[{"acknowledgement":"We thank all members of the Hannezo and Liberali groups for fruitful discussions, as well as C. Schwayer, G. Quintas, L. Capolupo, D. Bruckner and D. Pinheiro for reading the manuscript. We also thank Y. Wu and X. Wu from the Yang group for performing experiments in the last rounds of revision and the So group at the National Institute of Biological Sciences, Beijing, for helping with the light-sheet time-lapse experiments. This work received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme via grant agreement no. 758617 (to P.L.), Swiss National Foundation (SNF) (no. POOP3_157531 to P.L.), the ERC under the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 851288 (to E.H.) and the Austrian Science Fund (FWF) (no. P 31639 to E.H.). This work was supported by the National Natural Science Foundation of China via grant no.3247060387 (to Q.Y.) and the Strategic Priority Research Program of the Chinese Academy of Sciences (no. XDB0820000 to Q.Y.) . Open access funding provided by Institute of Science and Technology (IST Austria).","type":"journal_article","day":"28","status":"public","has_accepted_license":"1","arxiv":1,"date_created":"2025-03-09T23:01:28Z","doi":"10.1038/s41567-025-02792-1","corr_author":"1","ddc":["530"],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"scopus_import":"1","OA_type":"hybrid","title":"Mechanochemical bistability of intestinal organoids enables robust morphogenesis","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Springer Nature","pmid":1,"month":"02","publication":"Nature Physics","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","date_published":"2025-02-28T00:00:00Z","citation":{"mla":"Xue, Shi-lei, et al. “Mechanochemical Bistability of Intestinal Organoids Enables Robust Morphogenesis.” Nature Physics, vol. 21, 078104, Springer Nature, 2025, doi:10.1038/s41567-025-02792-1.","chicago":"Xue, Shi-lei, Qiutan Yang, Prisca Liberali, and Edouard B Hannezo. “Mechanochemical Bistability of Intestinal Organoids Enables Robust Morphogenesis.” Nature Physics. Springer Nature, 2025. https://doi.org/10.1038/s41567-025-02792-1.","ieee":"S. Xue, Q. Yang, P. Liberali, and E. B. Hannezo, “Mechanochemical bistability of intestinal organoids enables robust morphogenesis,” Nature Physics, vol. 21. Springer Nature, 2025.","ama":"Xue S, Yang Q, Liberali P, Hannezo EB. Mechanochemical bistability of intestinal organoids enables robust morphogenesis. Nature Physics. 2025;21. doi:10.1038/s41567-025-02792-1","short":"S. Xue, Q. Yang, P. Liberali, E.B. Hannezo, Nature Physics 21 (2025).","ista":"Xue S, Yang Q, Liberali P, Hannezo EB. 2025. Mechanochemical bistability of intestinal organoids enables robust morphogenesis. Nature Physics. 21, 078104.","apa":"Xue, S., Yang, Q., Liberali, P., & Hannezo, E. B. (2025). Mechanochemical bistability of intestinal organoids enables robust morphogenesis. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-02792-1"},"intvolume":" 21","article_number":"078104","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":21,"year":"2025","publication_status":"published","file":[{"date_created":"2025-08-05T12:12:03Z","checksum":"fb5e59be145b95f9851d3d7c9dbb85e6","creator":"dernst","success":1,"access_level":"open_access","file_id":"20129","content_type":"application/pdf","relation":"main_file","date_updated":"2025-08-05T12:12:03Z","file_size":16302436,"file_name":"2025_NaturePhysics_Xue.pdf"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-08-05T12:12:03Z","date_updated":"2025-09-30T10:47:36Z","PlanS_conform":"1","department":[{"_id":"EdHa"}],"author":[{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue","first_name":"Shi-lei"},{"last_name":"Yang","first_name":"Qiutan","full_name":"Yang, Qiutan"},{"first_name":"Prisca","last_name":"Liberali","full_name":"Liberali, Prisca"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B"}],"external_id":{"pmid":["40248571"],"isi":["001434072800001"],"arxiv":["2403.19900"]},"abstract":[{"lang":"eng","text":"Reproducible pattern and form generation during embryogenesis is poorly understood. Intestinal organoid morphogenesis involves a number of mechanochemical regulators such as cell-type-specific cytoskeletal forces and osmotically driven lumen volume changes. It is unclear how these forces are coordinated in time and space to ensure robust morphogenesis. Here we show how mechanosensitive feedback on cytoskeletal tension gives rise to morphological bistability in a minimal model of organoid morphogenesis. In the model, lumen volume changes can impact the epithelial shape via both direct mechanical and indirect mechanosensitive mechanisms. We find that both bulged and budded crypt states are possible and dependent on the history of volume changes. We test key modelling assumptions via biophysical and pharmacological experiments to demonstrate how bistability can explain experimental observations, such as the importance of the timing of lumen shrinkage and robustness of the final morphogenetic state to mechanical perturbations. This suggests that bistability arising from feedback between cellular tensions and fluid pressure could be a general mechanism that coordinates multicellular shape changes in developing systems."}],"article_type":"original","oa":1,"_id":"19373","ec_funded":1,"project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version"},{"volume":60,"year":"2025","type":"journal_article","day":"08","publication_status":"published","status":"public","date_created":"2025-03-09T23:01:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s10853-024-10582-y","scopus_import":"1","publication_identifier":{"issn":["0022-2461"],"eissn":["1573-4803"]},"date_updated":"2025-03-10T06:53:16Z","OA_type":"closed access","title":"The new PrNi6Si6 intermetallic: From crystal structure to thermal and electrical transport properties across a wide temperature range (2–900 K)","language":[{"iso":"eng"}],"publisher":"Springer Nature","department":[{"_id":"MaIb"}],"month":"02","author":[{"id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","full_name":"Singh, Saurabh","last_name":"Singh","first_name":"Saurabh"},{"first_name":"A.","last_name":"Provino","full_name":"Provino, A."},{"full_name":"Pallecchi, I.","last_name":"Pallecchi","first_name":"I."},{"full_name":"Caglieris, F.","first_name":"F.","last_name":"Caglieris"},{"full_name":"Mödlinger, M.","first_name":"M.","last_name":"Mödlinger"},{"full_name":"Mele, P.","first_name":"P.","last_name":"Mele"},{"first_name":"G.","last_name":"Latronico","full_name":"Latronico, G."},{"last_name":"Takeuchi","first_name":"T.","full_name":"Takeuchi, T."},{"full_name":"Manfrinetti, P.","last_name":"Manfrinetti","first_name":"P."}],"publication":"Journal of Materials Science","abstract":[{"text":"In the present study, the new ternary rare earth intermetallic compound PrNi6Si6 has been investigated. This work completes the study of the RNi6Si6 series (R = rare earth). While the RNi6Si6 compounds for R = La and Ce adopt the CeNi6Si6-type (tP52, P4/nbm, No. 125), surprisingly PrNi6Si6 crystallizes in the YNi6Si6 prototype (tP52, P − 4b2, No. 117) as do all the heavier lanthanides (but Lu). The YNi6Si6-type and its homolog CeNi6Si6 are two tetragonal ordered derivative of the cubic NaZn13-type structure. Lattice parameters for PrNi6Si6 are a = 7.7846(1) Å, c = 11.2144(1) Å, with a unit cell volume, Vobs = 679.585(5) Å3. The temperature dependence of the inverse magnetic susceptibility χ−1(T) follows the Curie–Weiss law, with calculated values of the effective magnetic moment (µeff) and Weiss temperature (Θpm) of 3.55 μB and − 4.5 K, respectively. While the observed µeff is very close to the theoretical value of 3.58 µB for the free Pr3+ ions, a negative value of the Weiss temperature suggests antiferromagnetic interactions in PrNi6Si6. Magnetization measurements confirm that PrNi₆Si₆ orders antiferromagnetically (AFM) below a Néel temperature (TN) of 9 K. The Ni atoms contribute negligibly to the magnetic properties of this phase. The specific heat of PrNi₆Si₆ is approximately 0.42 J K − 1 g − 1. Measurements of electric and thermal transport reveal that PrNi₆Si₆ exhibits metallic behavior across a wide temperature range of 2–900 K, accompanied by a relatively low thermal conductivity of around 6 W K − 1 m − 1 at room temperature. Such properties, together with its high-temperature refractory behavior, make PrNi₆Si₆ worthy of consideration in technological applications where fairly good electrical conductivity should be accompanied by a limited thermal conductivity.","lang":"eng"}],"article_processing_charge":"No","quality_controlled":"1","article_type":"original","date_published":"2025-02-08T00:00:00Z","citation":{"ista":"Singh S, Provino A, Pallecchi I, Caglieris F, Mödlinger M, Mele P, Latronico G, Takeuchi T, Manfrinetti P. 2025. The new PrNi6Si6 intermetallic: From crystal structure to thermal and electrical transport properties across a wide temperature range (2–900 K). Journal of Materials Science. 60, 100051.","apa":"Singh, S., Provino, A., Pallecchi, I., Caglieris, F., Mödlinger, M., Mele, P., … Manfrinetti, P. (2025). The new PrNi6Si6 intermetallic: From crystal structure to thermal and electrical transport properties across a wide temperature range (2–900 K). Journal of Materials Science. Springer Nature. https://doi.org/10.1007/s10853-024-10582-y","short":"S. Singh, A. Provino, I. Pallecchi, F. Caglieris, M. Mödlinger, P. Mele, G. Latronico, T. Takeuchi, P. Manfrinetti, Journal of Materials Science 60 (2025).","chicago":"Singh, Saurabh, A. Provino, I. Pallecchi, F. Caglieris, M. Mödlinger, P. Mele, G. Latronico, T. Takeuchi, and P. Manfrinetti. “The New PrNi6Si6 Intermetallic: From Crystal Structure to Thermal and Electrical Transport Properties across a Wide Temperature Range (2–900 K).” Journal of Materials Science. Springer Nature, 2025. https://doi.org/10.1007/s10853-024-10582-y.","ieee":"S. Singh et al., “The new PrNi6Si6 intermetallic: From crystal structure to thermal and electrical transport properties across a wide temperature range (2–900 K),” Journal of Materials Science, vol. 60. Springer Nature, 2025.","ama":"Singh S, Provino A, Pallecchi I, et al. The new PrNi6Si6 intermetallic: From crystal structure to thermal and electrical transport properties across a wide temperature range (2–900 K). Journal of Materials Science. 2025;60. doi:10.1007/s10853-024-10582-y","mla":"Singh, Saurabh, et al. “The New PrNi6Si6 Intermetallic: From Crystal Structure to Thermal and Electrical Transport Properties across a Wide Temperature Range (2–900 K).” Journal of Materials Science, vol. 60, 100051, Springer Nature, 2025, doi:10.1007/s10853-024-10582-y."},"_id":"19374","article_number":"100051","intvolume":" 60","oa_version":"None"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publication_status":"published","volume":15530,"year":"2025","date_updated":"2025-09-30T10:46:54Z","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Despite the advances in probabilistic model checking, the scalability of the verification methods remains limited. In particular, the state space often becomes extremely large when instantiating parameterized Markov decision processes (MDPs) even with moderate values. Synthesizing policies for such huge MDPs is beyond the reach of available tools. We propose a learning-based approach to obtain a reasonable policy for such huge MDPs.\r\n\r\nThe idea is to generalize optimal policies obtained by model-checking small instances to larger ones using decision-tree learning. Consequently, our method bypasses the need for explicit state-space exploration of large models, providing a practical solution to the state-space explosion problem. We demonstrate the efficacy of our approach by performing extensive experimentation on the relevant models from the quantitative verification benchmark set. The experimental results indicate that our policies perform well, even when the size of the model is orders of magnitude beyond the reach of state-of-the-art analysis tools."}],"author":[{"first_name":"Muqsit","last_name":"Azeem","full_name":"Azeem, Muqsit"},{"last_name":"Chakraborty","first_name":"Debraj","full_name":"Chakraborty, Debraj"},{"full_name":"Kanav, Sudeep","last_name":"Kanav","first_name":"Sudeep"},{"first_name":"Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mohammadsadegh","last_name":"Mohagheghi","full_name":"Mohagheghi, Mohammadsadegh"},{"full_name":"Mohr, Stefanie","last_name":"Mohr","first_name":"Stefanie"},{"last_name":"Weininger","first_name":"Maximilian","id":"02ab0197-cc70-11ed-ab61-918e71f56881","full_name":"Weininger, Maximilian"}],"external_id":{"isi":["001446577100005"],"arxiv":["2410.18293"]},"department":[{"_id":"KrCh"}],"oa_version":"Preprint","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"_id":"19375","ec_funded":1,"oa":1,"page":"97-120","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2410.18293"}],"arxiv":1,"doi":"10.1007/978-3-031-82703-7_5","date_created":"2025-03-09T23:01:29Z","status":"public","day":"23","type":"conference","acknowledgement":"This research was funded in part by the DFG project 427755713 GOPro, the DFG GRK 2428 (ConVeY), the MUNI Award in Science and Humanities (MUNI/I/1757/2021) of the Grant Agency of Masaryk University, and the EU under MSCA grant agreement 101034413 (IST-BRIDGE).","OA_type":"green","title":"1–2–3–Go! Policy synthesis for parameterized Markov decision processes via decision-tree learning and generalization","publication_identifier":{"isbn":["9783031827020"],"eissn":["1611-3349"],"issn":["0302-9743"]},"scopus_import":"1","article_processing_charge":"No","quality_controlled":"1","publication":"26th International Conference on Verification, Model Checking, and Abstract Interpretation","month":"01","language":[{"iso":"eng"}],"OA_place":"repository","publisher":"Springer Nature","intvolume":" 15530","date_published":"2025-01-23T00:00:00Z","citation":{"apa":"Azeem, M., Chakraborty, D., Kanav, S., Kretinsky, J., Mohagheghi, M., Mohr, S., & Weininger, M. (2025). 1–2–3–Go! Policy synthesis for parameterized Markov decision processes via decision-tree learning and generalization. In 26th International Conference on Verification, Model Checking, and Abstract Interpretation (Vol. 15530, pp. 97–120). Denver, CO, United States: Springer Nature. https://doi.org/10.1007/978-3-031-82703-7_5","ista":"Azeem M, Chakraborty D, Kanav S, Kretinsky J, Mohagheghi M, Mohr S, Weininger M. 2025. 1–2–3–Go! Policy synthesis for parameterized Markov decision processes via decision-tree learning and generalization. 26th International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 15530, 97–120.","short":"M. Azeem, D. Chakraborty, S. Kanav, J. Kretinsky, M. Mohagheghi, S. Mohr, M. Weininger, in:, 26th International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2025, pp. 97–120.","ama":"Azeem M, Chakraborty D, Kanav S, et al. 1–2–3–Go! Policy synthesis for parameterized Markov decision processes via decision-tree learning and generalization. In: 26th International Conference on Verification, Model Checking, and Abstract Interpretation. Vol 15530. Springer Nature; 2025:97-120. doi:10.1007/978-3-031-82703-7_5","chicago":"Azeem, Muqsit, Debraj Chakraborty, Sudeep Kanav, Jan Kretinsky, Mohammadsadegh Mohagheghi, Stefanie Mohr, and Maximilian Weininger. “1–2–3–Go! Policy Synthesis for Parameterized Markov Decision Processes via Decision-Tree Learning and Generalization.” In 26th International Conference on Verification, Model Checking, and Abstract Interpretation, 15530:97–120. Springer Nature, 2025. https://doi.org/10.1007/978-3-031-82703-7_5.","ieee":"M. Azeem et al., “1–2–3–Go! Policy synthesis for parameterized Markov decision processes via decision-tree learning and generalization,” in 26th International Conference on Verification, Model Checking, and Abstract Interpretation, Denver, CO, United States, 2025, vol. 15530, pp. 97–120.","mla":"Azeem, Muqsit, et al. “1–2–3–Go! Policy Synthesis for Parameterized Markov Decision Processes via Decision-Tree Learning and Generalization.” 26th International Conference on Verification, Model Checking, and Abstract Interpretation, vol. 15530, Springer Nature, 2025, pp. 97–120, doi:10.1007/978-3-031-82703-7_5."},"conference":{"location":"Denver, CO, United States","start_date":"2025-01-20","end_date":"2025-01-21","name":"VMCAI: Verification, Model Checking, and Abstract Interpretation"}},{"_id":"19393","oa_version":"Published Version","page":"192","oa":1,"author":[{"first_name":"Volker","last_name":"Karle","orcid":"0000-0002-6963-0129","full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"}],"abstract":[{"lang":"eng","text":"Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.\r\nWhile most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.\r\nIn this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.\r\nWe begin by establishing a theoretical bridge between periodically kicked rotors and \"crystalline\" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear\r\nmolecules provide an ideal experimental platform due to their abovementioned precise controllability.\r\nThe core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through\r\nmolecular alignment and rotational level populations.\r\nThese findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental\r\nphysics and developing quantum technologies."}],"department":[{"_id":"GradSch"},{"_id":"MiLe"}],"date_updated":"2026-04-07T11:48:53Z","alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"file_date_updated":"2025-03-20T08:02:35Z","degree_awarded":"PhD","file":[{"checksum":"d3ab25782c7ea38ce9910e57d25f6733","date_created":"2025-03-12T12:56:46Z","success":1,"creator":"vkarle","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"19394","file_size":10625143,"date_updated":"2025-03-12T12:56:46Z","file_name":"thesis_final.pdf"},{"relation":"source_file","content_type":"application/zip","file_id":"19400","date_updated":"2025-03-20T08:02:35Z","file_size":23119202,"file_name":"thesis.zip","checksum":"3ccfb0aeba4d860d71e18347913034e4","date_created":"2025-03-13T13:15:10Z","creator":"vkarle","access_level":"closed"}],"related_material":{"record":[{"id":"14851","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"12788"},{"status":"public","relation":"part_of_dissertation","id":"19425"},{"id":"9903","relation":"part_of_dissertation","status":"public"},{"id":"15004","status":"public","relation":"part_of_dissertation"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2025","publication_status":"published","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2025-03-13T00:00:00Z","citation":{"short":"V. Karle, Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors, Institute of Science and Technology Austria, 2025.","ista":"Karle V. 2025. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria.","apa":"Karle, V. (2025). Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19393","mla":"Karle, Volker. Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19393.","ama":"Karle V. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. 2025. doi:10.15479/AT-ISTA-19393","ieee":"V. Karle, “Non-equilibrium topological phases with periodically driven molecules and quantum rotors,” Institute of Science and Technology Austria, 2025.","chicago":"Karle, Volker. “Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19393."},"article_processing_charge":"No","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","month":"03","OA_type":"gold","title":"Non-equilibrium topological phases with periodically driven molecules and quantum rotors","corr_author":"1","ddc":["530"],"publication_identifier":{"eissn":["2663-337X"]},"status":"public","has_accepted_license":"1","doi":"10.15479/AT-ISTA-19393","date_created":"2025-03-12T13:04:59Z","type":"dissertation","day":"13"},{"title":"Cell-Surface Auxin Signaling: Linking molecular pathways to plant development","publication_identifier":{"eisbn":["978-3-99078-054-1"],"eissn":["2663-337X"]},"ddc":["580"],"corr_author":"1","doi":"10.15479/AT-ISTA-19395","date_created":"2025-03-12T14:25:42Z","has_accepted_license":"1","status":"public","day":"13","type":"dissertation","acknowledgement":"I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research.","citation":{"apa":"Monzer, A. (2025). Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19395","ista":"Monzer A. 2025. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.","short":"A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025.","ama":"Monzer A. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. 2025. doi:10.15479/AT-ISTA-19395","ieee":"A. Monzer, “Cell-Surface Auxin Signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.","chicago":"Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19395.","mla":"Monzer, Aline. Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19395."},"date_published":"2025-03-13T00:00:00Z","article_processing_charge":"No","month":"03","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","language":[{"iso":"eng"}],"date_updated":"2026-06-18T18:14:07Z","degree_awarded":"PhD","file_date_updated":"2025-04-01T07:55:27Z","supervisor":[{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12291"},{"status":"public","relation":"part_of_dissertation","id":"14826"},{"id":"19398","status":"public","relation":"part_of_dissertation"},{"id":"19399","relation":"part_of_dissertation","status":"public"}]},"file":[{"file_name":"Final Thesis Aline Monzer.pdf","file_size":13119670,"date_updated":"2025-03-12T14:14:49Z","content_type":"application/pdf","file_id":"19396","relation":"main_file","access_level":"open_access","creator":"amonzer","success":1,"date_created":"2025-03-12T14:14:49Z","checksum":"9a3dd03bb4ec6b9907a325c3c4e8a1d7"},{"date_created":"2025-03-12T14:15:19Z","checksum":"a353ce1ee2eabce37bca35499e76dbf1","creator":"amonzer","access_level":"closed","file_id":"19397","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":13774837,"date_updated":"2025-04-01T07:55:27Z","file_name":"Thesis Aline.docx"}],"publication_status":"published","year":"2025","oa_version":"Published Version","_id":"19395","oa":1,"page":"160","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood."}],"author":[{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"}]},{"OA_type":"green","title":"TMK interacting network of receptor like kinases for auxin canalization and beyond","ddc":["580"],"corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.02.28.640727"}],"doi":"10.1101/2025.02.28.640727","date_created":"2025-03-12T14:28:53Z","status":"public","has_accepted_license":"1","type":"preprint","day":"02","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.","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2025-03-02T00:00:00Z","citation":{"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. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.02.28.640727","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, 10.1101/2025.02.28.640727.","short":"A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal, E. Cervenova, J. Friml, BioRxiv (n.d.).","ama":"Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv. doi:10.1101/2025.02.28.640727","ieee":"A. Monzer et al., “TMK interacting network of receptor like kinases for auxin canalization and beyond,” bioRxiv. Cold Spring Harbor Laboratory.","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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2025.02.28.640727.","mla":"Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2025.02.28.640727."},"article_processing_charge":"No","publication":"bioRxiv","month":"03","language":[{"iso":"eng"}],"OA_place":"repository","publisher":"Cold Spring Harbor Laboratory","date_updated":"2026-06-18T18:13:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19395"}]},"publication_status":"draft","year":"2025","oa_version":"Published Version","_id":"19398","oa":1,"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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"author":[{"last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","last_name":"Rodriguez Solovey"},{"last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"first_name":"Michael","last_name":"Smejkal","full_name":"Smejkal, Michael","id":"79a5a1be-04a3-11f0-ba18-a1730e0b58e9"},{"first_name":"Ema","last_name":"Cervenova","full_name":"Cervenova, Ema","id":"9f185b95-04a3-11f0-8245-f5e32eeb470f"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}]},{"OA_type":"green","title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","corr_author":"1","ddc":["580"],"doi":"10.1101/2022.11.30.518503","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.11.30.518503"}],"date_created":"2025-03-13T08:36:48Z","status":"public","day":"20","type":"preprint","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).","date_published":"2025-02-20T00:00:00Z","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. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.11.30.518503","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, 10.1101/2022.11.30.518503.","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.).","ieee":"L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” bioRxiv. Cold Spring Harbor Laboratory.","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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2022.11.30.518503.","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. bioRxiv. doi:10.1101/2022.11.30.518503","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2022.11.30.518503."},"article_processing_charge":"No","publication":"bioRxiv","month":"02","language":[{"iso":"eng"}],"OA_place":"repository","publisher":"Cold Spring Harbor Laboratory","date_updated":"2026-06-18T18:14:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"20656","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19395"},{"relation":"dissertation_contains","status":"public","id":"20364"}]},"publication_status":"draft","year":"2025","oa_version":"Published Version","_id":"19399","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Cell surface receptor complexes for auxin signaling in plants","grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa":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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"author":[{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia"},{"first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia","last_name":"Zou","first_name":"Minxia"},{"first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"first_name":"Dmitrii","last_name":"Vladimirtsev","full_name":"Vladimirtsev, Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d"},{"first_name":"Marek","last_name":"Randuch","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"first_name":"Yongfan","last_name":"Yu","full_name":"Yu, Yongfan"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","last_name":"Gelová"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge"},{"first_name":"Jakub","last_name":"Hajny","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Meng","last_name":"Chen","full_name":"Chen, Meng"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan"},{"first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li"},{"full_name":"Marques-Bueno, Maria Mar","last_name":"Marques-Bueno","first_name":"Maria Mar"},{"id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","full_name":"Quddoos, Zainab","last_name":"Quddoos","first_name":"Zainab"},{"first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"last_name":"Kulich","first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","full_name":"Kulich, Ivan"},{"first_name":"Yvon","last_name":"Jaillais","full_name":"Jaillais, Yvon"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"},{"_id":"XiFe"}]},{"quality_controlled":"1","article_processing_charge":"Yes","publication":"Nature Communications","month":"03","pmid":1,"OA_place":"publisher","publisher":"Springer Nature","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 16","article_number":"2103","citation":{"mla":"Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” Nature Communications, vol. 16, 2103, Springer Nature, 2025, doi:10.1038/s41467-025-57252-4.","chicago":"Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-57252-4.","ieee":"M. Janik et al., “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors,” Nature Communications, vol. 16. Springer Nature, 2025.","ama":"Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. Nature Communications. 2025;16. doi:10.1038/s41467-025-57252-4","short":"M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger, S. Calcaterra, M. Botifoll, A. Garzón Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M. Pop, G. Katsaros, Nature Communications 16 (2025).","ista":"Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T, Calcaterra S, Botifoll M, Garzón Manjón A, Arbiol J, Chrastina D, Isella G, Pop IM, Katsaros G. 2025. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. Nature Communications. 16, 2103.","apa":"Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger, T., … Katsaros, G. (2025). Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-57252-4"},"date_published":"2025-03-01T00:00:00Z","date_created":"2025-03-16T23:01:23Z","doi":"10.1038/s41467-025-57252-4","arxiv":1,"status":"public","has_accepted_license":"1","day":"01","type":"journal_article","acknowledgement":"We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. We thank Simon Robson for proofreading the manuscript. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the HORIZON-RIA 101069515 project. This research was funded in whole or in part by the Austrian Science Fund (FWF) https://doi.org/10.55776/P32235, https://doi.org/10.55776/I5060 and https://doi.org/10.55776/P36507. For Open Access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. M.J. acknowledges funding from FellowQUTE 2024-01. K.R. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413. I.M.P. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission - NextGenerationEU (Regulation EU 2020/2094), through CSIC’s Quantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa programme from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD programme. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors acknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Centre at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM60.","DOAJ_listed":"1","title":"Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors","OA_type":"gold","scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"ddc":["530"],"corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"High kinetic inductance superconductors are gaining increasing interest for the realisation of qubits, amplifiers and detectors. Moreover, thanks to their high impedance, quantum buses made of such materials enable large zero-point fluctuations of the voltage, boosting the coupling rates to spin and charge qubits. However, fully exploiting the potential of disordered or granular superconductors is challenging, as their inductance and, therefore, impedance at high values are difficult to control. Here, we report a reproducible fabrication of granular aluminium resonators by developing a wireless ohmmeter, which allows in situ measurements during film deposition and, therefore, control of the kinetic inductance of granular aluminium films. Reproducible fabrication of circuits with impedances (inductances) exceeding 13 kΩ (1 nH per square) is now possible. By integrating a 7.9 kΩ resonator with a germanium double quantum dot, we demonstrate strong charge-photon coupling with a rate of gc/2π = 566 ± 2 MHz. This broadly applicable method opens the path for novel qubits and high-fidelity, long-distance two-qubit gates."}],"external_id":{"pmid":["40025007"],"arxiv":["2407.03079"],"isi":["001434774800001"]},"author":[{"first_name":"Marian","last_name":"Janik","full_name":"Janik, Marian","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87"},{"id":"53f93ea2-803f-11ed-ab7e-b283135794ef","full_name":"Roux, Kevin Etienne Robert","last_name":"Roux","first_name":"Kevin Etienne Robert"},{"id":"18777c01-896a-11ed-bdf8-e4851dc07d16","full_name":"Borja Espinosa, Carla N","last_name":"Borja Espinosa","first_name":"Carla N"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi","first_name":"Oliver"},{"full_name":"Baghdadi, Abdulhamid","id":"160D87FA-96B5-11E9-BF77-7626E6697425","first_name":"Abdulhamid","last_name":"Baghdadi"},{"first_name":"Thomas","last_name":"Adletzberger","full_name":"Adletzberger, Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"last_name":"Garzón Manjón","first_name":"Alba","full_name":"Garzón Manjón, Alba"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"first_name":"Ioan M.","last_name":"Pop","full_name":"Pop, Ioan M."},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros"}],"department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"M-Shop"}],"oa_version":"Published Version","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515","name":"Integrated Germanium Quantum Technology"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"_id":"19401","ec_funded":1,"oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"18144"},{"status":"public","relation":"research_data","id":"18886"}]},"file":[{"file_name":"2025_NatureComm_Janik.pdf","relation":"main_file","file_id":"19415","content_type":"application/pdf","date_updated":"2025-03-17T10:53:32Z","file_size":6364878,"access_level":"open_access","checksum":"a9383dd978ca2c50b7dded6c0bb2cd49","date_created":"2025-03-17T10:53:32Z","success":1,"creator":"dernst"}],"publication_status":"published","volume":16,"year":"2025","APC_amount":"7068 EUR","date_updated":"2026-05-20T06:34:51Z","file_date_updated":"2025-03-17T10:53:32Z"},{"ddc":["570"],"scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"OA_type":"gold","title":"Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles","DOAJ_listed":"1","acknowledgement":"This research was supported in part by the National Science Foundation under Grant No. 1844336 (J.S.), 2239567 (A.P), and MRSEC DMR-2308691 (A.G., N.P.K.) and the National Institutes of Health under Grant No. 1R35GM147170-01 (A.P). J.S. thanks Reinhard Lipowsky for discussions on stability of foams.\r\nOpen Access funding enabled and organized by Projekt DEAL.","type":"journal_article","day":"27","status":"public","has_accepted_license":"1","doi":"10.1038/s41467-025-57178-x","date_created":"2025-03-16T23:01:23Z","date_published":"2025-02-27T00:00:00Z","citation":{"chicago":"Gu, Andre A., Mehmet C Ucar, Peter Tran, Arthur Prindle, Neha P. Kamat, and Jan Steinkühler. “Remodeling of Lipid-Foam Prototissues by Network-Wide Tension Fluctuations Induced by Active Particles.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-57178-x.","ieee":"A. A. Gu, M. C. Ucar, P. Tran, A. Prindle, N. P. Kamat, and J. Steinkühler, “Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles,” Nature Communications, vol. 16. Springer Nature, 2025.","ama":"Gu AA, Ucar MC, Tran P, Prindle A, Kamat NP, Steinkühler J. Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles. Nature Communications. 2025;16. doi:10.1038/s41467-025-57178-x","mla":"Gu, Andre A., et al. “Remodeling of Lipid-Foam Prototissues by Network-Wide Tension Fluctuations Induced by Active Particles.” Nature Communications, vol. 16, 2026, Springer Nature, 2025, doi:10.1038/s41467-025-57178-x.","ista":"Gu AA, Ucar MC, Tran P, Prindle A, Kamat NP, Steinkühler J. 2025. Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles. Nature Communications. 16, 2026.","apa":"Gu, A. A., Ucar, M. C., Tran, P., Prindle, A., Kamat, N. P., & Steinkühler, J. (2025). Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-57178-x","short":"A.A. Gu, M.C. Ucar, P. Tran, A. Prindle, N.P. Kamat, J. Steinkühler, Nature Communications 16 (2025)."},"intvolume":" 16","article_number":"2026","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Springer Nature","pmid":1,"month":"02","publication":"Nature Communications","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","file_date_updated":"2025-03-17T09:43:27Z","date_updated":"2025-09-30T10:59:30Z","year":"2025","volume":16,"publication_status":"published","file":[{"file_name":"2025_NatureComm_Gu.pdf","file_size":2260791,"date_updated":"2025-03-17T09:43:27Z","relation":"main_file","file_id":"19411","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","checksum":"3bbae9b470c639005815342a39e96918","date_created":"2025-03-17T09:43:27Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_type":"original","oa":1,"_id":"19402","oa_version":"Published Version","department":[{"_id":"EdHa"}],"author":[{"full_name":"Gu, Andre A.","first_name":"Andre A.","last_name":"Gu"},{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","first_name":"Mehmet C"},{"last_name":"Tran","first_name":"Peter","full_name":"Tran, Peter"},{"full_name":"Prindle, Arthur","last_name":"Prindle","first_name":"Arthur"},{"full_name":"Kamat, Neha P.","first_name":"Neha P.","last_name":"Kamat"},{"last_name":"Steinkühler","first_name":"Jan","full_name":"Steinkühler, Jan"}],"external_id":{"pmid":["40016255"],"isi":["001435269000002"]},"abstract":[{"text":"Recent advances in the field of bottom-up synthetic biology have led to the development of synthetic cells that mimic some features of real cells, such as division, protein synthesis, or DNA replication. Larger assemblies of synthetic cells may be used to form prototissues. However, existing prototissues are limited by their relatively small lateral dimensions or their lack of remodeling ability. Here, we introduce a lipid-based tissue mimetic that can be easily prepared and functionalized, consisting of a millimeter-sized “lipid-foam” with individual micrometer-sized compartments bound by lipid bilayers. We characterize the structural and mechanical properties of the lipid-foam tissue mimetic, and we demonstrate self-healing capabilities enabled by the fluidity of the lipid bilayers. Upon inclusion of bacteria in the tissue compartments, we observe that the tissue mimetic exhibits network-wide tension fluctuations driven by membrane tension generation by the swimming bacteria. Active tension fluctuations facilitate the fluidization and reorganization of the prototissue, providing a versatile platform for understanding and mimicking biological tissues.","lang":"eng"}]},{"type":"journal_article","day":"01","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","date_created":"2025-03-16T23:01:24Z","arxiv":1,"doi":"10.1007/s00205-025-02088-x","status":"public","has_accepted_license":"1","corr_author":"1","ddc":["510"],"scopus_import":"1","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"OA_type":"hybrid","title":"BCS critical temperature on half-spaces","month":"04","pmid":1,"language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication":"Archive for Rational Mechanics and Analysis","date_published":"2025-04-01T00:00:00Z","citation":{"apa":"Roos, B., & Seiringer, R. (2025). BCS critical temperature on half-spaces. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-025-02088-x","ista":"Roos B, Seiringer R. 2025. BCS critical temperature on half-spaces. Archive for Rational Mechanics and Analysis. 249, 20.","short":"B. Roos, R. Seiringer, Archive for Rational Mechanics and Analysis 249 (2025).","ieee":"B. Roos and R. Seiringer, “BCS critical temperature on half-spaces,” Archive for Rational Mechanics and Analysis, vol. 249. Springer Nature, 2025.","chicago":"Roos, Barbara, and Robert Seiringer. “BCS Critical Temperature on Half-Spaces.” Archive for Rational Mechanics and Analysis. Springer Nature, 2025. https://doi.org/10.1007/s00205-025-02088-x.","ama":"Roos B, Seiringer R. BCS critical temperature on half-spaces. Archive for Rational Mechanics and Analysis. 2025;249. doi:10.1007/s00205-025-02088-x","mla":"Roos, Barbara, and Robert Seiringer. “BCS Critical Temperature on Half-Spaces.” Archive for Rational Mechanics and Analysis, vol. 249, 20, Springer Nature, 2025, doi:10.1007/s00205-025-02088-x."},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 249","article_number":"20","publication_status":"published","volume":249,"year":"2025","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"access_level":"open_access","checksum":"66803fb63a57987eb4f13ee2949bea77","date_created":"2025-03-17T10:07:45Z","success":1,"creator":"dernst","file_name":"2025_ArchiveRatMech_Roos.pdf","relation":"main_file","content_type":"application/pdf","file_id":"19412","date_updated":"2025-03-17T10:07:45Z","file_size":1224282}],"file_date_updated":"2025-03-17T10:07:45Z","date_updated":"2025-09-30T11:01:08Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"We study the BCS critical temperature on half-spaces in dimensions d =1, 2, 3 with Dirichlet or Neumann boundary conditions. We prove that the critical temperature on a half-space is strictly higher than on Rd, at least at weak coupling in d = 1, 2 and weak coupling and small chemical potential in d = 3. Furthermore, we show that the relative shift in critical temperature vanishes in the weak coupling limit.","lang":"eng"}],"author":[{"first_name":"Barbara","last_name":"Roos","orcid":"0000-0002-9071-5880","full_name":"Roos, Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"},{"last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"external_id":{"isi":["001435380100001"],"arxiv":["2306.05824"],"pmid":["40041541"]},"oa":1,"article_type":"original","oa_version":"Published Version","_id":"19403","project":[{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}]},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"intvolume":" 44","article_number":"115387","date_published":"2025-03-25T00:00:00Z","citation":{"mla":"Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” Cell Reports, vol. 44, no. 3, 115387, Elsevier, 2025, doi:10.1016/j.celrep.2025.115387.","ama":"Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. 2025;44(3). doi:10.1016/j.celrep.2025.115387","ieee":"S. Tavano et al., “BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation,” Cell Reports, vol. 44, no. 3. Elsevier, 2025.","chicago":"Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” Cell Reports. Elsevier, 2025. https://doi.org/10.1016/j.celrep.2025.115387.","short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (2025).","apa":"Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A., … Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2025.115387","ista":"Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R, Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. 44(3), 115387."},"article_processing_charge":"Yes","quality_controlled":"1","publication":"Cell Reports","pmid":1,"month":"03","language":[{"iso":"eng"}],"publisher":"Elsevier","OA_place":"publisher","OA_type":"gold","issue":"3","title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","ddc":["570"],"corr_author":"1","scopus_import":"1","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"date_created":"2025-03-16T23:01:24Z","doi":"10.1016/j.celrep.2025.115387","status":"public","has_accepted_license":"1","type":"journal_article","day":"25","DOAJ_listed":"1","acknowledgement":"We are grateful to the colleagues who contributed to this work with discussions, technical advice, and feedback on the manuscript: Irene Steccari, David Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship (ALTF 1159-2018).","oa_version":"Published Version","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"},{"name":"Mechanosensation in cell migration: the role of friction forces in cell polarization and directed migration","_id":"269CD5C4-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1159-2018"}],"_id":"19404","oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"author":[{"id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","full_name":"Tavano, Ste","orcid":"0000-0001-9970-7804","last_name":"Tavano","first_name":"Ste"},{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner"},{"last_name":"Tasciyan","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren"},{"last_name":"Tong","first_name":"Xin","id":"50F65CDC-AA30-11E9-A72B-8A12E6697425","full_name":"Tong, Xin"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland","last_name":"Kardos","first_name":"Roland"},{"first_name":"Alexandra","last_name":"Schauer","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["40057955"],"isi":["001443652700001"]},"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"date_updated":"2025-10-22T07:00:04Z","file_date_updated":"2025-03-17T10:26:54Z","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":9067797,"date_updated":"2025-03-17T10:26:54Z","file_id":"19413","content_type":"application/pdf","relation":"main_file","file_name":"2025_CellReports_Tavano.pdf","creator":"dernst","success":1,"date_created":"2025-03-17T10:26:54Z","checksum":"57e05dd1598c807af0afdb32cec039d3","access_level":"open_access"}],"publication_status":"published","volume":44,"year":"2025"},{"external_id":{"arxiv":["2410.00102"],"isi":["001414132600001"]},"author":[{"full_name":"Pinsonneault, Marc H.","last_name":"Pinsonneault","first_name":"Marc H."},{"last_name":"Zinn","first_name":"Joel C.","full_name":"Zinn, Joel C."},{"full_name":"Tayar, Jamie","last_name":"Tayar","first_name":"Jamie"},{"first_name":"Aldo","last_name":"Serenelli","full_name":"Serenelli, Aldo"},{"first_name":"Rafael A.","last_name":"García","full_name":"García, Rafael A."},{"last_name":"Mathur","first_name":"Savita","full_name":"Mathur, Savita"},{"last_name":"Vrard","first_name":"Mathieu","full_name":"Vrard, Mathieu"},{"full_name":"Elsworth, Yvonne P.","last_name":"Elsworth","first_name":"Yvonne P."},{"first_name":"Benoit","last_name":"Mosser","full_name":"Mosser, Benoit"},{"first_name":"Dennis","last_name":"Stello","full_name":"Stello, Dennis"},{"first_name":"Keaton J.","last_name":"Bell","full_name":"Bell, Keaton J."},{"last_name":"Bugnet","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000"},{"last_name":"Corsaro","first_name":"Enrico","full_name":"Corsaro, Enrico"},{"full_name":"Gaulme, Patrick","first_name":"Patrick","last_name":"Gaulme"},{"full_name":"Hekker, Saskia","last_name":"Hekker","first_name":"Saskia"},{"last_name":"Hon","first_name":"Marc","full_name":"Hon, Marc"},{"full_name":"Huber, Daniel","first_name":"Daniel","last_name":"Huber"},{"full_name":"Kallinger, Thomas","last_name":"Kallinger","first_name":"Thomas"},{"first_name":"Kaili","last_name":"Cao","full_name":"Cao, Kaili"},{"full_name":"Johnson, Jennifer A.","first_name":"Jennifer A.","last_name":"Johnson"},{"last_name":"Liagre","first_name":"Bastien","full_name":"Liagre, Bastien"},{"full_name":"Patton, Rachel A.","last_name":"Patton","first_name":"Rachel A."},{"last_name":"Santos","first_name":"Ângela R.G.","full_name":"Santos, Ângela R.G."},{"first_name":"Sarbani","last_name":"Basu","full_name":"Basu, Sarbani"},{"first_name":"Paul G.","last_name":"Beck","full_name":"Beck, Paul G."},{"full_name":"Beers, Timothy C.","first_name":"Timothy C.","last_name":"Beers"},{"full_name":"Chaplin, William J.","first_name":"William J.","last_name":"Chaplin"},{"full_name":"Cunha, Katia","first_name":"Katia","last_name":"Cunha"},{"full_name":"Frinchaboy, Peter M.","last_name":"Frinchaboy","first_name":"Peter M."},{"full_name":"Girardi, Léo","last_name":"Girardi","first_name":"Léo"},{"last_name":"Godoy-Rivera","first_name":"Diego","full_name":"Godoy-Rivera, Diego"},{"full_name":"Holtzman, Jon A.","last_name":"Holtzman","first_name":"Jon A."},{"full_name":"Jönsson, Henrik","first_name":"Henrik","last_name":"Jönsson"},{"last_name":"Mészáros","first_name":"Szabolcs","full_name":"Mészáros, Szabolcs"},{"full_name":"Reyes, Claudia","last_name":"Reyes","first_name":"Claudia"},{"last_name":"Rix","first_name":"Hans Walter","full_name":"Rix, Hans Walter"},{"full_name":"Shetrone, Matthew","last_name":"Shetrone","first_name":"Matthew"},{"first_name":"Verne V.","last_name":"Smith","full_name":"Smith, Verne V."},{"full_name":"Spoo, Taylor","first_name":"Taylor","last_name":"Spoo"},{"last_name":"Stassun","first_name":"Keivan G.","full_name":"Stassun, Keivan G."},{"full_name":"Wang, Ji","first_name":"Ji","last_name":"Wang"}],"abstract":[{"lang":"eng","text":"In the third APOKASC catalog, we present data for the complete sample of 15,808 evolved stars with APOGEE spectroscopic parameters and Kepler asteroseismology. We used 10 independent asteroseismic analysis techniques and anchor our system on fundamental radii derived from Gaia L and spectroscopic Teff. We provide evolutionary state, asteroseismic surface gravity, mass, radius, age, and the data used to derive them for 12,418 stars. This includes 10,036 exceptionally precise measurements, with median fractional uncertainties in \r\nvmax, Δν, mass, radius, and age of 0.6%, 0.6%, 3.8%, 1.8%, and 11.1%, respectively. We provide more limited data for 1624 additional stars that either have lower-quality data or are outside of our primary calibration domain. Using lower red giant branch (RGB) stars, we find a median age for the chemical thick disk of 9.14 ± 0.05(ran) ± 0.9(sys) Gyr with an age dispersion of 1.1 Gyr, consistent with our error model. We calibrate our red clump (RC) mass loss to derive an age consistent with the lower RGB and provide asymptotic GB and RGB ages for luminous stars. We also find a sharp upper-age boundary in the chemical thin disk. We find that scaling relations are precise and accurate on the lower RGB and RC, but they become more model dependent for more luminous giants and break down at the tip of the RGB. We recommend the use of multiple methods, calibration to a fundamental scale, and the use of stellar models to interpret frequency spacings."}],"department":[{"_id":"LiBu"}],"_id":"19405","oa_version":"Published Version","article_type":"original","oa":1,"file":[{"access_level":"open_access","success":1,"creator":"dernst","checksum":"a01a6645c6cb0b5cc75490f3339a2244","date_created":"2025-03-17T10:40:41Z","file_name":"2025_AstrophysicalJourSuppl_Pinsonneault.pdf","date_updated":"2025-03-17T10:40:41Z","file_size":4993506,"relation":"main_file","file_id":"19414","content_type":"application/pdf"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2025","volume":276,"publication_status":"published","date_updated":"2025-09-30T11:03:01Z","file_date_updated":"2025-03-17T10:40:41Z","publication":"Astrophysical Journal, Supplement Series","quality_controlled":"1","article_processing_charge":"Yes","publisher":"IOP Publishing","OA_place":"publisher","language":[{"iso":"eng"}],"month":"02","article_number":"69","intvolume":" 276","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Pinsonneault, Marc H., et al. “APOKASC-3: The Third Joint Spectroscopic and Asteroseismic Catalog for Evolved Stars in the Kepler Fields.” Astrophysical Journal, Supplement Series, vol. 276, no. 2, 69, IOP Publishing, 2025, doi:10.3847/1538-4365/ad9fef.","ieee":"M. H. Pinsonneault et al., “APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields,” Astrophysical Journal, Supplement Series, vol. 276, no. 2. IOP Publishing, 2025.","chicago":"Pinsonneault, Marc H., Joel C. Zinn, Jamie Tayar, Aldo Serenelli, Rafael A. García, Savita Mathur, Mathieu Vrard, et al. “APOKASC-3: The Third Joint Spectroscopic and Asteroseismic Catalog for Evolved Stars in the Kepler Fields.” Astrophysical Journal, Supplement Series. IOP Publishing, 2025. https://doi.org/10.3847/1538-4365/ad9fef.","ama":"Pinsonneault MH, Zinn JC, Tayar J, et al. APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields. Astrophysical Journal, Supplement Series. 2025;276(2). doi:10.3847/1538-4365/ad9fef","short":"M.H. Pinsonneault, J.C. Zinn, J. Tayar, A. Serenelli, R.A. García, S. Mathur, M. Vrard, Y.P. Elsworth, B. Mosser, D. Stello, K.J. Bell, L.A. Bugnet, E. Corsaro, P. Gaulme, S. Hekker, M. Hon, D. Huber, T. Kallinger, K. Cao, J.A. Johnson, B. Liagre, R.A. Patton, Â.R.G. Santos, S. Basu, P.G. Beck, T.C. Beers, W.J. Chaplin, K. Cunha, P.M. Frinchaboy, L. Girardi, D. Godoy-Rivera, J.A. Holtzman, H. Jönsson, S. Mészáros, C. Reyes, H.W. Rix, M. Shetrone, V.V. Smith, T. Spoo, K.G. Stassun, J. Wang, Astrophysical Journal, Supplement Series 276 (2025).","apa":"Pinsonneault, M. H., Zinn, J. C., Tayar, J., Serenelli, A., García, R. A., Mathur, S., … Wang, J. (2025). APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields. Astrophysical Journal, Supplement Series. IOP Publishing. https://doi.org/10.3847/1538-4365/ad9fef","ista":"Pinsonneault MH, Zinn JC, Tayar J, Serenelli A, García RA, Mathur S, Vrard M, Elsworth YP, Mosser B, Stello D, Bell KJ, Bugnet LA, Corsaro E, Gaulme P, Hekker S, Hon M, Huber D, Kallinger T, Cao K, Johnson JA, Liagre B, Patton RA, Santos ÂRG, Basu S, Beck PG, Beers TC, Chaplin WJ, Cunha K, Frinchaboy PM, Girardi L, Godoy-Rivera D, Holtzman JA, Jönsson H, Mészáros S, Reyes C, Rix HW, Shetrone M, Smith VV, Spoo T, Stassun KG, Wang J. 2025. APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields. Astrophysical Journal, Supplement Series. 276(2), 69."},"date_published":"2025-02-01T00:00:00Z","has_accepted_license":"1","status":"public","doi":"10.3847/1538-4365/ad9fef","arxiv":1,"date_created":"2025-03-16T23:01:24Z","acknowledgement":"We thank the anonymous referee for providing constructive comments that improved the paper. This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the NASA Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. M.H.P. acknowledges support from NASA grants 80NSSC24K0637 and 80NSSC18K1582. M.H.P., J.T., and P.M.F. acknowledge that part of this work was performed at the Aspen Center for Physics, which is supported by National Science Foundation grant PHY-1607611. M.H.P. acknowledges support from the Fundación Occident and the Instituto de Astrofísica de Canarias under the Visiting Researcher Programme 2022-2025 agreed between both institutions. A.S. acknowledges support by the Spanish Ministry of Science, Innovation and Universities through the grant PID2023-149918NB-I00 and the program Unidad de Excelencia Marìa de Maeztu CEX2020-001058-M, and by Generalitat de Catalunya through grant 2021-SGR-1526. S.B. acknowledges NSF grant AST-2205026. P.G.B. acknowledges support by the Spanish Ministry of Science and Innovation with the Ramón y Cajal fellowship Nos. RYC-2021-033137-I and MRR4032204. D.S. is supported by the Australian Research Council (DP190100666). P.G.B., D.G.R., and R.A.G. acknowledge support from the Spanish Ministry of Science and Innovation from grant No. PID2023-146453NB-100 (PLAtoSOnG). M.V. acknowledges support from NASA grant 80NSSC18K1582 and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 101019653). T.C.B. acknowledges partial support for this work from grant PHY 14-30152; Physics Frontier Center/JINA Center for the Evolution of the Elements (JINA-CEE), and OISE-1927130: The International Research Network for Nuclear Astrophysics (IReNA), awarded by the US National Science Foundation. The research leading to the presented results has received funding from the ERC Consolidator Grant DipolarSound (grant agreement No. 101000296). P.F. and T.S. acknowledges support from the National Science Foundation Astronomy and Astrophysics grants AST-1715662 and AST-2206541. S.M. acknowledges support by the Spanish Ministry of Science and Innovation with the Ramon y Cajal fellowship Nos. RYC-2015-17697, PID2019-107061GB-C66, and PID2023-149439NB-C41, and through AEI under the Severo Ochoa Centres of Excellence Programme 2020–2023 (CEX2019-000920-S). S.M. and D.G.R. acknowledge support from the Spanish Ministry of Science and Innovation (MICINN) from grant No. PID2019-107187GB-I00. D.G.R. acknowledges support from the Spanish Ministry of Science and Innovation (MICINN) with the Juan de la Cierva program under contract JDC2022-049054-I. L.B. gratefully acknowledges support from the European Research Council (ERC) under the Horizon Europe program (Calcifer; Starting grant agreement No. 101165631). A.R.G.S. acknowledges the support from the FCT through national funds and FEDER through COMPETE2020 (UIDB/04434/2020, UIDP/04434/2020, and 2022.03993.PTDC) and the support from the FCT through work contract No. 2020.02480.CEECIND/CP1631/CT0001.\r\n\r\nFunding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS acknowledges support and resources from the Center for High-Performance Computing at the University of Utah. The SDSS website is www.sdss4.org.\r\n\r\nSDSS is managed by the Astrophysical Research Consortium for the Participating Institutions of the SDSS Collaboration including the Brazilian Participation Group, the Carnegie Institution for Science, Carnegie Mellon University, Center for Astrophysics—Harvard & Smithsonian (CfA), the Chilean Participation Group, the French Participation Group, Instituto de Astrofísica de Canarias, The Johns Hopkins University, Kavli Institute for the Physics and Mathematics of the Universe (IPMU)/University of Tokyo, the Korean Participation Group, Lawrence Berkeley National Laboratory, Leibniz Institut für Astrophysik Potsdam (AIP), Max-Planck-Institut für Astronomie (MPIA Heidelberg), Max-Planck-Institut für Astrophysik (MPA Garching), Max-Planck-Institut für Extraterrestrische Physik (MPE), National Astronomical Observatories of China, New Mexico State University, New York University, University of Notre Dame, Observatório Nacional/MCTI, The Ohio State University, Pennsylvania State University, Shanghai Astronomical Observatory, United Kingdom Participation Group, Universidad Nacional Autónoma de México, University of Arizona, University of Colorado Boulder, University of Oxford, University of Portsmouth, University of Utah, University of Virginia, University of Washington, University of Wisconsin, Vanderbilt University, and Yale University.","DOAJ_listed":"1","day":"01","type":"journal_article","title":"APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields","issue":"2","OA_type":"gold","scopus_import":"1","publication_identifier":{"issn":["0067-0049"]},"ddc":["520"]},{"year":"2025","volume":246,"publication_status":"published","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T11:00:06Z","department":[{"_id":"XiFe"}],"author":[{"full_name":"Song, Xin","first_name":"Xin","last_name":"Song"},{"first_name":"Miao","last_name":"Zhang","full_name":"Zhang, Miao"},{"full_name":"Wang, Ting Ting","first_name":"Ting Ting","last_name":"Wang"},{"last_name":"Duan","first_name":"Yao Yuan","full_name":"Duan, Yao Yuan"},{"first_name":"Jie","last_name":"Ren","full_name":"Ren, Jie"},{"full_name":"Gao, Hu","first_name":"Hu","last_name":"Gao"},{"full_name":"Fan, Yan Jie","first_name":"Yan Jie","last_name":"Fan"},{"last_name":"Xia","first_name":"Qiang Ming","full_name":"Xia, Qiang Ming"},{"full_name":"Cao, Hui Xiang","first_name":"Hui Xiang","last_name":"Cao"},{"last_name":"Xie","first_name":"Kai Dong","full_name":"Xie, Kai Dong"},{"full_name":"Wu, Xiao Meng","first_name":"Xiao Meng","last_name":"Wu"},{"full_name":"Zhang, Fei","first_name":"Fei","last_name":"Zhang"},{"last_name":"Zhang","first_name":"Si Qi","full_name":"Zhang, Si Qi"},{"id":"11b5bbff-8b61-11ed-b69e-d8ddd6bce951","full_name":"Huang, Ying","last_name":"Huang","first_name":"Ying"},{"last_name":"Boualem","first_name":"Adnane","full_name":"Boualem, Adnane"},{"last_name":"Bendahmane","first_name":"Abdelhafid","full_name":"Bendahmane, Abdelhafid"},{"full_name":"Tan, Feng Quan","first_name":"Feng Quan","last_name":"Tan"},{"last_name":"Guo","first_name":"Wen Wu","full_name":"Guo, Wen Wu"}],"external_id":{"pmid":["39969116"],"isi":["001424915600001"]},"abstract":[{"lang":"eng","text":"Polyploidization is a common occurrence in the evolutionary history of flowering plants, significantly contributing to their adaptability and diversity. However, the molecular mechanisms behind these adaptive advantages are not well understood.\r\nThrough comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus genera, we discovered that genome doubling significantly enhances salt stress resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene production in the roots of tetraploid plants was associated with hypomethylation and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene production activates the transcription of reactive oxygen species scavenging genes and stress-related hormone biosynthesis genes. Consequently, tetraploid plants exhibited superior root functionality under salt stress, maintaining improved cytosolic K+/Na+ homeostasis.\r\nTo genetically validate the link between salt stress resilience and ACO1 expression, we generated overexpression and knockout lines, confirming the central role of ACO1 expression regulation following genome doubling in salt stress resilience.\r\nOur work elucidates the molecular mechanisms underlying the role of genome doubling in stress resilience. We also highlight the importance of chromatin dynamics in fine-tuning ethylene gene expression and activating salt stress resilience pathways, offering valuable insights into plant adaptation and crop genome evolution."}],"page":"176-191","article_type":"original","_id":"19406","oa_version":"None","acknowledgement":"We thank Prof. Qi Xie from the Institute of Genetics and Development, Chinese Academy of Sciences, for providing the YAO promoter-driven CRISPR/Cas9 vector, our colleague Dr Robert M. Larkin from Huazhong Agricultural University, and Dr Olivier Martin from IPS2 (INRAE, France) for critical reading of the manuscript. This research was financially supported by grants from the National Key Research & Development Program of China (2024YFD1200501), the National Natural Science Foundation of China (32172525 and 32202432), the Foundation of Hubei Hongshan laboratory (2021hszd009), the China Agricultural Research System (CARS-26) and the Department of Science and Technology of Hubei Province (2022BBA0019). A. Bendahmane is funded by the ANR BioAdapt (ANR-21-LCV3-0003), LabEx Saclay Plant Sciences (SPS) (ANR-10-LABX-40-SPS), and the NectarGland ERC Project (101095736).","day":"01","type":"journal_article","status":"public","doi":"10.1111/nph.20428","date_created":"2025-03-16T23:01:25Z","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"scopus_import":"1","OA_type":"closed access","issue":"1","title":"Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants","language":[{"iso":"eng"}],"publisher":"Wiley","month":"04","pmid":1,"publication":"New Phytologist","article_processing_charge":"No","quality_controlled":"1","date_published":"2025-04-01T00:00:00Z","citation":{"mla":"Song, Xin, et al. “Polyploidization Leads to Salt Stress Resilience via Ethylene Signaling in Citrus Plants.” New Phytologist, vol. 246, no. 1, Wiley, 2025, pp. 176–91, doi:10.1111/nph.20428.","ieee":"X. Song et al., “Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants,” New Phytologist, vol. 246, no. 1. Wiley, pp. 176–191, 2025.","chicago":"Song, Xin, Miao Zhang, Ting Ting Wang, Yao Yuan Duan, Jie Ren, Hu Gao, Yan Jie Fan, et al. “Polyploidization Leads to Salt Stress Resilience via Ethylene Signaling in Citrus Plants.” New Phytologist. Wiley, 2025. https://doi.org/10.1111/nph.20428.","ama":"Song X, Zhang M, Wang TT, et al. Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants. New Phytologist. 2025;246(1):176-191. doi:10.1111/nph.20428","short":"X. Song, M. Zhang, T.T. Wang, Y.Y. Duan, J. Ren, H. Gao, Y.J. Fan, Q.M. Xia, H.X. Cao, K.D. Xie, X.M. Wu, F. Zhang, S.Q. Zhang, Y. Huang, A. Boualem, A. Bendahmane, F.Q. Tan, W.W. Guo, New Phytologist 246 (2025) 176–191.","ista":"Song X, Zhang M, Wang TT, Duan YY, Ren J, Gao H, Fan YJ, Xia QM, Cao HX, Xie KD, Wu XM, Zhang F, Zhang SQ, Huang Y, Boualem A, Bendahmane A, Tan FQ, Guo WW. 2025. Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants. New Phytologist. 246(1), 176–191.","apa":"Song, X., Zhang, M., Wang, T. T., Duan, Y. Y., Ren, J., Gao, H., … Guo, W. W. (2025). Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants. New Phytologist. Wiley. https://doi.org/10.1111/nph.20428"},"intvolume":" 246"},{"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","month":"02","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Cambridge University Press","date_published":"2025-02-06T00:00:00Z","citation":{"mla":"Ballini, Francesco, et al. “On the L-Polynomials of Curves over Finite Fields.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, Cambridge University Press, 2025, doi:10.1017/prm.2025.7.","chicago":"Ballini, Francesco, Davide Lombardo, and Matteo Verzobio. “On the L-Polynomials of Curves over Finite Fields.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2025. https://doi.org/10.1017/prm.2025.7.","ieee":"F. Ballini, D. Lombardo, and M. Verzobio, “On the L-polynomials of curves over finite fields,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2025.","ama":"Ballini F, Lombardo D, Verzobio M. On the L-polynomials of curves over finite fields. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2025. doi:10.1017/prm.2025.7","short":"F. Ballini, D. Lombardo, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2025).","apa":"Ballini, F., Lombardo, D., & Verzobio, M. (2025). On the L-polynomials of curves over finite fields. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2025.7","ista":"Ballini F, Lombardo D, Verzobio M. 2025. On the L-polynomials of curves over finite fields. Proceedings of the Royal Society of Edinburgh Section A: Mathematics."},"doi":"10.1017/prm.2025.7","date_created":"2025-03-16T23:01:25Z","main_file_link":[{"url":"https://doi.org/10.1017/prm.2025.7","open_access":"1"}],"status":"public","type":"journal_article","day":"06","acknowledgement":"We thank Umberto Zannier for bringing the problem to our attention, for many useful suggestions, and especially for pointing out the relevance of the equidistribution results of Katz–Sarnak, noting that they imply the case q≫g0 of theorem 1.4. In addition, the first author would like to thank Umberto Zannier for his guidance during his undergraduate studies, on a topic that ultimately inspired much of the work in this article. We are grateful to J. Kaczorowski and A. Perelli for sharing their work [Reference Kaczorowski and Perelli28] before publication. We thank Christophe Ritzenthaler and Elisa Lorenzo García for their interesting comments on the first version of this article, Zhao Yu Ma for a comment about remark 3.12, and the anonymous referees for their helpful suggestions.","OA_type":"hybrid","title":"On the L-polynomials of curves over finite fields","corr_author":"1","ddc":["500"],"publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"We discuss, in a non-Archimedean setting, the distribution of the coefficients of L-polynomials of curves of genus g over Fq . Among other results, this allows us to prove that the Q-vector space spanned by such characteristic polynomials has dimension g + 1. We also state a conjecture about the Archimedean distribution of the number of rational points of curves over finite fields."}],"author":[{"first_name":"Francesco","last_name":"Ballini","full_name":"Ballini, Francesco"},{"full_name":"Lombardo, Davide","last_name":"Lombardo","first_name":"Davide"},{"first_name":"Matteo","last_name":"Verzobio","orcid":"0000-0002-0854-0306","full_name":"Verzobio, Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb"}],"external_id":{"isi":["001414690400001"]},"department":[{"_id":"TiBr"}],"oa_version":"Published Version","_id":"19407","oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication_status":"epub_ahead","year":"2025","date_updated":"2026-06-18T18:15:49Z"},{"title":"Exchange anisotropies in microwave-driven singlet-triplet qubits","OA_type":"gold","ddc":["530"],"corr_author":"1","has_accepted_license":"1","status":"public","date_created":"2025-03-17T08:57:09Z","doi":"10.15479/AT:ISTA:19409","acknowledgement":"We thank A. Crippa for helpful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project and the FWF Projects \r\nwith DOI:10.55776/F86 and DOI:10.55776/I5060. M.R.-R. acknowledges support from the Netherlands Organization of\r\n scientific Research (NWO) under Veni grant VI.Veni.212.223. The Research of S.B. and M.R.-R. was sponsored in part by the Army Research Office and was accomplished under Award Number: W911NF-23-1-0110.","day":"17","type":"research_data","contributor":[{"last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"last_name":"Schell","first_name":"Yona A","id":"fe39122d-06bb-11ec-a33b-9e22b40e40a5"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip"},{"last_name":"Calcaterra","first_name":"Stefano"},{"first_name":"Daniel ","last_name":"Chrastina"},{"first_name":"Giovanni ","last_name":"Isella"},{"last_name":"Rimbach-Russ","first_name":"Maximilian"},{"last_name":"Bosco","first_name":"Stefano"},{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"J. Saez Mollejo, (2025).","apa":"Saez Mollejo, J. (2025). Exchange anisotropies in microwave-driven singlet-triplet qubits. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:19409","ista":"Saez Mollejo J. 2025. Exchange anisotropies in microwave-driven singlet-triplet qubits, Institute of Science and Technology Austria, 10.15479/AT:ISTA:19409.","mla":"Saez Mollejo, Jaime. Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits. Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:19409.","chicago":"Saez Mollejo, Jaime. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:19409.","ieee":"J. Saez Mollejo, “Exchange anisotropies in microwave-driven singlet-triplet qubits.” Institute of Science and Technology Austria, 2025.","ama":"Saez Mollejo J. Exchange anisotropies in microwave-driven singlet-triplet qubits. 2025. doi:10.15479/AT:ISTA:19409"},"date_published":"2025-03-17T00:00:00Z","article_processing_charge":"No","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","month":"03","date_updated":"2026-05-20T06:42:16Z","file_date_updated":"2025-03-17T08:48:09Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"19424"}]},"file":[{"checksum":"1f21c8ea2196776aae51cc3a5d00e00b","date_created":"2025-03-17T08:48:09Z","success":1,"creator":"jsaezmol","access_level":"open_access","relation":"main_file","file_id":"19410","content_type":"application/x-zip-compressed","file_size":21971911,"date_updated":"2025-03-17T08:48:09Z","file_name":"AllDataPublished.zip"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","_id":"19409","project":[{"name":"Integrated Germanium Quantum Technology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"}],"oa_version":"Published Version","oa":1,"author":[{"full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"text":"This .zip file contains the data to reproduce the figures and supplementary figures of \"Exchange anisotropies in microwave-driven singlet-triplet qubits\" by Jaime Saez-Mollejo et al.\r\n","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}]},{"OA_type":"gold","title":"Sensitivity of self-aggregation and the key role of the free convection distance","issue":"3","ddc":["550"],"corr_author":"1","scopus_import":"1","publication_identifier":{"eissn":["1942-2466"]},"date_created":"2025-03-19T07:58:38Z","doi":"10.1029/2024MS004791","status":"public","has_accepted_license":"1","type":"journal_article","day":"18","acknowledgement":"This article is based on chapter 3 of AC Ph.D. thesis. The authors thank Graziano Giuliani for his coding assistance. We also thank Daniel Hernández-Deckers, Paolina Cerlini, and especially to Giovanni Biagioli for discussions and feedback. We also thank two reviewers for their insightful comments. AC was supported by a fellowship awarded by ICTP and by the European Union Horizon 2020 Marie Skłodowska-Curie grant agreement No. 101034413. CM acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041).","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_number":"e2024MS004791","intvolume":" 17","date_published":"2025-03-18T00:00:00Z","citation":{"mla":"Casallas Garcia, Alejandro, et al. “Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3, e2024MS004791, Wiley, 2025, doi:10.1029/2024MS004791.","ama":"Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. 2025;17(3). doi:10.1029/2024MS004791","ieee":"A. Casallas Garcia, A. M. Tompkins, C. J. Muller, and G. Thompson, “Sensitivity of self-aggregation and the key role of the free convection distance,” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3. Wiley, 2025.","chicago":"Casallas Garcia, Alejandro, A.M. Tompkins, Caroline J Muller, and G. Thompson. “Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.” Journal of Advances in Modeling Earth Systems. Wiley, 2025. https://doi.org/10.1029/2024MS004791.","short":"A. Casallas Garcia, A.M. Tompkins, C.J. Muller, G. Thompson, Journal of Advances in Modeling Earth Systems 17 (2025).","apa":"Casallas Garcia, A., Tompkins, A. M., Muller, C. J., & Thompson, G. (2025). Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2024MS004791","ista":"Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. 2025. Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. 17(3), e2024MS004791."},"article_processing_charge":"Yes","quality_controlled":"1","publication":"Journal of Advances in Modeling Earth Systems","month":"03","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Wiley","date_updated":"2025-09-30T11:04:38Z","file_date_updated":"2025-03-19T07:58:21Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"access_level":"open_access","date_created":"2025-03-19T07:58:21Z","checksum":"bc32677e63f8abb07b330f4a08da796d","creator":"acasalla","file_name":"Casallas_et_al_2025_dclr.pdf","file_id":"19417","content_type":"application/pdf","relation":"main_file","date_updated":"2025-03-19T07:58:21Z","file_size":18285343}],"publication_status":"published","volume":17,"year":"2025","oa_version":"Published Version","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"name":"Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041"}],"_id":"19416","ec_funded":1,"oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"Recently, Biagioli and Tompkins (2023, https://doi.org/10.1029/2022ms003231) used a simple stochastic model to derive a dimensionless parameter to predict convective self aggregation (SA) development, which was based on the derivation of the maximum free convective distance ($d_{clr}$) expected in the pre-aggregated, random state. Our goal is to test and further investigate this hypothesis, namely that $d_{clr}$ can predict SA occurrence, using an ensemble of twenty-four distinct combinations of horizontal mixing, planetary boundary layer (PBL), and microphysical parameterizations. We conclude that the key impact of parameterization schemes on SA is through their control of the number of convective cores and their relative spacing, $d_{clr}$, which itself is impacted by cold-pool (CP) properties and mean updraft core size. SA is more likely when the convective core count is small, while CPs modify convective spacing via suppression in their interiors and triggering by gust-front convergence and collisions. Each parameterization scheme emphasizes a different mechanism. Subgrid-scale horizontal turbulent mixing mainly affects SA through the determination of convective core size and thus spacing. The sensitivity to the microphysics is mainly through rain evaporation and the subsequent impact on CPs, while perturbations to the ice cloud microphysics have a limited effect. Non-local PBL mixing schemes promote SA primarily by increasing convective inhibition through inversion entrainment and altering low cloud amounts, leading to fewer convective cores and larger $d_{clr}$. "}],"author":[{"last_name":"Casallas Garcia","first_name":"Alejandro","id":"92081129-2d75-11ef-a48d-b04dd7a2385a","orcid":"0000-0002-1988-5035","full_name":"Casallas Garcia, Alejandro"},{"last_name":"Tompkins","first_name":"A.M.","full_name":"Tompkins, A.M."},{"last_name":"Muller","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"last_name":"Thompson","first_name":"G.","full_name":"Thompson, G."}],"external_id":{"isi":["001447023900001"]},"department":[{"_id":"CaMu"}]},{"date_updated":"2025-09-30T11:05:07Z","file_date_updated":"2025-03-20T09:46:20Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"date_updated":"2025-03-20T09:46:20Z","file_size":625974,"relation":"main_file","file_id":"19427","content_type":"application/pdf","file_name":"2025_JournLondonMath_Draganic.pdf","success":1,"creator":"dernst","checksum":"d8e0a03286a44c4f672709e3c829206e","date_created":"2025-03-20T09:46:20Z","access_level":"open_access"}],"publication_status":"published","year":"2025","volume":111,"oa_version":"Published Version","_id":"19418","ec_funded":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"The size-Ramsey number r^(H) of a graph H is the smallest number of edges a (host) graph G can have, such that for any red/blue colouring of G, there is a monochromatic copy of H in G. Recently, Conlon, Nenadov and Trujić showed that if H is a graph on n vertices and maximum degree three, then r^(H)=O(n8/5), improving upon the upper bound of n5/3+o(1) by Kohayakawa, Rödl, Schacht and Szemerédi. In this paper we show that r^(H)≤n3/2+o(1). While the previously used host graphs were vanilla binomial random graphs, we prove our result using a novel host graph construction. Our bound hits a natural barrier of the existing methods."}],"external_id":{"arxiv":["2207.05048"],"isi":["001450645400019"]},"author":[{"full_name":"Draganić, Nemanja","last_name":"Draganić","first_name":"Nemanja"},{"full_name":"Petrova, Kalina H","id":"554ff4e4-f325-11ee-b0c4-a10dbd523381","first_name":"Kalina H","last_name":"Petrova"}],"department":[{"_id":"MaKw"}],"title":"Size‐Ramsey numbers of graphs with maximum degree three","issue":"3","OA_type":"hybrid","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"scopus_import":"1","ddc":["510"],"arxiv":1,"doi":"10.1112/jlms.70116","date_created":"2025-03-19T09:03:37Z","has_accepted_license":"1","status":"public","type":"journal_article","day":"01","acknowledgement":"We would like to thank Rajko Nenadov and Miloš Trujić for helpful comments and discussions, as well as the anonymous referees for their very useful feedback, which improved the paper considerably. This research was supported by SNSF Project 217926. Part of this research was conducted while Nemanja Draganić was at ETH Zürich, Switzerland, and partially supported by SNSF Grant 200021_196965. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement Number: 101034413. Part of this research was conducted while Kalina Petrova was at the Department of Computer Science, ETH Zürich, Switzerland, supported by SNSF Grant CRSII5 173721.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 111","article_number":"e70116","citation":{"ieee":"N. Draganić and K. H. Petrova, “Size‐Ramsey numbers of graphs with maximum degree three,” Journal of the London Mathematical Society, vol. 111, no. 3. Wiley, 2025.","chicago":"Draganić, Nemanja, and Kalina H Petrova. “Size‐Ramsey Numbers of Graphs with Maximum Degree Three.” Journal of the London Mathematical Society. Wiley, 2025. https://doi.org/10.1112/jlms.70116.","ama":"Draganić N, Petrova KH. Size‐Ramsey numbers of graphs with maximum degree three. Journal of the London Mathematical Society. 2025;111(3). doi:10.1112/jlms.70116","mla":"Draganić, Nemanja, and Kalina H. Petrova. “Size‐Ramsey Numbers of Graphs with Maximum Degree Three.” Journal of the London Mathematical Society, vol. 111, no. 3, e70116, Wiley, 2025, doi:10.1112/jlms.70116.","apa":"Draganić, N., & Petrova, K. H. (2025). Size‐Ramsey numbers of graphs with maximum degree three. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.70116","ista":"Draganić N, Petrova KH. 2025. Size‐Ramsey numbers of graphs with maximum degree three. Journal of the London Mathematical Society. 111(3), e70116.","short":"N. Draganić, K.H. Petrova, Journal of the London Mathematical Society 111 (2025)."},"date_published":"2025-03-01T00:00:00Z","quality_controlled":"1","article_processing_charge":"No","publication":"Journal of the London Mathematical Society","month":"03","publisher":"Wiley","OA_place":"publisher","language":[{"iso":"eng"}]},{"year":"2025","publication_status":"published","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T11:05:55Z","department":[{"_id":"JiFr"}],"external_id":{"pmid":["39829340"],"isi":["001436802900001"]},"author":[{"id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","orcid":"0000-0001-6152-6637","full_name":"Tang, Han","last_name":"Tang","first_name":"Han"},{"last_name":"Chen","first_name":"L","full_name":"Chen, L"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"abstract":[{"lang":"eng","text":"Auxin and its PIN-FORMED (PIN) exporters are essential for tissue repair and regeneration in flowering plants. To gain insight into the evolution of this mechanism, we investigated their roles in leaves excised from Physcomitrium patens, a bryophyte known for its remarkable cell reprogramming capacity. We used various approaches to manipulate auxin levels, including exogenous application, pharmacological manipulations, and auxin biosynthesis mutants. We observed no significant effect on the rate of cell reprogramming. Rather, our analysis of auxin dynamics revealed a decrease in auxin levels upon excision, which was followed by a local increase before the reprogramming process began. Mutant analysis revealed that PpPINs are required for effective cell reprogramming, and endogenously expressed PpPINA-GFP accumulates polarly at sites that will develop into future filamentous stem cells. In addition, hyperpolarized PpPINA variants carrying mutated phosphorylation sites showed a marked delay in reprogramming, whereas endogenous or nonpolar versions do not have this effect. These results underscore that both the levels and the polarity of PpPINA are important for efficient cell reprogramming. Overall, these findings highlight the pivotal role of PIN polarity in plant regeneration. Furthermore, they suggest that understanding polarity mechanisms could have broader implications for improving regenerative processes across various plant species."}],"article_type":"original","_id":"19420","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"ec_funded":1,"oa_version":"None","acknowledgement":"The authors sincerely thank Dr Barbara Kloeckener Gruissem’s time and efforts in critical reading and constructive advice on the manuscript. The authors gratefully acknowledge Dr. Eva Sundberg for generously providing transgenic plants to support this study.\r\nThis work was supported by the European Research Council Advanced Grant (ETAP-742985 to H.T. and J.F.) and the Taiwan National Science and Technology Council (NSTC 112-2311-B-005-008 to H.T. and L.-H.C.).","day":"05","type":"journal_article","status":"public","date_created":"2025-03-19T09:44:19Z","doi":"10.1093/pcp/pcaf008","publication_identifier":{"eissn":["1471-9053"],"issn":["0032-0781"]},"scopus_import":"1","corr_author":"1","title":"Auxin fluctuation and PIN polarization in moss leaf cell reprogramming.","OA_type":"closed access","publisher":"Oxford University Press","language":[{"iso":"eng"}],"month":"03","pmid":1,"publication":"Plant and Cell Physiology","quality_controlled":"1","article_processing_charge":"No","citation":{"mla":"Tang, Han, et al. “Auxin Fluctuation and PIN Polarization in Moss Leaf Cell Reprogramming.” Plant and Cell Physiology, pcaf008, Oxford University Press, 2025, doi:10.1093/pcp/pcaf008.","chicago":"Tang, Han, L Chen, and Jiří Friml. “Auxin Fluctuation and PIN Polarization in Moss Leaf Cell Reprogramming.” Plant and Cell Physiology. Oxford University Press, 2025. https://doi.org/10.1093/pcp/pcaf008.","ieee":"H. Tang, L. Chen, and J. Friml, “Auxin fluctuation and PIN polarization in moss leaf cell reprogramming.,” Plant and Cell Physiology. Oxford University Press, 2025.","ama":"Tang H, Chen L, Friml J. Auxin fluctuation and PIN polarization in moss leaf cell reprogramming. Plant and Cell Physiology. 2025. doi:10.1093/pcp/pcaf008","short":"H. Tang, L. Chen, J. Friml, Plant and Cell Physiology (2025).","apa":"Tang, H., Chen, L., & Friml, J. (2025). Auxin fluctuation and PIN polarization in moss leaf cell reprogramming. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcaf008","ista":"Tang H, Chen L, Friml J. 2025. Auxin fluctuation and PIN polarization in moss leaf cell reprogramming. Plant and Cell Physiology., pcaf008."},"date_published":"2025-03-05T00:00:00Z","article_number":"pcaf008"},{"oa_version":"Published Version","_id":"19421","project":[{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"oa":1,"page":"1011-1016","article_type":"original","abstract":[{"lang":"eng","text":"The phytohormone auxin (Aux) is a principal endogenous developmental signal in plants. It mediates transcriptional reprogramming by a well-established canonical signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin ligase complex; after auxin perception, they associate with Aux/IAA transcriptional repressors and ubiquitinate them for degradation, thus enabling the activation of auxin response factor (ARF) transcription factors1,2,3. Here we revise this paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming and auxin-regulated development, including shoot, root, root hair growth and lateral root formation. Transgenic plants show that local cAMP production in the vicinity of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin perception and is sufficient to induce ARF-mediated transcription. These discoveries revise the canonical model of auxin signalling and establish TIR1/AFB-produced cAMP as a second messenger essential for transcriptional reprograming."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"author":[{"first_name":"Huihuang","last_name":"Chen","full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"first_name":"Linlin","last_name":"Qi","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"first_name":"Mengting","last_name":"Lu","full_name":"Lu, Mengting","id":"a8198a14-1ffe-11ee-8b67-d2bdff9d9178"},{"full_name":"Kwiatkowski, M","first_name":"M","last_name":"Kwiatkowski"},{"last_name":"Pei","first_name":"Yuanrong","id":"98605edc-6ce7-11ee-95f3-cc16b866efcd","full_name":"Pei, Yuanrong"},{"last_name":"Jaworski","first_name":"K","full_name":"Jaworski, K"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001437493900001"],"pmid":["40044868"]},"department":[{"_id":"JiFr"}],"PlanS_conform":"1","date_updated":"2026-04-28T13:42:45Z","file_date_updated":"2025-08-05T12:29:35Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"file":[{"date_updated":"2025-08-05T12:29:35Z","file_size":13549245,"relation":"main_file","content_type":"application/pdf","file_id":"20132","file_name":"2025_Nature_Chen.pdf","success":1,"creator":"dernst","checksum":"f5f18081003e7a1b8e372ecb7da82e7d","date_created":"2025-08-05T12:29:35Z","access_level":"open_access"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/updating-the-textbook/","description":"News on ISTA website","relation":"press_release"}],"record":[{"id":"19478","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","volume":640,"year":"2025","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 640","date_published":"2025-04-24T00:00:00Z","citation":{"ista":"Chen H, Qi L, Zou M, Lu M, Kwiatkowski M, Pei Y, Jaworski K, Friml J. 2025. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. 640, 1011–1016.","apa":"Chen, H., Qi, L., Zou, M., Lu, M., Kwiatkowski, M., Pei, Y., … Friml, J. (2025). TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08669-w","short":"H. Chen, L. Qi, M. Zou, M. Lu, M. Kwiatkowski, Y. Pei, K. Jaworski, J. Friml, Nature 640 (2025) 1011–1016.","ama":"Chen H, Qi L, Zou M, et al. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. 2025;640:1011-1016. doi:10.1038/s41586-025-08669-w","ieee":"H. Chen et al., “TIR1-produced cAMP as a second messenger in transcriptional auxin signalling,” Nature, vol. 640. Springer Nature, pp. 1011–1016, 2025.","chicago":"Chen, Huihuang, Linlin Qi, Minxia Zou, Mengting Lu, M Kwiatkowski, Yuanrong Pei, K Jaworski, and Jiří Friml. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-08669-w.","mla":"Chen, Huihuang, et al. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” Nature, vol. 640, Springer Nature, 2025, pp. 1011–16, doi:10.1038/s41586-025-08669-w."},"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication":"Nature","pmid":1,"month":"04","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Springer Nature","OA_type":"hybrid","title":"TIR1-produced cAMP as a second messenger in transcriptional auxin signalling","corr_author":"1","ddc":["580"],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"date_created":"2025-03-19T09:44:39Z","doi":"10.1038/s41586-025-08669-w","has_accepted_license":"1","status":"public","day":"24","type":"journal_article","acknowledgement":"We are grateful to J. Callis and H.-Q. Yang for sharing materials and to M. Estelle and S. Kepinski for inspiring discussions. This research was supported by the Laboratory Support Facility, the Plant Facility and the Imaging and Optics Facility of the Institute of Science and Technology Austria. This project has received funding from the European Research Council (101142681 CYNIPS) and Austrian Science Fund (P 37051-B). L.Q. was supported by the National Natural Science Foundation of China (grant no. 32470327). M.Z. was supported by the Interdisciplinary Project Committee of the Institute of Science and Technology Austria, and Y.P. was supported by an EMBO Postdoctoral Fellowship (ALTF 38-2023). Open access funding provided by Institute of Science and Technology (IST Austria)."},{"day":"05","type":"journal_article","acknowledgement":"We thank X. Yang for providing published inbred lines and helping with data analysis; and S. Huang, C. Jiang, G. Bi, C. Liu and S. Zhang for helpful discussions. The transgenic maize lines were generated by the Center for Crop Functional Genomics and Molecular Breeding of China Agricultural University. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500 to J.Z.), the National Natural Science Foundation of China (32170265 and 32441022 to J.Z.), the Chinese Universities Scientific Fund (2024TC084 to J.Z.), the Pinduoduo-China Agricultural University Research Fund (PC2024B01005 to J.Z.), the Hainan Provincial Natural Science Foundation of China (323CXTD379 to J.Z.), and the Central Guidance on Local Science and Technology Development Fund of Shanxi Province (YDZJSX2024D040 to C.T. and J.Z.).","date_created":"2025-03-19T09:44:55Z","doi":"10.1038/s41477-025-01934-w","status":"public","has_accepted_license":"1","scopus_import":"1","publication_identifier":{"issn":["2055-0278"]},"ddc":["580"],"title":"Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize","OA_type":"green","pmid":1,"month":"03","OA_place":"repository","publisher":"Springer Nature","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","publication":"Nature Plants","citation":{"short":"G. Jia, G. Chen, Z. Zhang, C. Tian, Y. Wang, J. Luo, K. Zhang, X. Zhao, X. Zhao, Z. Li, L. Sun, W. Yang, Y. Guo, J. Friml, Z. Gong, J. Zhang, Nature Plants 11 (2025).","apa":"Jia, G., Chen, G., Zhang, Z., Tian, C., Wang, Y., Luo, J., … Zhang, J. (2025). Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-025-01934-w","ista":"Jia G, Chen G, Zhang Z, Tian C, Wang Y, Luo J, Zhang K, Zhao X, Zhao X, Li Z, Sun L, Yang W, Guo Y, Friml J, Gong Z, Zhang J. 2025. Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize. Nature Plants. 11, 5207.","mla":"Jia, G., et al. “Ferredoxin-Mediated Mechanism for Efficient Nitrogen Utilization in Maize.” Nature Plants, vol. 11, 5207, Springer Nature, 2025, doi:10.1038/s41477-025-01934-w.","ama":"Jia G, Chen G, Zhang Z, et al. Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize. Nature Plants. 2025;11. doi:10.1038/s41477-025-01934-w","chicago":"Jia, G, G Chen, Z Zhang, C Tian, Y Wang, J Luo, K Zhang, et al. “Ferredoxin-Mediated Mechanism for Efficient Nitrogen Utilization in Maize.” Nature Plants. Springer Nature, 2025. https://doi.org/10.1038/s41477-025-01934-w.","ieee":"G. Jia et al., “Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize,” Nature Plants, vol. 11. Springer Nature, 2025."},"date_published":"2025-03-05T00:00:00Z","article_number":"5207","intvolume":" 11","publication_status":"published","volume":11,"year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"file":[{"date_updated":"2025-11-12T07:50:45Z","file_size":2714177,"relation":"main_file","content_type":"application/pdf","file_id":"20634","file_name":"2025_NaturePlants_Jia_submitted.pdf","success":1,"creator":"dernst","checksum":"caeaf1a8bc3e1435e8c995d1d9df5390","date_created":"2025-11-12T07:50:45Z","access_level":"open_access"}],"file_date_updated":"2025-11-12T07:50:45Z","date_updated":"2025-11-12T07:52:06Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Nitrogen (N) is an essential macronutrient for plant development and, ultimately, yield. Identifying the genetic components and mechanisms underlying N use efficiency in maize (Zea mays L.) is thus of great importance. Nitrate (NO3−) is the preferred inorganic N source in maize. Here we performed a genome-wide association study of shoot NO3− accumulation in maize seedlings grown under low-NO3− conditions, identifying the ferredoxin family gene ZmFd4 as a major contributor to this trait. ZmFd4 interacts and co-localizes with nitrite reductases (ZmNiRs) in chloroplasts to promote their enzymatic activity. Furthermore, ZmFd4 forms a high-affinity heterodimer with its closest paralogue, ZmFd9, in a NO3−-sensitive manner. Although ZmFd4 exerts similar biochemical functions as ZmFd9, ZmFd4 and ZmFd9 interaction limits their ability to associate with ZmNiRs and stimulate their activity. Knockout lines for ZmFd4 with decreased NO3− contents exhibit more efficient NO3− assimilation, and field experiments show consistently improved N utilization and grain yield under N-deficient conditions. Our work thus provides molecular and mechanistic insights into the natural variation in N utilization, instrumental for genetic improvement of yield in maize and, potentially, in other crops."}],"external_id":{"isi":["001437953800001"],"pmid":["40044942"]},"author":[{"full_name":"Jia, G","last_name":"Jia","first_name":"G"},{"last_name":"Chen","first_name":"G","full_name":"Chen, G"},{"last_name":"Zhang","first_name":"Z","full_name":"Zhang, Z"},{"last_name":"Tian","first_name":"C","full_name":"Tian, C"},{"last_name":"Wang","first_name":"Y","full_name":"Wang, Y"},{"first_name":"J","last_name":"Luo","full_name":"Luo, J"},{"full_name":"Zhang, K","first_name":"K","last_name":"Zhang"},{"first_name":"X","last_name":"Zhao","full_name":"Zhao, X"},{"last_name":"Zhao","first_name":"X","full_name":"Zhao, X"},{"last_name":"Li","first_name":"Z","full_name":"Li, Z"},{"last_name":"Sun","first_name":"L","full_name":"Sun, L"},{"first_name":"W","last_name":"Yang","full_name":"Yang, W"},{"first_name":"Y","last_name":"Guo","full_name":"Guo, Y"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"full_name":"Gong, Z","last_name":"Gong","first_name":"Z"},{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"}],"oa":1,"article_type":"original","oa_version":"Submitted Version","_id":"19422"}]