[{"publication_status":"draft","das_tickbox":"1","related_material":{"record":[{"id":"20656","status":"public","relation":"later_version"},{"id":"20364","status":"public","relation":"dissertation_contains"},{"id":"19395","relation":"dissertation_contains","status":"public"}]},"doi":"10.1101/2022.11.30.518503","author":[{"full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"full_name":"Fiedler, Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","full_name":"Zou, Minxia","last_name":"Zou"},{"last_name":"Giannini","full_name":"Giannini, Caterina","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"first_name":"Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","last_name":"Vladimirtsev","full_name":"Vladimirtsev, Dmitrii"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","full_name":"Randuch, Marek","last_name":"Randuch"},{"first_name":"Yongfan","last_name":"Yu","full_name":"Yu, Yongfan"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","last_name":"Gelová"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge"},{"orcid":"0000-0003-2140-7195","last_name":"Hajny","full_name":"Hajny, Jakub","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Meng","full_name":"Chen, Meng","last_name":"Chen"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"first_name":"Maria Mar","full_name":"Marques-Bueno, Maria Mar","last_name":"Marques-Bueno"},{"id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","first_name":"Zainab","full_name":"Quddoos, Zainab","last_name":"Quddoos"},{"first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","full_name":"Molnar, Gergely"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan","full_name":"Kulich, Ivan","last_name":"Kulich"},{"last_name":"Jaillais","full_name":"Jaillais, Yvon","first_name":"Yvon"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"oa_version":"Published Version","corr_author":"1","month":"02","publication":"bioRxiv","oa":1,"status":"public","ddc":["580"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"19399","OA_place":"repository","date_created":"2025-03-13T08:36:48Z","ec_funded":1,"abstract":[{"text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena.","lang":"eng"}],"acknowledgement":"We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova for help with manuscript preparation; J. Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at ISTA for their excellent service and assistance. The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant 32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural Science Foundation of China (32321001).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","main_file_link":[{"url":"https://doi.org/10.1101/2022.11.30.518503","open_access":"1"}],"article_processing_charge":"No","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"ALTF 985-2016","name":"Cell surface receptor complexes for auxin signaling in plants","_id":"26060676-B435-11E9-9278-68D0E5697425"}],"title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","citation":{"apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>","chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>.","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” <i>bioRxiv</i>. .","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>","ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv, <a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais, J. Friml, BioRxiv (n.d.)."},"type":"preprint","year":"2025","date_updated":"2026-08-14T09:33:45Z","day":"20","department":[{"_id":"JiFr"},{"_id":"XiFe"}],"language":[{"iso":"eng"}],"date_published":"2025-02-20T00:00:00Z"},{"publication_status":"draft","das_tickbox":"1","related_material":{"record":[{"id":"19395","relation":"dissertation_contains","status":"public"}]},"doi":"10.1101/2025.02.28.640727","author":[{"first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","full_name":"Monzer, Aline"},{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","full_name":"Zou, Minxia","last_name":"Zou"},{"full_name":"Smejkal, Michael","last_name":"Smejkal","id":"79a5a1be-04a3-11f0-ba18-a1730e0b58e9","first_name":"Michael"},{"first_name":"Ema","id":"9f185b95-04a3-11f0-8245-f5e32eeb470f","last_name":"Cervenova","full_name":"Cervenova, Ema"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"oa_version":"Published Version","corr_author":"1","oa":1,"status":"public","month":"03","publication":"bioRxiv","ddc":["580"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_created":"2025-03-12T14:28:53Z","tmp":{"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","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"OA_place":"repository","_id":"19398","abstract":[{"text":"Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.","lang":"eng"}],"acknowledgement":"We deeply appreciate M. Wrzaczek’s constructive input and insightful discussions, which significantly enriched this work. We thank L. Fiedler for helping with the heat map and for the discussions. We also thank the facilities at ISTA, the imaging and optics (IOF) and Lab Support (LSF) facilities for their service and assistance.","OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2025.02.28.640727","open_access":"1"}],"citation":{"short":"A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal, E. Cervenova, J. Friml, BioRxiv (n.d.).","mla":"Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","ista":"Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova E, Friml J. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv, <a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","ama":"Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>","apa":"Monzer, A., Mazur, E., Rodriguez Solovey, L., Gallei, M. C., Zou, M., Smejkal, M., … Friml, J. (n.d.). TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>","ieee":"A. Monzer <i>et al.</i>, “TMK interacting network of receptor like kinases for auxin canalization and beyond,” <i>bioRxiv</i>. .","chicago":"Monzer, Aline, Ewa Mazur, Lesia Rodriguez Solovey, Michelle C Gallei, Minxia Zou, Michael Smejkal, Ema Cervenova, and Jiří Friml. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>."},"title":"TMK interacting network of receptor like kinases for auxin canalization and beyond","year":"2025","type":"preprint","day":"02","date_updated":"2026-08-14T09:33:45Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"date_published":"2025-03-02T00:00:00Z","language":[{"iso":"eng"}]},{"publication_identifier":{"isbn":["9783959773720"]},"type":"conference","year":"2025","file_date_updated":"2026-02-18T09:02:33Z","day":"30","date_updated":"2026-08-20T06:28:00Z","has_accepted_license":"1","department":[{"_id":"MoHe"}],"date_published":"2025-06-30T00:00:00Z","language":[{"iso":"eng"}],"OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","conference":{"start_date":"2025-07-08","location":"Aarhus, Denmark","name":"ICALP: Automata, Languages and Programming","end_date":"2025-07-11"},"project":[{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"Z00422","name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"volume":334,"title":"Incremental approximate maximum flow via residual graph sparsification","citation":{"ieee":"G. Goranci, M. Henzinger, H. Räcke, and A. Sricharan, “Incremental approximate maximum flow via residual graph sparsification,” in <i>52nd International Colloquium on Automata, Languages, and Programming</i>, Aarhus, Denmark, 2025, vol. 334, p. 91:1-91:20.","apa":"Goranci, G., Henzinger, M., Räcke, H., &#38; Sricharan, A. (2025). Incremental approximate maximum flow via residual graph sparsification. In <i>52nd International Colloquium on Automata, Languages, and Programming</i> (Vol. 334, p. 91:1-91:20). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">https://doi.org/10.4230/lipics.icalp.2025.91</a>","chicago":"Goranci, Gramoz, Monika Henzinger, Harald Räcke, and A. Sricharan. “Incremental Approximate Maximum Flow via Residual Graph Sparsification.” In <i>52nd International Colloquium on Automata, Languages, and Programming</i>, 334:91:1-91:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. <a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">https://doi.org/10.4230/lipics.icalp.2025.91</a>.","ama":"Goranci G, Henzinger M, Räcke H, Sricharan A. Incremental approximate maximum flow via residual graph sparsification. In: <i>52nd International Colloquium on Automata, Languages, and Programming</i>. Vol 334. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025:91:1-91:20. doi:<a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">10.4230/lipics.icalp.2025.91</a>","short":"G. Goranci, M. Henzinger, H. Räcke, A. Sricharan, in:, 52nd International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, p. 91:1-91:20.","ista":"Goranci G, Henzinger M, Räcke H, Sricharan A. 2025. Incremental approximate maximum flow via residual graph sparsification. 52nd International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 334, 91:1-91:20.","mla":"Goranci, Gramoz, et al. “Incremental Approximate Maximum Flow via Residual Graph Sparsification.” <i>52nd International Colloquium on Automata, Languages, and Programming</i>, vol. 334, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, p. 91:1-91:20, doi:<a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">10.4230/lipics.icalp.2025.91</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","_id":"21280","page":"91:1-91:20","date_created":"2026-02-17T08:26:06Z","scopus_import":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We give an algorithm that, with high probability, maintains a (1-ε)-approximate s-t maximum flow in undirected, uncapacitated n-vertex graphs undergoing m edge insertions in Õ(m+ n F^*/ε) total update time, where F^{*} is the maximum flow on the final graph. This is the first algorithm to achieve polylogarithmic amortized update time for dense graphs (m = Ω(n²)), and more generally, for graphs where F^* = Õ(m/n). At the heart of our incremental algorithm is the residual graph sparsification technique of Karger and Levine [SICOMP '15], originally designed for computing exact maximum flows in the static setting. Our main contributions are (i) showing how to maintain such sparsifiers for approximate maximum flows in the incremental setting and (ii) generalizing the cut sparsification framework of Fung et al. [SICOMP '19] from undirected graphs to balanced directed graphs."}],"acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI\r\n10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Harald Räcke: This project has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 498605858 and 470029389.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","corr_author":"1","publication":"52nd International Colloquium on Automata, Languages, and Programming","month":"06","oa":1,"status":"public","quality_controlled":"1","ddc":["000"],"doi":"10.4230/lipics.icalp.2025.91","file":[{"file_name":"2025_ICALP_Goranci.pdf","creator":"dernst","date_created":"2026-02-18T09:02:33Z","success":1,"date_updated":"2026-02-18T09:02:33Z","checksum":"c178cf554e44204b9f64ebd9b54cf7ba","file_size":944824,"content_type":"application/pdf","file_id":"21315","relation":"main_file","access_level":"open_access"}],"author":[{"last_name":"Goranci","full_name":"Goranci, Gramoz","first_name":"Gramoz"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"first_name":"A.","last_name":"Sricharan","full_name":"Sricharan, A."}],"oa_version":"Published Version","external_id":{"arxiv":["2502.09105"]},"related_material":{"record":[{"id":"22716","relation":"later_version","status":"public"}]},"arxiv":1,"alternative_title":["LIPIcs"],"publication_status":"published","intvolume":"       334"},{"alternative_title":["LNCS"],"publication_status":"published","intvolume":"     16007","related_material":{"record":[{"id":"22664","relation":"dissertation_contains","status":"public"}]},"doi":"10.1007/978-3-032-01913-4_5","author":[{"full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606","last_name":"Auerbach","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt"},{"last_name":"Cueto Noval","orcid":"0000-0002-2505-4246","full_name":"Cueto Noval, Miguel","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"full_name":"Erol, Boran","last_name":"Erol","first_name":"Boran"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"oa_version":"Preprint","publication":"45th Annual International Cryptology Conference","month":"08","oa":1,"status":"public","quality_controlled":"1","_id":"21262","OA_place":"repository","page":"141-172","date_created":"2026-02-17T07:41:04Z","acknowledgement":"B. Auerbach and B. Erol—Conducted part of this work at ISTA.","abstract":[{"text":"Continuous Group Key Agreement (CGKA) is the primitive underlying secure group messaging. It allows a large group of N users to maintain a shared secret key that is frequently rotated by the\r\ngroup members in order to achieve forward secrecy and post compromise security. The group messaging scheme Messaging Layer Security (MLS) standardized by the IETF makes use of a CGKA called TreeKEM which arranges the N group members in a binary tree. Here, each node is associated with a public-key, each user is assigned one of the leaves, and a user knows the corresponding secret keys from their leaf to the root. To update the key material known to them, a user must just replace keys at log(N) nodes, which requires them to create and upload log(N) ciphertexts. Such updates must be processed sequentially by all users, which for large groups is impractical. To allow for concurrent updates, TreeKEM uses the “propose and commit” paradigm, where multiple users can concurrently propose to update (by just sampling a fresh leaf key), and a single user can then commit to all proposals at once. Unfortunately, this process destroys the binary tree structure as the tree gets pruned and some nodes must be “blanked” at the cost of increasing the in-degree of others, which makes the commit operation, as well as, future commits more costly. In the worst case, the update cost (in terms of uploaded ciphertexts) per user can grow from log(N) to Ω(N). In this work we provide two main contributions. First, we show that MLS’ communication complexity is bad not only in the worst case but also if the proposers and committers are chosen at random: even if there’s just one update proposal for every commit the expected cost is already over √N, and it approaches N as this ratio changes towards more proposals. Our second contribution is a new variant of propose and commit for\r\nTreeKEM which for moderate amounts of update proposals per commit provably achieves an update cost of Θ(log(N)) assuming the proposers and committers are chosen at random.","lang":"eng"}],"publisher":"Springer Nature","OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2025/1035"}],"conference":{"start_date":"2025-08-17","name":"CRYPTO: International Cryptology Conference","end_date":"2025-08-21","location":"Santa Barbara, CA, United States"},"volume":16007,"title":"Continuous group-key agreement: Concurrent updates without pruning","citation":{"ieee":"B. Auerbach, M. Cueto Noval, B. Erol, and K. Z. Pietrzak, “Continuous group-key agreement: Concurrent updates without pruning,” in <i>45th Annual International Cryptology Conference</i>, Santa Barbara, CA, United States, 2025, vol. 16007, pp. 141–172.","ama":"Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. Continuous group-key agreement: Concurrent updates without pruning. In: <i>45th Annual International Cryptology Conference</i>. Vol 16007. Springer Nature; 2025:141-172. doi:<a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">10.1007/978-3-032-01913-4_5</a>","apa":"Auerbach, B., Cueto Noval, M., Erol, B., &#38; Pietrzak, K. Z. (2025). Continuous group-key agreement: Concurrent updates without pruning. In <i>45th Annual International Cryptology Conference</i> (Vol. 16007, pp. 141–172). Santa Barbara, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">https://doi.org/10.1007/978-3-032-01913-4_5</a>","chicago":"Auerbach, Benedikt, Miguel Cueto Noval, Boran Erol, and Krzysztof Z Pietrzak. “Continuous Group-Key Agreement: Concurrent Updates without Pruning.” In <i>45th Annual International Cryptology Conference</i>, 16007:141–72. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">https://doi.org/10.1007/978-3-032-01913-4_5</a>.","ista":"Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. 2025. Continuous group-key agreement: Concurrent updates without pruning. 45th Annual International Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 16007, 141–172.","mla":"Auerbach, Benedikt, et al. “Continuous Group-Key Agreement: Concurrent Updates without Pruning.” <i>45th Annual International Cryptology Conference</i>, vol. 16007, Springer Nature, 2025, pp. 141–72, doi:<a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">10.1007/978-3-032-01913-4_5</a>.","short":"B. Auerbach, M. Cueto Noval, B. Erol, K.Z. Pietrzak, in:, 45th Annual International Cryptology Conference, Springer Nature, 2025, pp. 141–172."},"type":"conference","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783032019134"],"issn":["0302-9743"],"isbn":["9783032019127"]},"year":"2025","day":"17","date_updated":"2026-08-21T10:53:16Z","department":[{"_id":"KrPi"}],"date_published":"2025-08-17T00:00:00Z","language":[{"iso":"eng"}]},{"external_id":{"isi":["001428076100015"],"pmid":["39972227"]},"pmid":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/an-electrifying-turn-in-an-age-old-quest/","relation":"press_release","description":"News on ISTA website"}],"record":[{"relation":"dissertation_contains","status":"public","id":"20203"},{"status":"public","relation":"dissertation_contains","id":"22684"}]},"doi":"10.1038/s41586-024-08530-6","author":[{"full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A"},{"full_name":"Pertl, Felix","last_name":"Pertl","orcid":"0000-0003-0463-5794","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix"},{"last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"last_name":"Sauer","full_name":"Sauer, Markus","first_name":"Markus"},{"first_name":"Annette","full_name":"Foelske, Annette","last_name":"Foelske"},{"first_name":"Markus","last_name":"Ostermann","full_name":"Ostermann, Markus"},{"first_name":"Christian M.","full_name":"Pichler, Christian M.","last_name":"Pichler"},{"full_name":"Wang, Yongkang","last_name":"Wang","first_name":"Yongkang"},{"first_name":"Yuki","full_name":"Nagata, Yuki","last_name":"Nagata"},{"first_name":"Mischa","full_name":"Bonn, Mischa","last_name":"Bonn"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"}],"file":[{"file_name":"2025_Nature_Sobarzo.pdf","creator":"dernst","date_created":"2025-03-04T10:05:18Z","success":1,"date_updated":"2025-03-04T10:05:18Z","content_type":"application/pdf","file_id":"19289","file_size":3807415,"access_level":"open_access","relation":"main_file","checksum":"fecf302274dd3218d3e7dd22f39a6c0c"}],"oa_version":"Published Version","issue":"8051","publication_status":"published","article_number":"664-669","intvolume":"       638","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}],"volume":638,"title":"Spontaneous ordering of identical materials into a triboelectric series","citation":{"mla":"Sobarzo Ponce, Juan Carlos A., et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>, vol. 638, no. 8051, 664–669, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>.","ista":"Sobarzo Ponce JCA, Pertl F, Balazs D, Costanzo T, Sauer M, Foelske A, Ostermann M, Pichler CM, Wang Y, Nagata Y, Bonn M, Waitukaitis SR. 2025. Spontaneous ordering of identical materials into a triboelectric series. Nature. 638(8051), 664–669.","short":"J.C.A. Sobarzo Ponce, F. Pertl, D. Balazs, T. Costanzo, M. Sauer, A. Foelske, M. Ostermann, C.M. Pichler, Y. Wang, Y. Nagata, M. Bonn, S.R. Waitukaitis, Nature 638 (2025).","ieee":"J. C. A. Sobarzo Ponce <i>et al.</i>, “Spontaneous ordering of identical materials into a triboelectric series,” <i>Nature</i>, vol. 638, no. 8051. Springer Nature, 2025.","apa":"Sobarzo Ponce, J. C. A., Pertl, F., Balazs, D., Costanzo, T., Sauer, M., Foelske, A., … Waitukaitis, S. R. (2025). Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>","chicago":"Sobarzo Ponce, Juan Carlos A, Felix Pertl, Daniel Balazs, Tommaso Costanzo, Markus Sauer, Annette Foelske, Markus Ostermann, et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>.","ama":"Sobarzo Ponce JCA, Pertl F, Balazs D, et al. Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. 2025;638(8051). doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>"},"type":"journal_article","year":"2025","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"file_date_updated":"2025-03-04T10:05:18Z","day":"20","date_updated":"2026-08-27T11:42:43Z","department":[{"_id":"ScWa"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2025-02-20T00:00:00Z","corr_author":"1","isi":1,"month":"02","publication":"Nature","status":"public","oa":1,"quality_controlled":"1","ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"_id":"19278","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","date_created":"2025-03-02T23:01:52Z","scopus_import":"1","ec_funded":1,"article_type":"original","abstract":[{"text":"When two insulating, neutral materials are contacted and separated, they exchange electrical charge1. Experiments have long suggested that this ‘contact electrification’ is transitive, with different materials ordering into ‘triboelectric series’ based on the sign of charge acquired2. At the same time, the effect is plagued by unpredictability, preventing consensus on the mechanism and casting doubt on the rhyme and reason that series imply3. Here we expose an unanticipated connection between the unpredictability and order in contact electrification: nominally identical materials initially exchange charge randomly and intransitively, but—over repeated experiments—order into triboelectric series. We find that this evolution is driven by the act of contact itself—samples with more contacts in their history charge negatively to ones with fewer contacts. Capturing this ‘contact bias’ in a minimal model, we recreate both the initial randomness and ultimate order in numerical simulations and use it experimentally to force the appearance of a triboelectric series of our choosing. With a set of surface-sensitive techniques to search for the underlying alterations contact creates, we only find evidence of nanoscale morphological changes, pointing to a mechanism strongly coupled with mechanics. Our results highlight the centrality of contact history in contact electrification and suggest that focusing on the unpredictability that has long plagued the effect may hold the key to understanding it.","lang":"eng"}],"acknowledgement":"This project has received financing from the European Research Council grant agreement no. 949120 under the European Union’s Horizon 2020 research and innovation programme. The Analytical Instrumentation Center of the TU Wien acknowledges support by the FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state of Lower Austria and the European Regional Development Fund under grant no. WST3-F-542638/004-2021. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing facility, Electron Microscopy Facility and Lab Support Facility. We thank J. Garcia-Suarez and G. Anciaux for the suggestion to look into the roughness power spectral density. We thank I.-M. Strugaru for help with testing the device for Young’s modulus measurements. Open access funding provided by Institute of Science and Technology (IST Austria).","publisher":"Springer Nature"},{"arxiv":1,"intvolume":"       135","PlanS_conform":"1","issue":"14","article_number":"146202","publication_status":"published","oa_version":"Published Version","author":[{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix","full_name":"Pertl, Felix","last_name":"Pertl","orcid":"0000-0003-0463-5794"},{"full_name":"Lenton, Isaac C","last_name":"Lenton","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C"},{"full_name":"Cramer, Tobias","last_name":"Cramer","first_name":"Tobias"},{"last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"dernst","file_name":"2025_PhysReviewLetters_Pertl.pdf","date_created":"2025-10-23T09:32:31Z","success":1,"date_updated":"2025-10-23T09:32:31Z","file_id":"20522","content_type":"application/pdf","file_size":1692251,"access_level":"open_access","relation":"main_file","checksum":"7e45e89b8db0b7f01e63185c68e4b0f9"}],"doi":"10.1103/lcsm-xxty","related_material":{"record":[{"id":"20523","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"22684"}]},"external_id":{"arxiv":["2502.12718"],"isi":["001587263900003"]},"publisher":"American Physical Society","ec_funded":1,"abstract":[{"lang":"eng","text":"Kelvin probe force microscopy (KPFM) is widely used in stationary and dynamic studies of contact electrification. An obvious question that connects these two has been overlooked: when are charge dynamics too fast for stationary studies to be meaningful? Using a rapid transfer system to quickly perform KPFM after contact, we find the dynamics are too fast in all but the best insulators. Our data further suggest that dynamics are caused by bulk as opposed to surface conductivity, and that charge-transfer heterogeneity is less prevalent than previously suggested."}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the Nanofabrication Facility and Lab Support Facility.","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"20481","OA_place":"publisher","date_created":"2025-10-16T13:13:29Z","scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"}],"quality_controlled":"1","ddc":["530"],"publication":"Physical Review Letters","month":"09","status":"public","oa":1,"corr_author":"1","isi":1,"language":[{"iso":"eng"}],"date_published":"2025-09-30T00:00:00Z","has_accepted_license":"1","department":[{"_id":"ScWa"}],"file_date_updated":"2025-10-23T09:32:31Z","date_updated":"2026-08-27T11:42:43Z","day":"30","type":"journal_article","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"year":"2025","title":"No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces","citation":{"ista":"Pertl F, Lenton IC, Cramer T, Waitukaitis SR. 2025. No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. Physical Review Letters. 135(14), 146202.","mla":"Pertl, Felix, et al. “No Time for Surface Charge: How Bulk Conductivity Hides Charge Patterns from Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.” <i>Physical Review Letters</i>, vol. 135, no. 14, 146202, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/lcsm-xxty\">10.1103/lcsm-xxty</a>.","short":"F. Pertl, I.C. Lenton, T. Cramer, S.R. Waitukaitis, Physical Review Letters 135 (2025).","ama":"Pertl F, Lenton IC, Cramer T, Waitukaitis SR. No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. <i>Physical Review Letters</i>. 2025;135(14). doi:<a href=\"https://doi.org/10.1103/lcsm-xxty\">10.1103/lcsm-xxty</a>","ieee":"F. Pertl, I. C. Lenton, T. Cramer, and S. R. Waitukaitis, “No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces,” <i>Physical Review Letters</i>, vol. 135, no. 14. American Physical Society, 2025.","chicago":"Pertl, Felix, Isaac C Lenton, Tobias Cramer, and Scott R Waitukaitis. “No Time for Surface Charge: How Bulk Conductivity Hides Charge Patterns from Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/lcsm-xxty\">https://doi.org/10.1103/lcsm-xxty</a>.","apa":"Pertl, F., Lenton, I. C., Cramer, T., &#38; Waitukaitis, S. R. (2025). No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/lcsm-xxty\">https://doi.org/10.1103/lcsm-xxty</a>"},"project":[{"grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020"}],"volume":135,"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"external_id":{"pmid":["41034200"],"isi":["001586620700015"]},"DOAJ_listed":"1","pmid":1,"related_material":{"record":[{"id":"22770","relation":"research_data","status":"public"}]},"doi":"10.1038/s41467-025-63852-x","author":[{"full_name":"King, Daniel S.","last_name":"King","first_name":"Daniel S."},{"last_name":"Kim","full_name":"Kim, Dongjin","first_name":"Dongjin"},{"full_name":"Zhong, Peichen","last_name":"Zhong","first_name":"Peichen"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","last_name":"Cheng","full_name":"Cheng, Bingqing"}],"file":[{"checksum":"34b6005d349bbff85839c4e51d6c8725","content_type":"application/pdf","file_size":4907055,"file_id":"20460","access_level":"open_access","relation":"main_file","file_name":"2025_NatureComm_King.pdf","creator":"dernst","date_created":"2025-10-13T07:54:51Z","success":1,"date_updated":"2025-10-13T07:54:51Z"}],"researchdata_availability":"no","oa_version":"Published Version","publication_status":"published","article_number":"8763","PlanS_conform":"1","das_tickbox":"1","intvolume":"        16","OA_type":"gold","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","volume":16,"supplementarymaterial":"no","citation":{"apa":"King, D. S., Kim, D., Zhong, P., &#38; Cheng, B. (2025). Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>","ama":"King DS, Kim D, Zhong P, Cheng B. Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>","ieee":"D. S. King, D. Kim, P. Zhong, and B. Cheng, “Machine learning of charges and long-range interactions from energies and forces,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","chicago":"King, Daniel S., Dongjin Kim, Peichen Zhong, and Bingqing Cheng. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>.","mla":"King, Daniel S., et al. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>, vol. 16, 8763, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>.","ista":"King DS, Kim D, Zhong P, Cheng B. 2025. Machine learning of charges and long-range interactions from energies and forces. Nature Communications. 16, 8763.","short":"D.S. King, D. Kim, P. Zhong, B. Cheng, Nature Communications 16 (2025)."},"title":"Machine learning of charges and long-range interactions from energies and forces","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","year":"2025","date_updated":"2026-08-27T12:16:47Z","day":"01","file_date_updated":"2025-10-13T07:54:51Z","department":[{"_id":"BiCh"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2025-10-01T00:00:00Z","isi":1,"corr_author":"1","oa":1,"status":"public","month":"10","publication":"Nature Communications","quality_controlled":"1","ddc":["000"],"dataavailabilitystatement":"The training sets, training scripts, MD input files, and trained CACE potentials are available at https://github.com/BingqingCheng/cace-lr-fit; see https://doi.org/10.5281/zenodo.16415061. Source data for all figures are provided with this paper. Source data are provided with this paper.","date_created":"2025-10-12T22:01:25Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","_id":"20452","article_type":"original","acknowledgement":"We thank Chunyi Zhang for providing the TiO2(101)/NaCl+NaOH+HCl(aq) dataset and for useful discussions. We thank Jia-Xin Zhu for providing the Pt(111)/KF(aq) dataset. We thank Tsz Wai Ko and Jonas Finkler for useful discussions and for the DFT-optimized Au2-MgO(001) structures. We thank Junmin Chen for discussions. D.K and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship.","abstract":[{"lang":"eng","text":"Accurate modeling of long-range forces is critical in atomistic simulations, as they play a central role in determining the properties of material and chemical systems. However, standard machine learning interatomic potentials (MLIPs) often rely on short-range approximations, limiting their applicability to systems with significant electrostatics and dispersion forces. We recently introduced the Latent Ewald Summation (LES) method, which captures long-range electrostatics without explicitly learning atomic charges or charge equilibration. We benchmark LES on diverse and challenging systems, including charged molecules, ionic liquids, electrolyte solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces, and solid-solid interfaces. Here we show that LES can reproduce the exact atomic charges for classical systems with fixed charges and can infer dipole and quadrupole moments, as well as the dipole derivative with respect to atomic positions, for quantum mechanical systems. Moreover, LES can achieve better accuracy in energy and force predictions compared to methods that explicitly learn from charges."}],"publisher":"Springer Nature"},{"ddc":["000"],"oa":1,"status":"public","month":"07","publisher":"Repository","date_created":"2026-08-27T12:13:55Z","OA_place":"repository","_id":"22770","citation":{"mla":"Cheng, Bingqing, et al. <i>BingqingCheng/Cace-Lr-Fit: V0</i>. Repository, 2025, doi:<a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>.","ista":"Cheng B, King D, Kim D, Zhong P. 2025. BingqingCheng/cace-lr-fit: V0, Repository, <a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>.","short":"B. Cheng, D. King, D. Kim, P. Zhong, (2025).","ieee":"B. Cheng, D. King, D. Kim, and P. Zhong, “BingqingCheng/cace-lr-fit: V0.” Repository, 2025.","chicago":"Cheng, Bingqing, Daniel King, Dongjin Kim, and Peichen Zhong. “BingqingCheng/Cace-Lr-Fit: V0.” Repository, 2025. <a href=\"https://doi.org/10.5281/zenodo.16415060\">https://doi.org/10.5281/zenodo.16415060</a>.","apa":"Cheng, B., King, D., Kim, D., &#38; Zhong, P. (2025). BingqingCheng/cace-lr-fit: V0. Repository. <a href=\"https://doi.org/10.5281/zenodo.16415060\">https://doi.org/10.5281/zenodo.16415060</a>","ama":"Cheng B, King D, Kim D, Zhong P. BingqingCheng/cace-lr-fit: V0. 2025. doi:<a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>"},"related_material":{"record":[{"id":"20452","relation":"used_in_publication","status":"public"}]},"title":"BingqingCheng/cace-lr-fit: V0","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"green","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.16415061","open_access":"1"}],"department":[{"_id":"BiCh"}],"date_published":"2025-07-24T00:00:00Z","oa_version":"None","year":"2025","type":"research_data_reference","doi":"10.5281/zenodo.16415060","date_updated":"2026-08-27T12:16:48Z","author":[{"first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"first_name":"Daniel","last_name":"King","full_name":"King, Daniel"},{"first_name":"Dongjin","last_name":"Kim","full_name":"Kim, Dongjin"},{"first_name":"Peichen","full_name":"Zhong, Peichen","last_name":"Zhong"}],"day":"24"},{"status":"public","oa":1,"month":"05","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["514","519","532","004"],"date_created":"2025-05-12T15:12:28Z","page":"155","OA_place":"publisher","_id":"19684","degree_awarded":"PhD","supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","abstract":[{"text":"The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate.","lang":"eng"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Yalniz, Gökhan. <i>Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>.","ista":"Yalniz G. 2025. Transition to turbulence: Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.","short":"G. Yalniz, Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025.","apa":"Yalniz, G. (2025). <i>Transition to turbulence: Data-, solution-, and pattern-driven approaches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>","chicago":"Yalniz, Gökhan. “Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>.","ama":"Yalniz G. Transition to turbulence: Data-, solution-, and pattern-driven approaches. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>","ieee":"G. Yalniz, “Transition to turbulence: Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025."},"title":"Transition to turbulence: Data-, solution-, and pattern-driven approaches","project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"date_updated":"2026-09-02T08:16:32Z","day":"13","file_date_updated":"2025-05-12T15:43:28Z","year":"2025","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","language":[{"iso":"eng"}],"date_published":"2025-05-13T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"has_accepted_license":"1","publication_status":"published","alternative_title":["ISTA Thesis"],"doi_confirm":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9558"},{"relation":"part_of_dissertation","status":"public","id":"12105"},{"relation":"part_of_dissertation","status":"public","id":"13274"},{"status":"public","relation":"part_of_dissertation","id":"14466"},{"status":"public","relation":"part_of_dissertation","id":"7563"}]},"author":[{"full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan"}],"file":[{"checksum":"0e452642b79f13633f1595bde71a67e3","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"19685","file_size":20058169,"date_created":"2025-05-12T15:13:28Z","date_updated":"2025-05-12T15:13:28Z","success":1,"file_name":"Gökhan Yalnız - PhD thesis.pdf","creator":"gyalniz"},{"date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:15:59Z","creator":"gyalniz","file_name":"Movie 2A.1.mp4","file_id":"19686","content_type":"video/mp4","file_size":37763743,"relation":"supplementary_material","access_level":"open_access","checksum":"921099d76adab2df784ce12ce41cfb22","description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).","title":"Chapter 2 - Movie 2A.1"},{"creator":"gyalniz","file_name":"Movie 3A.1.mp4","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:16:09Z","description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.1","access_level":"open_access","relation":"supplementary_material","content_type":"video/mp4","file_size":3902655,"file_id":"19687","checksum":"0ae5ac7d9896003c0c4207dd746808dc"},{"creator":"gyalniz","file_name":"Movie 3A.2.mp4","date_created":"2025-05-12T15:16:21Z","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 3 - Movie 3A.2","description":"Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","checksum":"ef8d270e066c1a9c3cb5ae46acf945e6","content_type":"video/mp4","file_id":"19688","file_size":7043169,"relation":"supplementary_material","access_level":"open_access"},{"date_created":"2025-05-12T15:16:36Z","date_updated":"2025-05-12T15:43:28Z","creator":"gyalniz","file_name":"Movie 3A.3.mp4","content_type":"video/mp4","file_id":"19689","file_size":7748659,"access_level":"open_access","relation":"supplementary_material","checksum":"7ed871f428100d6827ac9b0e8ca8e985","description":"Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.3"},{"title":"Chapter 3 - Movie 3A.4","description":"Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","checksum":"dd5a252e1da00c8f303588e22e2baeef","access_level":"open_access","relation":"supplementary_material","file_id":"19690","file_size":5873052,"content_type":"video/mp4","creator":"gyalniz","file_name":"Movie 3A.4.mp4","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:16:50Z"},{"date_created":"2025-05-12T15:17:11Z","date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 4A.1.mp4","creator":"gyalniz","checksum":"5ac58b86810698db28cbfc28f351ff70","file_size":9209327,"file_id":"19691","content_type":"video/mp4","access_level":"open_access","relation":"supplementary_material","title":"Chapter 4 - Movie 4A.1","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit."},{"date_created":"2025-05-12T15:17:43Z","date_updated":"2025-05-12T15:43:28Z","creator":"gyalniz","file_name":"Movie 5A.1.mp4","checksum":"ac877f1e1ef39439911bf37cb1793b8e","access_level":"open_access","relation":"supplementary_material","content_type":"video/mp4","file_id":"19692","file_size":5893993,"title":"Chapter 5 - Movie 5A.1","description":"Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain."},{"checksum":"fd17eabb70129ceaa414e40924d1d2fe","content_type":"video/mp4","file_size":3990352,"file_id":"19693","access_level":"open_access","relation":"supplementary_material","title":"Chapter 5 - Movie 5A.2","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:17:49Z","creator":"gyalniz","file_name":"Movie 5A.2.mp4"},{"date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:17:58Z","creator":"gyalniz","file_name":"Movie 5A.3.mp4","checksum":"32f904497ab0bbee38f0788d96b91454","file_size":5171009,"content_type":"video/mp4","file_id":"19694","access_level":"open_access","relation":"supplementary_material","title":"Chapter 5 - Movie 5A.3","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is a zoom-in of the full (L_x = L_z) domain."},{"file_name":"Gökhan Yalnız - PhD thesis.zip","creator":"gyalniz","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:27:10Z","checksum":"f313261b9bb12dfb943fead8318954c6","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","file_size":18991996,"file_id":"19695"}],"doi":"10.15479/AT-ISTA-19684","oa_version":"Published Version"},{"OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination","grant_number":"CZI01"},{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"volume":5,"title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","citation":{"ama":"Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2). doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>","chicago":"Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>.","ieee":"J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol. 5, no. 2. Elsevier, 2025.","apa":"Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>","ista":"Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211.","mla":"Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no. 2, 100211, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>.","short":"J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025)."},"year":"2025","type":"journal_article","publication_identifier":{"eissn":["2667-0747"]},"file_date_updated":"2025-06-10T07:24:46Z","day":"11","date_updated":"2026-09-03T09:36:24Z","has_accepted_license":"1","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"date_published":"2025-06-11T00:00:00Z","corr_author":"1","month":"06","publication":"Biophysical Reports","oa":1,"status":"public","ddc":["570"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"19795","scopus_import":"1","date_created":"2025-06-08T22:01:22Z","ec_funded":1,"article_type":"original","abstract":[{"text":"Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.","lang":"eng"}],"acknowledgement":"We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).","publisher":"Elsevier","DOAJ_listed":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20206"},{"status":"public","relation":"dissertation_contains","id":"22744"}]},"doi":"10.1016/j.bpr.2025.100211","author":[{"orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425"},{"last_name":"Semenov","full_name":"Semenov, Nikolai","first_name":"Nikolai","id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger"},{"first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","orcid":"0000-0003-2311-2112","full_name":"Javoor, Manjunath"},{"last_name":"Zens","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tavakoli","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"id":"EE8452B8-C26A-11E9-B157-E80CE6697425","first_name":"Marek","full_name":"Suplata, Marek","last_name":"Suplata"},{"full_name":"Jahr, Wiebke","last_name":"Jahr","orcid":"0000-0003-0201-2315","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","first_name":"Andreas","full_name":"Wartak, Andreas","last_name":"Wartak"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian Km","first_name":"Florian Km","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann 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Nikol","last_name":"Zorin"},{"last_name":"Nguyen","full_name":"Nguyen, Akemi L.","first_name":"Akemi L."},{"first_name":"Georgiy","id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05","orcid":"0009-0002-3999-3735","last_name":"Ivanian","full_name":"Ivanian, Georgiy"},{"first_name":"Jamie","full_name":"Woych, Jamie","last_name":"Woych"},{"last_name":"Arnold","full_name":"Arnold, Rebecca C","first_name":"Rebecca C","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f"},{"full_name":"Ortega Gurrola, Alonso","last_name":"Ortega Gurrola","first_name":"Alonso"},{"full_name":"Shvartsman, Arik","last_name":"Shvartsman","first_name":"Arik"},{"last_name":"Barbieri","full_name":"Barbieri, Francesca","first_name":"Francesca","id":"a9492887-8972-11ed-ae7b-bfae10998254"},{"last_name":"Toma","full_name":"Toma, Florina-Alexandra","first_name":"Florina-Alexandra","id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5"},{"first_name":"Gary J.","full_name":"Gorbsky, Gary J.","last_name":"Gorbsky"},{"first_name":"Marko E.","full_name":"Horb, Marko E.","last_name":"Horb"},{"first_name":"Hollis T.","last_name":"Cline","full_name":"Cline, Hollis T."},{"first_name":"Timothy F.","last_name":"Shay","full_name":"Shay, Timothy F."},{"first_name":"Darcy B.","last_name":"Kelley","full_name":"Kelley, Darcy B."},{"last_name":"Yamaguchi","full_name":"Yamaguchi, Ayako","first_name":"Ayako"},{"first_name":"Mark","last_name":"Shein-Idelson","full_name":"Shein-Idelson, Mark"},{"first_name":"Maria Antonietta","full_name":"Tosches, Maria Antonietta","last_name":"Tosches"},{"orcid":"0000-0001-9242-5601","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","first_name":"Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"file":[{"file_id":"19790","content_type":"application/pdf","file_size":11936258,"relation":"main_file","access_level":"open_access","checksum":"a83a4cb58f5941096d3ad91ca0172594","date_updated":"2025-06-04T05:43:27Z","date_created":"2025-06-04T05:43:27Z","success":1,"file_name":"2025_DevelopmentalCell_Jaeger.pdf","creator":"dernst"}],"doi":"10.1016/j.devcel.2024.10.025","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"22667"},{"id":"22803","relation":"research_data","status":"public"}]},"pmid":1,"external_id":{"pmid":["39603234"],"isi":["001444798600001"]},"publisher":"Elsevier","acknowledgement":"We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion, and support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru (Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination; our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC, and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.); FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund (FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.); EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).","abstract":[{"lang":"eng","text":"Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution."}],"article_type":"original","page":"794-812.e6","scopus_import":"1","date_created":"2024-02-20T09:20:32Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"15016","OA_place":"publisher","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"quality_controlled":"1","ddc":["570"],"status":"public","oa":1,"publication":"Developmental Cell","month":"03","isi":1,"corr_author":"1","date_published":"2025-03-10T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"day":"10","date_updated":"2026-09-04T10:11:04Z","file_date_updated":"2025-06-04T05:43:27Z","type":"journal_article","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"year":"2025","citation":{"ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6.","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>, vol. 60, no. 5, Elsevier, 2025, p. 794–812.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>.","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.","apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. 2025;60(5):794-812.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>","chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>.","ieee":"E. C. B. Jaeger <i>et al.</i>, “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” <i>Developmental Cell</i>, vol. 60, no. 5. Elsevier, p. 794–812.e6, 2025."},"title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","volume":60,"project":[{"name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","grant_number":"FTI21-D-046","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits"},{"_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e","grant_number":"F7814","name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity"}],"article_processing_charge":"Yes (via OA deal)","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"hybrid"},{"date_published":"2025-08-03T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"ToHe"}],"file_date_updated":"2025-09-08T08:46:31Z","date_updated":"2026-09-05T15:59:18Z","day":"03","year":"2025","type":"conference","publication_identifier":{"issn":["2154-817X"],"isbn":["9798400714542"]},"title":"Monitoring robustness and individual fairness","citation":{"apa":"Gupta, A., Henzinger, T. A., Kueffner, K., Mallik, K., &#38; Pape, D. (2025). Monitoring robustness and individual fairness. In <i>Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i> (Vol. 2, pp. 790–801). Toronto, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3711896.3737054\">https://doi.org/10.1145/3711896.3737054</a>","ama":"Gupta A, Henzinger TA, Kueffner K, Mallik K, Pape D. Monitoring robustness and individual fairness. In: <i>Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>. Vol 2. Association for Computing Machinery; 2025:790-801. doi:<a href=\"https://doi.org/10.1145/3711896.3737054\">10.1145/3711896.3737054</a>","ieee":"A. Gupta, T. A. Henzinger, K. Kueffner, K. Mallik, and D. Pape, “Monitoring robustness and individual fairness,” in <i>Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, Toronto, Canada, 2025, vol. 2, pp. 790–801.","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Konstantin Kueffner, Kaushik Mallik, and David Pape. “Monitoring Robustness and Individual Fairness.” In <i>Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, 2:790–801. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3711896.3737054\">https://doi.org/10.1145/3711896.3737054</a>.","short":"A. Gupta, T.A. Henzinger, K. Kueffner, K. Mallik, D. Pape, in:, Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Association for Computing Machinery, 2025, pp. 790–801.","ista":"Gupta A, Henzinger TA, Kueffner K, Mallik K, Pape D. 2025. Monitoring robustness and individual fairness. Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining. KDD: Conference on Knowledge Discovery and Data Mining vol. 2, 790–801.","mla":"Gupta, Ashutosh, et al. “Monitoring Robustness and Individual Fairness.” <i>Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, vol. 2, Association for Computing Machinery, 2025, pp. 790–801, doi:<a href=\"https://doi.org/10.1145/3711896.3737054\">10.1145/3711896.3737054</a>."},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"volume":2,"article_processing_charge":"No","conference":{"start_date":"2025-08-03","name":"KDD: Conference on Knowledge Discovery and Data Mining","end_date":"2025-08-07","location":"Toronto, Canada"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","ec_funded":1,"abstract":[{"text":"In automated decision-making, it is desirable that outputs of decision-makers be robust to slight perturbations in their inputs, a property that may be called input-output robustness. Input-output robustness appears in various different forms in the literature, such as robustness of AI models to adversarial or semantic perturbations and individual fairness of AI models that make decisions about humans. We propose runtime monitoring of input-output robustness of deployed, black-box AI models, where the goal is to design monitors that would observe one long execution sequence of the model, and would raise an alarm whenever it is detected that two similar inputs from the past led to dissimilar outputs. This way, monitoring will complement existing offline ''robustification'' approaches to increase the trustworthiness of AI decision-makers. We show that the monitoring problem can be cast as the fixed-radius nearest neighbor (FRNN) search problem, which, despite being well-studied, lacks suitable online solutions. We present our tool Clemont, which offers a number of lightweight monitors, some of which use upgraded online variants of existing FRNN algorithms, and one uses a novel algorithm based on binary decision diagrams--a data-structure commonly used in software and hardware verification. We have also developed an efficient parallelization technique that can substantially cut down the computation time of monitors for which the distance between input-output pairs is measured using the L∞norm. Using standard benchmarks from the literature of adversarial and semantic robustness and individual fairness, we perform a comparative study of different monitors in Clemont, and demonstrate their effectiveness in correctly detecting robustness violations at runtime.","lang":"eng"}],"acknowledgement":"This work was supported in part by the ERC project ERC-2020-AdG 101020093 and the SBI Foundation Hub for Data Science &Analytics, IIT Bombay.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"20292","OA_place":"publisher","date_created":"2025-09-07T22:01:33Z","page":"790-801","scopus_import":"1","quality_controlled":"1","ddc":["000"],"month":"08","publication":"Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining","oa":1,"status":"public","corr_author":"1","oa_version":"Published Version","author":[{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin","full_name":"Kueffner, Konstantin","orcid":"0000-0001-8974-2542","last_name":"Kueffner"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","last_name":"Mallik"},{"first_name":"David","full_name":"Pape, David","last_name":"Pape"}],"file":[{"file_size":7745940,"content_type":"application/pdf","file_id":"20310","relation":"main_file","access_level":"open_access","checksum":"81e18cdf9ca5f6dfa79425b326ea9725","creator":"dernst","file_name":"2025_KDD_Gupta.pdf","success":1,"date_updated":"2025-09-08T08:46:31Z","date_created":"2025-09-08T08:46:31Z"}],"doi":"10.1145/3711896.3737054","related_material":{"link":[{"url":"https://github.com/ariez-xyz/clemont","relation":"software"}],"record":[{"relation":"dissertation_contains","status":"for_moderation","id":"22808"}]},"external_id":{"arxiv":["2506.00496"]},"arxiv":1,"intvolume":"         2","publication_status":"published"},{"external_id":{"arxiv":["2507.20711"]},"related_material":{"record":[{"id":"22808","status":"for_moderation","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0002-0783-904X","last_name":"Cano Cordoba","full_name":"Cano Cordoba, Filip","first_name":"Filip","id":"708cad98-e86a-11ef-8098-bdae2d7c6af1"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724"},{"orcid":"0000-0001-8974-2542","last_name":"Kueffner","full_name":"Kueffner, Konstantin","first_name":"Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515"}],"doi":"10.1007/978-3-032-05435-7_1","oa_version":"Preprint","alternative_title":["LNCS"],"publication_status":"published","intvolume":"     16087","arxiv":1,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2507.20711"}],"conference":{"start_date":"2025-09-15","location":"Graz, Austria","name":"RV: Runtime Verification","end_date":"2025-09-19"},"OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Algorithmic fairness: A runtime perspective","citation":{"ama":"Cano Cordoba F, Henzinger TA, Kueffner K. Algorithmic fairness: A runtime perspective. In: <i>25th International Conference on Runtime Verification</i>. Vol 16087. Springer Nature; 2025:1-21. doi:<a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">10.1007/978-3-032-05435-7_1</a>","ieee":"F. Cano Cordoba, T. A. Henzinger, and K. Kueffner, “Algorithmic fairness: A runtime perspective,” in <i>25th International Conference on Runtime Verification</i>, Graz, Austria, 2025, vol. 16087, pp. 1–21.","apa":"Cano Cordoba, F., Henzinger, T. A., &#38; Kueffner, K. (2025). Algorithmic fairness: A runtime perspective. In <i>25th International Conference on Runtime Verification</i> (Vol. 16087, pp. 1–21). Graz, Austria: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">https://doi.org/10.1007/978-3-032-05435-7_1</a>","chicago":"Cano Cordoba, Filip, Thomas A Henzinger, and Konstantin Kueffner. “Algorithmic Fairness: A Runtime Perspective.” In <i>25th International Conference on Runtime Verification</i>, 16087:1–21. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">https://doi.org/10.1007/978-3-032-05435-7_1</a>.","short":"F. Cano Cordoba, T.A. Henzinger, K. Kueffner, in:, 25th International Conference on Runtime Verification, Springer Nature, 2025, pp. 1–21.","mla":"Cano Cordoba, Filip, et al. “Algorithmic Fairness: A Runtime Perspective.” <i>25th International Conference on Runtime Verification</i>, vol. 16087, Springer Nature, 2025, pp. 1–21, doi:<a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">10.1007/978-3-032-05435-7_1</a>.","ista":"Cano Cordoba F, Henzinger TA, Kueffner K. 2025. Algorithmic fairness: A runtime perspective. 25th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 16087, 1–21."},"project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"volume":16087,"day":"13","date_updated":"2026-09-05T15:59:18Z","type":"conference","year":"2025","publication_identifier":{"eisbn":["9783032054357"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"date_published":"2025-09-13T00:00:00Z","department":[{"_id":"ToHe"}],"month":"09","publication":"25th International Conference on Runtime Verification","status":"public","oa":1,"corr_author":"1","quality_controlled":"1","_id":"21090","OA_place":"repository","date_created":"2026-01-29T16:01:41Z","page":"1-21","publisher":"Springer Nature","ec_funded":1,"abstract":[{"lang":"eng","text":"Fairness in AI is traditionally studied as a static property evaluated once, over a fixed dataset. However, real-world AI systems operate sequentially, with outcomes and environments evolving over time. This paper proposes a framework for analysing fairness as a runtime property. Using a minimal yet expressive model based on sequences of coin tosses with possibly evolving biases, we study the problems of monitoring and enforcing fairness expressed in either toss outcomes or coin biases. Since there is no one-size-fits-all solution for either problem, we provide a summary of monitoring and enforcement strategies, parametrised by environment dynamics, prediction horizon, and confidence thresholds. For both problems, we present general results under simple or minimal assumptions. We survey existing solutions for the monitoring problem for Markovian and additive dynamics, and existing solutions for the enforcement problem in static settings with known dynamics."}],"acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093."},{"file":[{"access_level":"closed","relation":"source_file","file_id":"20209","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25798848,"checksum":"36b87c17d12c7bf5955d6d812acb8d77","embargo_to":"open_access","date_updated":"2026-09-03T22:30:03Z","date_created":"2025-08-22T08:22:10Z","creator":"yiqwang","file_name":"2025_Wang_Yiqun_Thesis.docx"},{"date_updated":"2026-09-03T22:30:03Z","date_created":"2025-08-22T10:32:30Z","creator":"yiqwang","file_name":"2025_Wang_Yiqun_Thesis.pdf","checksum":"8d7a2383f66377da675d379ec30ea0fe","embargo":"2026-09-03","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"20211","file_size":12628313}],"author":[{"last_name":"Wang","full_name":"Wang, Yiqun","first_name":"Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425"}],"doi":"10.15479/AT-ISTA-20117","oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"18063"}]},"alternative_title":["ISTA Thesis"],"publication_status":"published","file_date_updated":"2026-09-03T22:30:03Z","date_updated":"2026-09-03T22:30:04Z","day":"04","type":"dissertation","year":"2025","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"date_published":"2025-08-04T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"has_accepted_license":"1","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","citation":{"chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>.","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025."},"_id":"20117","OA_place":"publisher","page":"108","date_created":"2025-08-04T15:24:21Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","month":"08","status":"public","oa":1,"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"ddc":["580"]},{"oa_version":"Published Version","doi":"10.15479/AT-ISTA-20212","author":[{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889","last_name":"Miranda"}],"file":[{"checksum":"3331f76bbef74ff4908e2d2c9262045c","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20230","file_size":32887334,"date_updated":"2026-08-26T22:30:02Z","date_created":"2025-08-26T09:03:50Z","embargo_to":"open_access","creator":"omiranda","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx"},{"date_created":"2025-08-26T09:05:55Z","date_updated":"2026-08-26T22:30:02Z","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf","creator":"omiranda","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":28636240,"file_id":"20231","checksum":"02509d50cff8e35c5bcbf71e8d658176","embargo":"2026-08-26"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17425"}]},"publication_status":"published","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"date_published":"2025-08-22T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-063-3"],"issn":["2663-337X"]},"type":"dissertation","year":"2025","date_updated":"2026-08-26T22:30:03Z","day":"22","file_date_updated":"2026-08-26T22:30:02Z","project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"}],"citation":{"mla":"Miranda, Osvaldo. <i>Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>.","ista":"Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria.","short":"O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025.","ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025.","apa":"Miranda, O. (2025). <i>Unraveling the role of Pten in cortical stem cell lineage progression using MADM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>","chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>.","ama":"Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>"},"title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253).","supervisor":[{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"publisher":"Institute of Science and Technology Austria","keyword":["Pten","mtor","cortical development","MADM","Mapk"],"degree_awarded":"PhD","page":"119","date_created":"2025-08-22T14:07:00Z","OA_place":"publisher","_id":"20212","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"corr_author":"1","oa":1,"status":"public","month":"08"},{"OA_embargo":"12","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","citation":{"chicago":"Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>.","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>","mla":"Elkrewi, Marwan N. <i>Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>.","ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.","short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2025-03-14T00:00:00Z","type":"dissertation","publication_identifier":{"isbn":["9783990780534"],"eissn":["2663-337X"]},"year":"2025","file_date_updated":"2026-03-26T23:30:03Z","day":"14","date_updated":"2026-07-06T13:48:33Z","ddc":["570","576"],"acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","month":"03","oa":1,"status":"public","acknowledgement":"My PhD work was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).","abstract":[{"text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. ","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"degree_awarded":"PhD","_id":"19386","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","page":"170","date_created":"2025-03-11T12:54:31Z","related_material":{"record":[{"id":"12248","relation":"part_of_dissertation","status":"public"},{"id":"10767","status":"public","relation":"part_of_dissertation"},{"id":"15009","status":"public","relation":"part_of_dissertation"},{"id":"14613","relation":"part_of_dissertation","status":"public"},{"id":"17890","status":"public","relation":"part_of_dissertation"},{"id":"10167","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","doi":"10.15479/AT-ISTA-19386","file":[{"file_name":"Thesis_Marwan_Elkrewi.docx","creator":"melkrewi","embargo_to":"open_access","date_created":"2025-03-26T07:06:56Z","date_updated":"2026-03-26T23:30:03Z","file_size":25019680,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"19462","access_level":"closed","relation":"source_file","checksum":"5549a8216c07e4c39281648912d72246"},{"checksum":"aed2ba9965aa89b3414deae1ae9f4321","embargo":"2026-03-26","relation":"main_file","access_level":"open_access","file_id":"19463","file_size":17294844,"content_type":"application/pdf","creator":"melkrewi","file_name":"Thesis_Marwan_Elkrewi.pdf","date_updated":"2026-03-26T23:30:03Z","date_created":"2025-03-26T07:06:22Z"}],"author":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"}],"alternative_title":["ISTA Thesis"],"publication_status":"published"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","OA_embargo":"6","title":"Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry","citation":{"apa":"Wald, S. (2025). <i>Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>","ama":"Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>","ieee":"S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry,” Institute of Science and Technology Austria, 2025.","chicago":"Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>.","short":"S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry, Institute of Science and Technology Austria, 2025.","mla":"Wald, Sebastian. <i>Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>.","ista":"Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria."},"year":"2025","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-075-6"]},"type":"dissertation","file_date_updated":"2026-06-15T22:30:03Z","date_updated":"2026-07-24T08:07:28Z","day":"11","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2025-12-11T00:00:00Z","corr_author":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"12","status":"public","oa":1,"ddc":["530"],"keyword":["entanglement-enhanced atom interferometry","cavity QED","spin-squeezing","dipole trap","quantum optics"],"degree_awarded":"PhD","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"_id":"20798","OA_place":"publisher","page":"152","date_created":"2025-12-11T11:48:11Z","abstract":[{"text":"Atom interferometers measure the relative phase shifts between coherent matter-wave paths\r\nthat arise from interactions with external fields or inertial forces. Due to their exceptional\r\nphase sensitivity, atom interferometers became an essential tool for precision measurements\r\nand fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However, their measurement precision is limited by quantum projection noise,\r\nwhich arises from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates with absolute precision. The generation of entanglement between the atoms offers a\r\npath to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis thesis reports on the development of an atom interferometer experiment designed to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity that mediates all relevant atom-light interactions. The\r\ncavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates on the fundamental theoretical framework, the cavity design, and the full\r\noptical setup, including the detailed configuration of the developed laser stabilization methods.\r\nExperimentally, continuous loading methods were explored, resulting in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control\r\nwas verified via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity coupling.\r\nThese presented results establish the experimental groundwork for the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"doi_confirm":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14759"}]},"doi":"10.15479/AT-ISTA-20798","file":[{"file_name":"2025_Wald_Sebastian_Thesis.pdf","creator":"swald","date_updated":"2026-06-15T22:30:03Z","date_created":"2025-12-12T11:53:42Z","embargo":"2026-06-15","checksum":"1be72faf529a5e8a2d03cb3d5f808b77","content_type":"application/pdf","file_size":47536855,"file_id":"20809","access_level":"open_access","relation":"main_file"},{"access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","file_size":40127601,"file_id":"20810","checksum":"8c3a1904dceb4bcd04bc9f14b2594bab","embargo_to":"open_access","date_created":"2025-12-12T11:54:55Z","date_updated":"2026-06-15T22:30:03Z","file_name":"2025_Wald_Sebastian_Thesis.zip","creator":"swald"}],"author":[{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","full_name":"Wald, Sebastian","orcid":"0000-0002-5869-1604","last_name":"Wald"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"publication_status":"published","das_tickbox":"1"},{"OA_embargo":"6 months","volume":45,"title":"Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans","citation":{"ama":"Stratigi A, Soler-García M, Krout M, et al. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. 2025;45(13). doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>","apa":"Stratigi, A., Soler-García, M., Krout, M., Shukla, S., de Bono, M., Richmond, J. E., &#38; Laurent, P. (2025). Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>","ieee":"A. Stratigi <i>et al.</i>, “Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans,” <i>Journal of Neuroscience</i>, vol. 45, no. 13. Society for Neuroscience, 2025.","chicago":"Stratigi, Aikaterini, Miguel Soler-García, Mia Krout, Shikha Shukla, Mario de Bono, Janet E. Richmond, and Patrick Laurent. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2025. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>.","short":"A. Stratigi, M. Soler-García, M. Krout, S. Shukla, M. de Bono, J.E. Richmond, P. Laurent, Journal of Neuroscience 45 (2025).","mla":"Stratigi, Aikaterini, et al. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>, vol. 45, no. 13, e1767232024, Society for Neuroscience, 2025, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>.","ista":"Stratigi A, Soler-García M, Krout M, Shukla S, de Bono M, Richmond JE, Laurent P. 2025. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 45(13), e1767232024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"MaDe"}],"language":[{"iso":"eng"}],"date_published":"2025-03-26T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"year":"2025","file_date_updated":"2025-09-27T22:30:02Z","day":"26","date_updated":"2026-07-28T11:30:41Z","ddc":["570"],"quality_controlled":"1","isi":1,"publication":"Journal of Neuroscience","month":"03","oa":1,"status":"public","article_type":"original","abstract":[{"lang":"eng","text":"A dynamic interplay between fast synaptic signals and slower neuromodulatory signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits. The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance remain uncertain. We designed a genetic screen to isolate genes involved in the peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin (snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1). We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans, and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies [developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C. elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1 signaling alters the synapsin and actin cytoskeleton and increases neuropeptide release by cholinergic motor neurons, which secondarily affects the presynaptic vesicle cycle. Together, these results clarify the dominant mechanisms of action of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I balance in DEE70."}],"acknowledgement":"P.L. is a research associate of the Belgian National Fund for Scientific Research (FRS-FNRS). K.S., M.S.-G., S.S., and P.L. are supported by grants from the FRS-FNRS. This work was supported by an Advanced ERC Grant (269058 ACMO) to M.D.B. We thank the team of Alexander Gottschalk for the snn-1(S9A) strain. We thank the Imaging Facility of the Faculty of Medicine (LiMiF) of the Universite Libre de Bruxelles, supported by FRS-FNRS. This work made use of instruments in the Electron Microscopy Core of the University of Illinois Chicago Research Resources Center as well as the BioCryo facility of Northwestern University's NUANCE Center, which has received support from the SHyNE Resource (NSF ECCS-2025633), the IIN, and Northwestern's MRSEC program (NSF DMR-2308691). Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440).","publisher":"Society for Neuroscience","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","_id":"19498","date_created":"2025-04-06T22:01:32Z","scopus_import":"1","pmid":1,"external_id":{"isi":["001460952700001"],"pmid":["39919830"]},"oa_version":"Published Version","doi":"10.1523/JNEUROSCI.1767-23.2024","file":[{"file_size":3111735,"content_type":"application/pdf","file_id":"19525","relation":"main_file","access_level":"open_access","embargo":"2025-09-27","checksum":"7befc0168f4cd5bd2b0fcff9e2a94784","file_name":"2025_JourNeuroscience_Stratigi.pdf","creator":"dernst","date_updated":"2025-09-27T22:30:02Z","date_created":"2025-04-07T11:57:19Z"}],"author":[{"last_name":"Stratigi","full_name":"Stratigi, Aikaterini","first_name":"Aikaterini"},{"last_name":"Soler-García","full_name":"Soler-García, Miguel","first_name":"Miguel"},{"full_name":"Krout, Mia","last_name":"Krout","first_name":"Mia"},{"full_name":"Shukla, Shikha","last_name":"Shukla","first_name":"Shikha"},{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario"},{"first_name":"Janet E.","last_name":"Richmond","full_name":"Richmond, Janet E."},{"full_name":"Laurent, Patrick","last_name":"Laurent","first_name":"Patrick"}],"intvolume":"        45","issue":"13","publication_status":"published","article_number":"e1767232024"},{"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"year":"2025","file_date_updated":"2026-01-29T23:30:03Z","day":"24","date_updated":"2026-04-16T12:20:43Z","department":[{"_id":"JoFi"},{"_id":"GradSch"}],"has_accepted_license":"1","date_published":"2025-01-24T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"title":"Microwave-optic interconnects for superconducting circuits","citation":{"ieee":"G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,” Institute of Science and Technology Austria, 2025.","ama":"Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>","apa":"Arnold, G. M. (2025). <i>Microwave-optic interconnects for superconducting circuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>","chicago":"Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>.","ista":"Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria.","mla":"Arnold, Georg M. <i>Microwave-Optic Interconnects for Superconducting Circuits</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>.","short":"G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits, Institute of Science and Technology Austria, 2025."},"degree_awarded":"PhD","_id":"18871","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"OA_place":"publisher","date_created":"2025-01-24T10:28:39Z","page":"135","ec_funded":1,"acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020 research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN) and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n","abstract":[{"text":"\"Can we do this with a new type of computer - a quantum computer?\". This famous\r\nquotation of the brilliant Richard Feynman within a conference talk on \"Simulating physics\r\nwith computers.” is often reverently praised as the origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical. Now, 43 years later, the theoretical framework of how such\r\na computer can operate has been developed. Two main important concepts for a potential\r\nquantum supremacy, superposition and entanglement, have been exploited to design quantum\r\nalgorithms to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis still far from being certain, in fact the race between the most promising platforms such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well\r\nas spin qubits has recently intensified. If one also includes the most mature applications of\r\nquantum communication technologies, secure quantum key distribution and quantum random\r\nnumber generators, as part of a quantum information technology ecosystem, we are confronted\r\nwith a plethora of different materials, concepts, and also operation frequencies. While\r\nsuperconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently, a quantum frequency converter or microwave-optic transducer is required\r\nto interface the different frequency domains or establish a long-range network connection\r\nwith suitable telecom fibers. In fact, the combination of different frequency regimes is also\r\nan essential part in our classical modern communication network, where computations are\r\nperformed in electrical circuits and the information exchange over longer distances happens\r\nvia optical fibers. However, the specific challenges specific to building a quantum computer,\r\nalso apply to the development of such a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the carrier of information, i.e. the smallest possible quantity, the signal\r\ncan easily be corrupted by other noise sources which needs to be avoided by all means. This\r\nis also the reason why microwave quantum computers operate at temperature environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals cannot be copied which would be a typical\r\nstrategy to account for errors in classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic transducers: While quantum computers are operating in one specific frequency\r\ndomain, microwave-optic transducers combine microwave and optical fields in one device.\r\nThis results in the particular challenge that high-energy optical radiation, which is usually\r\nwell-shielded from superconducting microwave quantum processors, are now an essential part\r\nof the device. The concomitant optical radiation in the operating transducer will inevitably\r\nhave a detrimental effect on the superconducting microwave components. Together with the\r\nrequirement of minimal background noise for quantum-limited operation as described above,\r\nv\r\nheating from the absorption of optical photons within the same device where single microwave\r\nexcitations are processed forms a formidable challenge.\r\nThis thesis aims to address this challenge by developing microwave-optic transducers where\r\nthe impact of optical absorption on superconducting circuits in general and superconducting\r\nqubits specifically can be mitigated. In our first approach, we developed a compact device\r\nwith optimized interaction strengths between the different frequency domains. This minimizes\r\nthe optical powers used for transducer operation and thus the optical absorption heating. This\r\nwork was - to the best of our knowledge - the first comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately, we saw that the optical absorption heating added\r\nnoise way above a single excitation. Consequently, a potential quantum signal would have\r\nbeen buried in the noise, added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional microwave-optic transducer instead\r\nof an integrated device. The larger heat capacity of the macroscopic device with a size\r\nof a few millimeters can absorb a larger fraction of the optical heating before it increases\r\nthe temperature of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat the microwave-optic transducer can be operated in a regime in which optical fields don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic\r\ntransducers in conjunction with microwave quantum processors and brings the integration and\r\nseamless orchestration of different frequency components in a quantum network a step closer.\r\n","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"corr_author":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"01","oa":1,"status":"public","ddc":["530"],"acknowledged_ssus":[{"_id":"SSU"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.15479/at:ista:18871","author":[{"full_name":"Arnold, Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M"}],"file":[{"access_level":"closed","relation":"source_file","file_size":18856130,"content_type":"application/x-zip-compressed","file_id":"18946","checksum":"71872702e8f46c275eaea44efc4d304f","creator":"cchlebak","file_name":"tex for upload.zip","embargo_to":"open_access","date_created":"2025-01-29T08:38:08Z","date_updated":"2026-01-29T23:30:03Z"},{"creator":"cchlebak","file_name":"ISTThesisGA2022_final.pdf","date_created":"2025-01-29T08:38:34Z","date_updated":"2026-01-29T23:30:03Z","checksum":"dfaa06591970f4bff163705802fad56d","embargo":"2026-01-29","file_id":"18947","content_type":"application/pdf","file_size":17344760,"access_level":"open_access","relation":"main_file"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6609"},{"status":"public","relation":"part_of_dissertation","id":"8529"},{"relation":"part_of_dissertation","status":"public","id":"18953"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9114"},{"id":"13200","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"publication_status":"published"},{"publication_status":"published","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","doi":"10.15479/AT-ISTA-19745","file":[{"access_level":"closed","relation":"source_file","file_size":103879193,"file_id":"19748","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"1a2d1525d19347fbb879ef57c02951bf","embargo_to":"open_access","date_updated":"2025-11-27T23:30:02Z","date_created":"2025-05-28T07:38:17Z","creator":"cchlebak","file_name":"NikolaCanigova_Thesis_final.docx"},{"embargo":"2025-11-27","checksum":"c1d8f9a40a8e19fcf895373f4b773a46","file_size":194530600,"file_id":"19749","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_updated":"2025-11-27T23:30:02Z","date_created":"2025-05-28T07:39:53Z","file_name":"NikolaCanigova_Thesis_final_PDFA2a_fixed.pdf","creator":"cchlebak"}],"author":[{"orcid":"0000-0002-8518-5926","last_name":"Canigova","full_name":"Canigova, Nikola","first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"14274","relation":"part_of_dissertation","status":"public"}]},"abstract":[{"text":"Cell migration is a crucial process in animal development and maintenance. It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment, where cells can switch between\r\nmigration modes as they encounter new environmental cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration strategy when encountering geometrically,\r\nmechanically and chemically distinct environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy, extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable. Instead, the cells use topography of the\r\nenvironment to propel their cell body forward. To migrate efficiently in the maze of different\r\npore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions into much denser environments with limited choice of large pores. In such invasive\r\ntransitions it is unclear if the cells can cross tight pores without the use of adhesions and\r\nextracellular proteolysis and whether they maintain the nucleus in the cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen gels, geometrically defined\r\nmicrochannels with constrictions and simplistic under agarose migration assay, we provide\r\na comprehensive characterization of invasive migration of dendritic cells. We show that\r\nduring invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody into the dense environment. In collagen gels, we show that dendritic cells can invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading\r\nto a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile force is simultaneously necessary for reverting the nucleus back to\r\nthe cell front after invasion and maintaining this positioning during permissive migration.\r\nA functional role of the reorientation was uncovered in the first collaboration project.\r\nA prominent central actin pool was identified around the MTOC, especially pronounced in\r\ndense and compressive environments. The actin pool was shown to generate pushing forces\r\nto dilate the space for cell translocation. These forces are only necessary in non-permissive\r\nenvironments, where the nucleus reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive environments where space generation is dispensable, the\r\nMTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second collaboration project, we investigated the effects of distinct chemical\r\nenvironments on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas explained by their ability to modulate and even self-generate chemokine gradients. This\r\nallows the cells to migrate faster and more persistent in uniform chemokine fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial\r\nplayer in this process, both sensing the signal and internalizing the chemokine to create a sink.","lang":"eng"}],"acknowledgement":"This project has received funding from the Austrian Science Fund (FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","ec_funded":1,"supervisor":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","page":"133","date_created":"2025-05-26T08:49:00Z","OA_place":"publisher","_id":"19745","ddc":["570"],"corr_author":"1","oa":1,"status":"public","month":"05","department":[{"_id":"MiSi"},{"_id":"GradSch"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2025-05-27T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-058-9"],"issn":["2663-337X"]},"year":"2025","type":"dissertation","day":"27","date_updated":"2026-06-18T17:34:48Z","file_date_updated":"2025-11-27T23:30:02Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"}],"OA_embargo":"6","citation":{"ama":"Canigova N. Adaptive strategies of dendritic cell migration in response to environmental cues. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>","apa":"Canigova, N. (2025). <i>Adaptive strategies of dendritic cell migration in response to environmental cues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>","ieee":"N. Canigova, “Adaptive strategies of dendritic cell migration in response to environmental cues,” Institute of Science and Technology Austria, 2025.","chicago":"Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>.","short":"N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues, Institute of Science and Technology Austria, 2025.","mla":"Canigova, Nikola. <i>Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>.","ista":"Canigova N. 2025. Adaptive strategies of dendritic cell migration in response to environmental cues. Institute of Science and Technology Austria."},"title":"Adaptive strategies of dendritic cell migration in response to environmental cues","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No"}]