephanie J.","last_name":"Eder"},{"last_name":"Lev","first_name":"Itamar","full_name":"Lev, Itamar"},{"full_name":"Englmaier, Lukas","first_name":"Lukas","last_name":"Englmaier"},{"last_name":"Bhandari","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","full_name":"Bhandari, Pradeep"},{"last_name":"Fietz","full_name":"Fietz, Simone A.","first_name":"Simone A."},{"first_name":"Wolfgang","full_name":"Härtig, Wolfgang","last_name":"Härtig"},{"last_name":"Renaux","full_name":"Renaux, Estelle","first_name":"Estelle"},{"last_name":"Villunger","full_name":"Villunger, Andreas","first_name":"Andreas"},{"last_name":"Hökfelt","first_name":"Tomas","full_name":"Hökfelt, Tomas"},{"last_name":"Zimmer","first_name":"Manuel","full_name":"Zimmer, Manuel"},{"last_name":"Clotman","full_name":"Clotman, Frédéric","first_name":"Frédéric"},{"last_name":"Harkany","full_name":"Harkany, Tibor","first_name":"Tibor"}],"has_accepted_license":"1","intvolume":"        15","isi":1,"OA_place":"publisher","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"status":"public","oa":1,"pmid":1},{"volume":386,"oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"corr_author":"1","title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","publication_status":"published","quality_controlled":"1","oa":1,"pmid":1,"status":"public","isi":1,"OA_place":"repository","intvolume":"       386","issue":"6718","author":[{"last_name":"Fabrèges","full_name":"Fabrèges, Dimitri","first_name":"Dimitri"},{"full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643"},{"full_name":"Moghe, Prachiti","first_name":"Prachiti","last_name":"Moghe"},{"first_name":"Alison","full_name":"Kickuth, Alison","last_name":"Kickuth"},{"first_name":"Takafumi","full_name":"Ichikawa, Takafumi","last_name":"Ichikawa"},{"last_name":"Iwatani","full_name":"Iwatani, Chizuru","first_name":"Chizuru"},{"last_name":"Tsukiyama","full_name":"Tsukiyama, Tomoyuki","first_name":"Tomoyuki"},{"last_name":"Daniel","first_name":"Nathalie","full_name":"Daniel, Nathalie"},{"first_name":"Julie","full_name":"Gering, Julie","last_name":"Gering"},{"full_name":"Stokkermans, Anniek","first_name":"Anniek","last_name":"Stokkermans"},{"last_name":"Wolny","full_name":"Wolny, Adrian","first_name":"Adrian"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"last_name":"Duranthon","first_name":"Véronique","full_name":"Duranthon, Véronique"},{"last_name":"Uhlman","first_name":"Virginie","full_name":"Uhlman, Virginie"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"last_name":"Hiiragi","full_name":"Hiiragi, Takashi","first_name":"Takashi"}],"month":"10","department":[{"_id":"EdHa"}],"year":"2024","type":"journal_article","OA_type":"green","publication_identifier":{"eissn":["1095-9203"]},"day":"11","publisher":"AAAS","publication":"Science","article_number":"eadh1145","date_published":"2024-10-11T00:00:00Z","doi":"10.1126/science.adh1145","external_id":{"pmid":["39388574"],"isi":["001422132300018"]},"date_created":"2024-10-20T22:02:06Z","acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","article_type":"original","main_file_link":[{"open_access":"1","url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf"}],"citation":{"apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>.","ieee":"D. Fabrèges <i>et al.</i>, “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” <i>Science</i>, vol. 386, no. 6718. AAAS, 2024.","short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. 2024;386(6718). doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>","chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>."},"_id":"18446","article_processing_charge":"No","abstract":[{"text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning.","lang":"eng"}],"scopus_import":"1","date_updated":"2025-09-08T14:22:13Z"},{"doi":"10.1109/OMN61224.2024.10685279","date_created":"2024-10-20T22:02:07Z","acknowledgement":"The authors acknowledge the financial support of the project HfPT – Health from Portugal, with the reference n.° C644937233-00000047, co-funded by Component C5 – Capitalisation and Business Innovation under the Portuguese Resilience and Recovery Plan, through the NextGenerationEU Fund.","external_id":{"isi":["001327768000060"]},"status":"public","_id":"18450","citation":{"apa":"Quintero, S., Relvas, M., Aranda, M., Nodal, F., Dieguez, L., &#38; Abalde-Cela, S. (2024). Portable Raman platform for SERS droplets microfludics. In <i>2024 International Conference on Optical MEMS and Nanophotonics</i>. San Sebastian, Spain: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">https://doi.org/10.1109/OMN61224.2024.10685279</a>","ieee":"S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, and S. Abalde-Cela, “Portable Raman platform for SERS droplets microfludics,” in <i>2024 International Conference on Optical MEMS and Nanophotonics</i>, San Sebastian, Spain, 2024.","ama":"Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. Portable Raman platform for SERS droplets microfludics. In: <i>2024 International Conference on Optical MEMS and Nanophotonics</i>. Institute of Electrical and Electronics Engineers; 2024. doi:<a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">10.1109/OMN61224.2024.10685279</a>","chicago":"Quintero, Sergio, Maria Relvas, Marta Aranda, Fernando Nodal, Lorena Dieguez, and Sara Abalde-Cela. “Portable Raman Platform for SERS Droplets Microfludics.” In <i>2024 International Conference on Optical MEMS and Nanophotonics</i>. Institute of Electrical and Electronics Engineers, 2024. <a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">https://doi.org/10.1109/OMN61224.2024.10685279</a>.","short":"S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, S. Abalde-Cela, in:, 2024 International Conference on Optical MEMS and Nanophotonics, Institute of Electrical and Electronics Engineers, 2024.","mla":"Quintero, Sergio, et al. “Portable Raman Platform for SERS Droplets Microfludics.” <i>2024 International Conference on Optical MEMS and Nanophotonics</i>, Institute of Electrical and Electronics Engineers, 2024, doi:<a href=\"https://doi.org/10.1109/OMN61224.2024.10685279\">10.1109/OMN61224.2024.10685279</a>.","ista":"Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. 2024. Portable Raman platform for SERS droplets microfludics. 2024 International Conference on Optical MEMS and Nanophotonics. OMN: Conference on Optical MEMS and Nanophotonics."},"isi":1,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"In this work we present the engineering of a portable platform for sensing SERS signals in droplets microfluidics. This system comprised not only the read-out platform but also a design for the microfluidic devices optimized to enhanced the obtained SERS signals."}],"scopus_import":"1","date_updated":"2025-09-08T14:19:49Z","author":[{"last_name":"Quintero","first_name":"Sergio","full_name":"Quintero, Sergio"},{"last_name":"Relvas","full_name":"Relvas, Maria","first_name":"Maria"},{"full_name":"Aranda, Marta","first_name":"Marta","last_name":"Aranda"},{"full_name":"Nodal, Fernando","first_name":"Fernando","id":"8ad43d5a-1ffe-11ee-8b67-8176f59de781","last_name":"Nodal","orcid":"0009-0006-4119-4376"},{"last_name":"Dieguez","first_name":"Lorena","full_name":"Dieguez, Lorena"},{"last_name":"Abalde-Cela","first_name":"Sara","full_name":"Abalde-Cela, Sara"}],"conference":{"name":"OMN: Conference on Optical MEMS and Nanophotonics","end_date":"2024-08-01","location":"San Sebastian, Spain","start_date":"2024-07-28"},"year":"2024","month":"09","department":[{"_id":"GradSch"}],"oa_version":"None","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798350384925"],"issn":["2160-5033"],"eissn":["2160-5041"]},"type":"conference","OA_type":"closed access","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Portable Raman platform for SERS droplets microfludics","publication_status":"published","day":"27","publication":"2024 International Conference on Optical MEMS and Nanophotonics","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","date_published":"2024-09-27T00:00:00Z"},{"ddc":["540"],"status":"public","OA_place":"publisher","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"pmid":1,"oa":1,"author":[{"full_name":"Zhou, Yu","first_name":"Yu","last_name":"Zhou"},{"last_name":"Shaukat","full_name":"Shaukat, Ahmed","first_name":"Ahmed"},{"last_name":"Seitsonen","full_name":"Seitsonen, Jani","first_name":"Jani"},{"id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0","last_name":"Rigoni","full_name":"Rigoni, Carlo","first_name":"Carlo"},{"last_name":"Timonen","first_name":"Jaakko V.I.","full_name":"Timonen, Jaakko V.I."},{"last_name":"Kostiainen","first_name":"Mauri A.","full_name":"Kostiainen, Mauri A."}],"intvolume":"        11","issue":"45","has_accepted_license":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Protein cage directed assembly of binary nanoparticle superlattices","volume":11,"DOAJ_listed":"1","oa_version":"Published Version","quality_controlled":"1","publication_status":"published","file_date_updated":"2025-01-13T09:16:25Z","_id":"18451","citation":{"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.","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>","short":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen, Advanced Science 11 (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>"},"article_processing_charge":"Yes","doi":"10.1002/advs.202408416","article_type":"original","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.","external_id":{"pmid":["39401426"],"isi":["001330745600001"]},"date_created":"2024-10-20T22:02:07Z","scopus_import":"1","date_updated":"2025-09-08T14:20:31Z","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."}],"publication_identifier":{"eissn":["2198-3844"]},"type":"journal_article","OA_type":"gold","year":"2024","department":[{"_id":"RaKl"}],"month":"12","publication":"Advanced Science","file":[{"file_id":"18834","date_created":"2025-01-13T09:16:25Z","content_type":"application/pdf","success":1,"checksum":"00451eeb2c9eecf1ff41ad243c793a51","access_level":"open_access","file_name":"2024_AdvancedScience_Zhou.pdf","file_size":7040083,"date_updated":"2025-01-13T09:16:25Z","creator":"dernst","relation":"main_file"}],"publisher":"Wiley","date_published":"2024-12-04T00:00:00Z","article_number":"2408416","day":"04"},{"quality_controlled":"1","file_date_updated":"2025-01-13T09:11:09Z","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"9259-9266","language":[{"iso":"eng"}],"title":"Response matching for generating materials and molecules","corr_author":"1","arxiv":1,"volume":20,"oa_version":"Published Version","author":[{"last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing"}],"intvolume":"        20","issue":"20","has_accepted_license":"1","ddc":["540"],"status":"public","isi":1,"OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"pmid":1,"publisher":"American Chemical Society","file":[{"file_id":"18832","date_created":"2025-01-13T09:11:09Z","content_type":"application/pdf","success":1,"checksum":"aca0011bba4846140809b5af583daa9a","access_level":"open_access","file_name":"2024_JCTC_Cheng.pdf","date_updated":"2025-01-13T09:11:09Z","file_size":4758251,"relation":"main_file","creator":"dernst"}],"publication":"Journal of Chemical Theory and Computation","date_published":"2024-10-22T00:00:00Z","day":"22","OA_type":"hybrid","type":"journal_article","publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]},"month":"10","department":[{"_id":"BiCh"}],"year":"2024","scopus_import":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/cace"}]},"date_updated":"2025-09-08T14:21:30Z","abstract":[{"text":"Diffusion models have recently emerged as powerful tools for the generation of new molecular and material structures. The key insight is that the noise in these models is related to the response of the atoms to displacement, and the denoising step is thus analogous to the geometry relaxation of atomistic systems starting from a random structure. Building on this, we present a generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching this response is closely related to score matching in diffusion models. Another important aspect of state-of-the-art diffusion models is the incorporation of physical symmetries such as translation, rotation, and periodicity. RM employs a machine learning interatomic potential and random structure search as the denoising model, inherently respecting these symmetries and exploiting the locality of atomic interactions. RM handles both molecules and bulk materials under the same framework. Its efficiency and generalization are demonstrated on three systems: a small organic molecular data set, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration.","lang":"eng"}],"citation":{"mla":"Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” <i>Journal of Chemical Theory and Computation</i>, vol. 20, no. 20, American Chemical Society, 2024, pp. 9259–66, doi:<a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">10.1021/acs.jctc.4c00998</a>.","ista":"Cheng B. 2024. Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. 20(20), 9259–9266.","ieee":"B. Cheng, “Response matching for generating materials and molecules,” <i>Journal of Chemical Theory and Computation</i>, vol. 20, no. 20. American Chemical Society, pp. 9259–9266, 2024.","short":"B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266.","chicago":"Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">https://doi.org/10.1021/acs.jctc.4c00998</a>.","ama":"Cheng B. Response matching for generating materials and molecules. <i>Journal of Chemical Theory and Computation</i>. 2024;20(20):9259-9266. doi:<a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">10.1021/acs.jctc.4c00998</a>","apa":"Cheng, B. (2024). Response matching for generating materials and molecules. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">https://doi.org/10.1021/acs.jctc.4c00998</a>"},"_id":"18452","article_processing_charge":"Yes (in subscription journal)","doi":"10.1021/acs.jctc.4c00998","external_id":{"arxiv":["2405.09057"],"isi":["001330001500001"],"pmid":["39365029"]},"date_created":"2024-10-20T22:02:07Z","acknowledgement":"B.C. thanks Chris Pickard for enlightening discussions.","article_type":"original"},{"author":[{"last_name":"Janacek","full_name":"Janacek, DP","first_name":"DP"},{"last_name":"Kolb","full_name":"Kolb, M","first_name":"M"},{"first_name":"L","full_name":"Schulz, L","last_name":"Schulz"},{"full_name":"Mergner, J","first_name":"J","last_name":"Mergner"},{"first_name":"B","full_name":"Kuster, B","last_name":"Kuster"},{"full_name":"Glanc, Matous","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","last_name":"Glanc"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"Ten Tusscher, K","first_name":"K","last_name":"Ten Tusscher"},{"first_name":"C","full_name":"Schwechheimer, C","last_name":"Schwechheimer"},{"last_name":"Hammes","full_name":"Hammes, UZ","first_name":"UZ"}],"issue":"14","intvolume":"        59","has_accepted_license":"1","status":"public","ddc":["570"],"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"OA_place":"publisher","isi":1,"pmid":1,"oa":1,"quality_controlled":"1","publication_status":"published","file_date_updated":"2025-01-13T09:20:15Z","page":"S1534-5807(24)00569-0","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport","volume":59,"oa_version":"Published Version","scopus_import":"1","date_updated":"2025-09-08T14:33:17Z","abstract":[{"lang":"eng","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."}],"_id":"18465","citation":{"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>.","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.","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>","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.","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>.","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.","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>"},"article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.devcel.2024.09.020","article_type":"original","date_created":"2024-10-23T08:41:27Z","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.","external_id":{"pmid":["39413780"],"isi":["001390774300001"]},"publication":"Developmental Cell","publisher":"Elsevier","file":[{"success":1,"access_level":"open_access","checksum":"34423ee9fb4e30334f3572eddf1da2ae","date_created":"2025-01-13T09:20:15Z","file_id":"18835","content_type":"application/pdf","file_size":3675955,"date_updated":"2025-01-13T09:20:15Z","creator":"dernst","relation":"main_file","file_name":"2024_DevelopmentalCell_Janacek.pdf"}],"date_published":"2024-12-16T00:00:00Z","day":"16","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"type":"journal_article","OA_type":"hybrid","year":"2024","department":[{"_id":"JiFr"}],"month":"12"},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","file":[{"file_name":"2024_PNAS_McDonough.pdf","file_size":1299095,"date_updated":"2024-11-04T10:29:43Z","relation":"main_file","creator":"dernst","file_id":"18501","date_created":"2024-11-04T10:29:43Z","content_type":"application/pdf","success":1,"checksum":"73db3c87b35753e0f4324417f164a35e","access_level":"open_access"}],"publisher":"National Academy of Sciences","article_number":"e2406335121","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"date_published":"2024-10-29T00:00:00Z","day":"29","publication_identifier":{"eissn":["1091-6490"]},"type":"journal_article","OA_type":"hybrid","year":"2024","department":[{"_id":"BeVi"}],"month":"10","scopus_import":"1","date_updated":"2025-09-08T14:31:58Z","abstract":[{"lang":"eng","text":"The dominance of beneficial mutations is a key evolutionary parameter affecting the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate. A leading method to infer it is to compare the relative rates of adaptive substitution for X-linked and autosomal genes, which—according to a classic model by Charlesworth et al. (1987)—is a simple function of the dominance of new beneficial mutations. Recent evidence that rates of adaptive substitution are faster for X-linked genes implies, accordingly, that beneficial mutations are usually recessive. However, this conclusion is incompatible with leading theories of dominance, which predict that beneficial mutations tend to be dominant or overdominant with respect to fitness. To address this incompatibility, we use Fisher’s geometric model to predict the distribution of fitness effects of new mutations and the relative rates of positively selected substitution on the X and autosomes. Previous predictions of faster-X theory emerge as a special case of our model in which the phenotypic effects of mutations are small relative to the distance to the phenotypic optimum. But as mutational effects become large relative to the optimum, we observe an elevated tempo of positively selected substitutions on the X relative to the autosomes across a broader range of dominance conditions, including those predicted by theories of dominance. Our results imply that, contrary to previous models, dominant and overdominant beneficial mutations can plausibly generate patterns of faster-X adaptation. We discuss resulting implications for genomic studies of adaptation and inferences of dominance."}],"_id":"18479","citation":{"ista":"Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2406335121.","mla":"Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>.","ieee":"Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>.","ama":"Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>","apa":"Mcdonough, Y., Ruzicka, F., &#38; Connallon, T. (2024). Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>"},"article_processing_charge":"Yes (in subscription journal)","doi":"10.1073/pnas.2406335121","article_type":"original","ec_funded":1,"acknowledgement":"This work was supported by funds from the Australian Research Council and The School of Biological Sciences at Monash University. F.R. was funded by a H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous reviewers for suggestions that substantially improved the paper and breadth of the analysis.","date_created":"2024-10-27T23:01:44Z","external_id":{"pmid":["39436652"],"isi":["001359216400017"]},"quality_controlled":"1","publication_status":"published","file_date_updated":"2024-11-04T10:29:43Z","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","volume":121,"oa_version":"Published Version","author":[{"last_name":"Mcdonough","full_name":"Mcdonough, Yasmine","first_name":"Yasmine"},{"last_name":"Ruzicka","id":"347955dd-57b0-11ee-9095-c28bdd368f4b","first_name":"Filip","full_name":"Ruzicka, Filip"},{"last_name":"Connallon","first_name":"Tim","full_name":"Connallon, Tim"}],"issue":"44","intvolume":"       121","has_accepted_license":"1","ddc":["570"],"status":"public","OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"isi":1,"pmid":1,"oa":1},{"department":[{"_id":"MaHe"}],"month":"10","year":"2024","type":"journal_article","OA_type":"gold","publication_identifier":{"eissn":["2041-1723"]},"day":"21","file":[{"file_name":"2024_NatureComm_dosSantos.pdf","date_updated":"2024-11-04T10:37:56Z","file_size":7358742,"relation":"main_file","creator":"dernst","date_created":"2024-11-04T10:37:56Z","file_id":"18502","content_type":"application/pdf","success":1,"access_level":"open_access","checksum":"b936b1c047f41cd427f00e3dc79327d3"}],"publisher":"Springer Nature","publication":"Nature Communications","date_published":"2024-10-21T00:00:00Z","article_number":"9063","doi":"10.1038/s41467-024-53127-2","date_created":"2024-10-27T23:01:44Z","acknowledgement":"We are thankful to Michelle Reyzer from the Vanderbilt Mass Spectrometry Research Center for assistance with MALDI-MS imaging and analysis, to the outstanding team at the Vanderbilt Mouse Metabolic Phenotyping Center for all the assistance with in vivo glucose homeostasis tests (DK135073, 1S10RR028101-01). We also thank the University of Michigan Animal Phenotyping Core for conducting the bomb calorimetry experiments (1U2CDK110768, DK020575, and DK089503). This research was supported by recruitment funds from the Vanderbilt’s Department of Molecular Physiology and Biophysics and NIH grants 1R03DK127484, 5U24DK097771, and 1R01DK138141 to RAeD, by a grant from the Canadian Institutes of Health Research (CIHR; 487188) to PEM, by and NIH DK132669 to D.D. PEM holds the Canada Research Chair in Islet Biology.","external_id":{"isi":["001426270600023"],"pmid":["39433757"]},"article_type":"original","citation":{"apa":"Dos Santos, C., Cambraia, A., Shrestha, S., Cutler, M., Cottam, M., Perkins, G., … Arrojo E Drigo, R. (2024). Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53127-2\">https://doi.org/10.1038/s41467-024-53127-2</a>","chicago":"Dos Santos, Cristiane, Amanda Cambraia, Shristi Shrestha, Melanie Cutler, Matthew Cottam, Guy Perkins, Varda Lev-Ram, et al. “Calorie Restriction Increases Insulin Sensitivity to Promote Beta Cell Homeostasis and Longevity in Mice.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53127-2\">https://doi.org/10.1038/s41467-024-53127-2</a>.","ieee":"C. Dos Santos <i>et al.</i>, “Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"C. Dos Santos, A. Cambraia, S. Shrestha, M. Cutler, M. Cottam, G. Perkins, V. Lev-Ram, B. Roy, C. Acree, K.Y. Kim, T. Deerinck, D. Dean, J.P. Cartailler, P.E. Macdonald, M. Hetzer, M. Ellisman, R. Arrojo E Drigo, Nature Communications 15 (2024).","ama":"Dos Santos C, Cambraia A, Shrestha S, et al. Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53127-2\">10.1038/s41467-024-53127-2</a>","mla":"Dos Santos, Cristiane, et al. “Calorie Restriction Increases Insulin Sensitivity to Promote Beta Cell Homeostasis and Longevity in Mice.” <i>Nature Communications</i>, vol. 15, 9063, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53127-2\">10.1038/s41467-024-53127-2</a>.","ista":"Dos Santos C, Cambraia A, Shrestha S, Cutler M, Cottam M, Perkins G, Lev-Ram V, Roy B, Acree C, Kim KY, Deerinck T, Dean D, Cartailler JP, Macdonald PE, Hetzer M, Ellisman M, Arrojo E Drigo R. 2024. Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice. Nature Communications. 15, 9063."},"_id":"18480","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Caloric restriction (CR) can extend the organism life- and health-span by improving glucose homeostasis. How CR affects the structure-function of pancreatic beta cells remains unknown. We used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis reveal that CR activates transcription factors important for beta cell identity and homeostasis, while imaging metabolomics demonstrates that beta cells upon CR are more energetically competent. In fact, high-resolution microscopy show that CR reduces beta cell mitophagy to increase mitochondria mass and the potential for ATP generation. However, CR beta cells have impaired adaptive proliferation in response to high fat diet feeding. Finally, we show that long-term CR delays the onset of beta cell aging hallmarks and promotes cell longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function during aging and diabetes."}],"scopus_import":"1","date_updated":"2025-09-08T14:32:38Z","DOAJ_listed":"1","volume":15,"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"title":"Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice","file_date_updated":"2024-11-04T10:37:56Z","publication_status":"published","quality_controlled":"1","oa":1,"pmid":1,"status":"public","ddc":["570"],"isi":1,"OA_place":"publisher","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        15","has_accepted_license":"1","author":[{"first_name":"Cristiane","full_name":"Dos Santos, Cristiane","last_name":"Dos Santos"},{"full_name":"Cambraia, Amanda","first_name":"Amanda","last_name":"Cambraia"},{"last_name":"Shrestha","first_name":"Shristi","full_name":"Shrestha, Shristi"},{"last_name":"Cutler","full_name":"Cutler, Melanie","first_name":"Melanie"},{"last_name":"Cottam","first_name":"Matthew","full_name":"Cottam, Matthew"},{"first_name":"Guy","full_name":"Perkins, Guy","last_name":"Perkins"},{"last_name":"Lev-Ram","first_name":"Varda","full_name":"Lev-Ram, Varda"},{"first_name":"Birbickram","full_name":"Roy, Birbickram","last_name":"Roy"},{"last_name":"Acree","full_name":"Acree, Christopher","first_name":"Christopher"},{"first_name":"Keun Young","full_name":"Kim, Keun Young","last_name":"Kim"},{"full_name":"Deerinck, Thomas","first_name":"Thomas","last_name":"Deerinck"},{"last_name":"Dean","first_name":"Danielle","full_name":"Dean, Danielle"},{"last_name":"Cartailler","full_name":"Cartailler, Jean Philippe","first_name":"Jean Philippe"},{"last_name":"Macdonald","first_name":"Patrick E.","full_name":"Macdonald, Patrick E."},{"orcid":"0000-0002-2111-992X","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"Hetzer, Martin W"},{"last_name":"Ellisman","full_name":"Ellisman, Mark","first_name":"Mark"},{"last_name":"Arrojo E Drigo","first_name":"Rafael","full_name":"Arrojo E Drigo, Rafael"}]},{"year":"2024","department":[{"_id":"AnKi"}],"month":"10","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"type":"journal_article","OA_type":"gold","day":"14","article_number":"e1012508","date_published":"2024-10-14T00:00:00Z","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"publication":"PLoS Computational Biology","file":[{"creator":"dernst","relation":"main_file","file_size":3732443,"date_updated":"2024-10-29T11:59:09Z","file_name":"2024_PloSComBio_Ho.pdf","checksum":"42fa714459943cb3961b40fab8fd82c8","access_level":"open_access","success":1,"content_type":"application/pdf","file_id":"18487","date_created":"2024-10-29T11:59:09Z"}],"publisher":"Public Library of Science","article_type":"original","external_id":{"pmid":["39401260"],"isi":["001331700300003"]},"acknowledgement":"We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","date_created":"2024-10-27T23:01:45Z","doi":"10.1371/journal.pcbi.1012508","article_processing_charge":"No","_id":"18481","citation":{"apa":"Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., &#38; Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>","ama":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. 2024;20. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>","ieee":"R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” <i>PLoS Computational Biology</i>, vol. 20. Public Library of Science, 2024.","chicago":"Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>.","short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","mla":"Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>, vol. 20, e1012508, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>.","ista":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508."},"abstract":[{"text":"A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.","lang":"eng"}],"date_updated":"2026-04-07T12:31:58Z","scopus_import":"1","related_material":{"record":[{"id":"20393","relation":"dissertation_contains","status":"public"}]},"oa_version":"Published Version","volume":20,"DOAJ_listed":"1","title":"Dynamics of morphogen source formation in a growing tissue","corr_author":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","file_date_updated":"2024-10-29T11:59:09Z","quality_controlled":"1","pmid":1,"oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","isi":1,"status":"public","ddc":["570"],"has_accepted_license":"1","intvolume":"        20","APC_amount":"3197,23 EUR","author":[{"first_name":"Richard D.J.G.","full_name":"Ho, Richard D.J.G.","last_name":"Ho"},{"first_name":"Kasumi","full_name":"Kishi, Kasumi","last_name":"Kishi","orcid":"0000-0001-6060-4795","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Majka","first_name":"Maciej","full_name":"Majka, Maciej"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna"},{"full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","last_name":"Zagórski"}]},{"day":"01","date_published":"2024-06-01T00:00:00Z","publication":"Automation and Remote Control","publisher":"Springer Nature","year":"2024","month":"06","department":[{"_id":"GradSch"}],"publication_identifier":{"eissn":["1608-3032"],"issn":["0005-1179"]},"type":"journal_article","OA_type":"closed access","abstract":[{"text":"This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a shift to a vector x0 ∈ \r\nRn. The goal is to find t0 and x0. In the special case of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev center and the Chebyshev radius of A. This paper focuses on the case in which A and B are defined with their black-box support functions. An algorithm for solving such problems efficiently is suggested. The algorithm has a superlinear convergence rate, and it can solve hundred-dimensional test problems in a reasonable time, but some additional conditions on A and B are required to guarantee the presence of convergence. Additionally, the behavior of the algorithm for a simple special case is investigated, which leads to a number of theoretical results. Perturbations of this special case are also studied.","lang":"eng"}],"date_updated":"2025-09-08T14:27:08Z","scopus_import":"1","article_type":"original","external_id":{"isi":["001338721700007"]},"acknowledgement":"The author is grateful to Maxim Balashov for setting the problem, providing useful literature, important discussions and text review. Also, I thank Dmitry Tsarev and Kseniia Petukhova for meaningful talks and support.","date_created":"2024-10-27T23:01:45Z","doi":"10.1134/S0005117924060031","article_processing_charge":"No","_id":"18482","citation":{"short":"P. Arkhipov, Automation and Remote Control 85 (2024) 522–532.","chicago":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” <i>Automation and Remote Control</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1134/S0005117924060031\">https://doi.org/10.1134/S0005117924060031</a>.","ieee":"P. Arkhipov, “An algorithm for finding the generalized Chebyshev center of sets defined via their support functions,” <i>Automation and Remote Control</i>, vol. 85, no. 6. Springer Nature, pp. 522–532, 2024.","ama":"Arkhipov P. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. <i>Automation and Remote Control</i>. 2024;85(6):522-532. doi:<a href=\"https://doi.org/10.1134/S0005117924060031\">10.1134/S0005117924060031</a>","mla":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” <i>Automation and Remote Control</i>, vol. 85, no. 6, Springer Nature, 2024, pp. 522–32, doi:<a href=\"https://doi.org/10.1134/S0005117924060031\">10.1134/S0005117924060031</a>.","ista":"Arkhipov P. 2024. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 85(6), 522–532.","apa":"Arkhipov, P. (2024). An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. <i>Automation and Remote Control</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0005117924060031\">https://doi.org/10.1134/S0005117924060031</a>"},"publication_status":"published","quality_controlled":"1","oa_version":"None","volume":85,"title":"An algorithm for finding the generalized Chebyshev center of sets defined via their support functions","corr_author":"1","page":"522-532","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"6","intvolume":"        85","author":[{"last_name":"Arkhipov","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","first_name":"Pavel","full_name":"Arkhipov, Pavel"}],"isi":1,"status":"public"},{"author":[{"first_name":"Vadim","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"first_name":"Edmond","full_name":"Koudjinan, Edmond","last_name":"Koudjinan","orcid":"0000-0003-2640-4049","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E"},{"full_name":"Zhang, Ke","first_name":"Ke","last_name":"Zhang"}],"intvolume":"        34","has_accepted_license":"1","ddc":["510"],"status":"public","isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","oa":1,"quality_controlled":"1","file_date_updated":"2025-01-13T09:14:24Z","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"1973-2007","language":[{"iso":"eng"}],"title":"Birkhoff conjecture for nearly centrally symmetric domains","corr_author":"1","arxiv":1,"volume":34,"oa_version":"Published Version","scopus_import":"1","date_updated":"2025-09-08T14:27:45Z","abstract":[{"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.","lang":"eng"}],"citation":{"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>","ista":"Kaloshin V, Koudjinan E, Zhang K. 2024. Birkhoff conjecture for nearly centrally symmetric domains. Geometric and Functional Analysis. 34, 1973–2007.","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>","short":"V. Kaloshin, E. Koudjinan, K. Zhang, Geometric and Functional Analysis 34 (2024) 1973–2007.","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.","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>."},"_id":"18483","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00039-024-00695-6","ec_funded":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).","external_id":{"isi":["001329804200001"],"arxiv":["2306.12301"]},"date_created":"2024-10-27T23:01:45Z","article_type":"original","file":[{"success":1,"checksum":"e7fcd9f78beb40408c7d858ac0625e27","access_level":"open_access","file_id":"18833","date_created":"2025-01-13T09:14:24Z","content_type":"application/pdf","date_updated":"2025-01-13T09:14:24Z","file_size":2260980,"creator":"dernst","relation":"main_file","file_name":"2024_GeometricFunctionalAnalysis_Kaloshin.pdf"}],"publisher":"Springer Nature","publication":"Geometric and Functional Analysis","date_published":"2024-12-01T00:00:00Z","project":[{"grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"}],"day":"01","OA_type":"hybrid","type":"journal_article","publication_identifier":{"issn":["1016-443X"],"eissn":["1420-8970"]},"department":[{"_id":"VaKa"}],"month":"12","year":"2024"},{"date_updated":"2025-09-08T14:26:29Z","scopus_import":"1","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."}],"article_processing_charge":"Yes","citation":{"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.","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>","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>.","short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).","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>.","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.","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>"},"_id":"18488","external_id":{"arxiv":["2403.12325"],"isi":["001346198800001"]},"ec_funded":1,"date_created":"2024-10-29T16:04:05Z","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).","article_type":"original","doi":"10.1103/prxquantum.5.040311","date_published":"2024-10-23T00:00:00Z","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"article_number":"040311","publisher":"American Physical Society","file":[{"file_name":"2024_PRXQuantum_Ljubotina.pdf","file_size":1151431,"date_updated":"2024-10-30T08:59:09Z","relation":"main_file","creator":"dernst","date_created":"2024-10-30T08:59:09Z","file_id":"18489","content_type":"application/pdf","success":1,"access_level":"open_access","checksum":"2e057ba021744d0a74602517935326b3"}],"publication":"PRX Quantum","day":"23","type":"journal_article","OA_type":"gold","publication_identifier":{"eissn":["2691-3399"]},"month":"10","department":[{"_id":"MaSe"}],"year":"2024","author":[{"first_name":"Marko","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","last_name":"Petrova","full_name":"Petrova, Elena","first_name":"Elena"},{"last_name":"Schuch","full_name":"Schuch, Norbert","first_name":"Norbert"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"APC_amount":"3711,01 EUR","has_accepted_license":"1","issue":"4","intvolume":"         5","isi":1,"OA_place":"publisher","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","ddc":["530"],"oa":1,"quality_controlled":"1","file_date_updated":"2024-10-30T08:59:09Z","publication_status":"published","corr_author":"1","title":"Tangent space generators of matrix product states and exact floquet quantum scars","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa_version":"Published Version","DOAJ_listed":"1","volume":5}]