[{"corr_author":"1","title":"Quantum rotor in a two-dimensional mesoscopic Bose gas","year":"2025","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"creator":"dernst","checksum":"7bed8c68c36d495540491bd0579e33e4","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2025_SciPostPhys_Suchorowski.pdf","date_created":"2025-03-10T07:08:21Z","date_updated":"2025-03-10T07:08:21Z","success":1,"file_id":"19376","file_size":1124066}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.21468/SciPostPhys.18.2.059","publisher":"SciPost Foundation","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"author":[{"last_name":"Suchorowski","full_name":"Suchorowski, Michał","first_name":"Michał"},{"last_name":"Badamshina","full_name":"Badamshina, Alina","first_name":"Alina"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"last_name":"Tomza","first_name":"Michał","full_name":"Tomza, Michał"},{"first_name":"Artem","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525"}],"month":"02","OA_place":"publisher","status":"public","file_date_updated":"2025-03-10T07:08:21Z","issue":"2","article_type":"original","_id":"19371","quality_controlled":"1","publication_status":"published","date_created":"2025-03-09T23:01:28Z","abstract":[{"lang":"eng","text":"We investigate a molecular quantum rotor in a two-dimensional Bose-Einstein condensate. The focus is on studying the angulon quasiparticle concept in the crossover from few- to many-body physics. To this end, we formulate the problem in real space and solve it with a mean-field approach in the frame co-rotating with the impurity. We show that the system starts to feature angulon characteristics when the size of the bosonic cloud is large enough to screen the rotor. More importantly, we demonstrate the departure from the angulon picture for large system sizes or large angular momenta where the properties of the system are determined by collective excitations of the Bose gas."}],"type":"journal_article","citation":{"ama":"Suchorowski M, Badamshina A, Lemeshko M, Tomza M, Volosniev A. Quantum rotor in a two-dimensional mesoscopic Bose gas. SciPost Physics. 2025;18(2). doi:10.21468/SciPostPhys.18.2.059","short":"M. Suchorowski, A. Badamshina, M. Lemeshko, M. Tomza, A. Volosniev, SciPost Physics 18 (2025).","ista":"Suchorowski M, Badamshina A, Lemeshko M, Tomza M, Volosniev A. 2025. Quantum rotor in a two-dimensional mesoscopic Bose gas. SciPost Physics. 18(2), 059.","apa":"Suchorowski, M., Badamshina, A., Lemeshko, M., Tomza, M., & Volosniev, A. (2025). Quantum rotor in a two-dimensional mesoscopic Bose gas. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/SciPostPhys.18.2.059","chicago":"Suchorowski, Michał, Alina Badamshina, Mikhail Lemeshko, Michał Tomza, and Artem Volosniev. “Quantum Rotor in a Two-Dimensional Mesoscopic Bose Gas.” SciPost Physics. SciPost Foundation, 2025. https://doi.org/10.21468/SciPostPhys.18.2.059.","mla":"Suchorowski, Michał, et al. “Quantum Rotor in a Two-Dimensional Mesoscopic Bose Gas.” SciPost Physics, vol. 18, no. 2, 059, SciPost Foundation, 2025, doi:10.21468/SciPostPhys.18.2.059.","ieee":"M. Suchorowski, A. Badamshina, M. Lemeshko, M. Tomza, and A. Volosniev, “Quantum rotor in a two-dimensional mesoscopic Bose gas,” SciPost Physics, vol. 18, no. 2. SciPost Foundation, 2025."},"oa":1,"arxiv":1,"date_updated":"2025-04-14T07:48:55Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"059","acknowledgement":"We thank Fabian Brauneis, Arthur Christianen and Pietro Massignan for useful discussions. M. S. and A. G. V. would like to thank the Institut Henri Poincaré\r\n(UAR 839 CNRS-Sorbonne Université) and the LabEx CARMIN (ANR-10-LABX-59-01) for\r\ntheir support and hospitality during the final stages of completion of this work. M.S.\r\nand M.T. acknowledge the National Science Centre, Poland, within Sonata Bis Grant No.\r\n2020/38/E/ST2/00564. M.L. acknowledges support by the European Research Council (ERC)\r\nStarting Grant No.801770 (ANGULON). M.S. acknowledges the National Science Centre,\r\nPoland, within Preludium Grant No. 2023/49/N/ST2/03820. We gratefully acknowledge\r\nPoland’s high-performance Infrastructure PLGrid ACK Cyfronet AGH for providing computer\r\nfacilities and support within computational grant no PLG/2023/016878.","article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","publication_identifier":{"eissn":["2542-4653"]},"DOAJ_listed":"1","date_published":"2025-02-19T00:00:00Z","department":[{"_id":"MiLe"}],"ddc":["530"],"volume":18,"language":[{"iso":"eng"}],"intvolume":" 18","ec_funded":1,"day":"19","OA_type":"gold","publication":"SciPost Physics","external_id":{"arxiv":["2407.06046"]},"has_accepted_license":"1"},{"OA_type":"green","publication":"Probability and Mathematical Physics","external_id":{"arxiv":["2306.16373"]},"intvolume":" 6","day":"23","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"volume":6,"date_published":"2025-02-23T00:00:00Z","scopus_import":"1","oa_version":"Preprint","publication_identifier":{"issn":["2690-0998"],"eissn":["2690-1005"]},"acknowledgement":"M.B. gratefully acknowledges funding from the ERC Advanced Grant ERC-AdG CLaQS, grant agreement n. 83478.","article_processing_charge":"No","abstract":[{"text":"We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field.","lang":"eng"}],"date_created":"2025-03-09T23:01:28Z","type":"journal_article","arxiv":1,"citation":{"ieee":"M. Brooks and D. J. Mitrouskas, “ Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling,” Probability and Mathematical Physics, vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025.","mla":"Brooks, Morris, and David Johannes Mitrouskas. “ Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325, doi:10.2140/pmp.2025.6.281.","chicago":"Brooks, Morris, and David Johannes Mitrouskas. “ Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2025. https://doi.org/10.2140/pmp.2025.6.281.","apa":"Brooks, M., & Mitrouskas, D. J. (2025). Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2025.6.281","ista":"Brooks M, Mitrouskas DJ. 2025. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 6(1), 281–325.","short":"M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025) 281–325.","ama":"Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 2025;6(1):281-325. doi:10.2140/pmp.2025.6.281"},"oa":1,"date_updated":"2025-03-10T07:19:02Z","quality_controlled":"1","publication_status":"published","issue":"1","article_type":"original","_id":"19372","month":"02","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.16373","open_access":"1"}],"status":"public","OA_place":"repository","author":[{"full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","first_name":"Morris","last_name":"Brooks","orcid":"0000-0002-6249-0928"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes"}],"doi":"10.2140/pmp.2025.6.281","publisher":"Mathematical Sciences Publishers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"281-325","title":" Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling","year":"2025","corr_author":"1"},{"file":[{"date_updated":"2025-08-05T12:12:03Z","success":1,"file_id":"20129","file_name":"2025_NaturePhysics_Xue.pdf","date_created":"2025-08-05T12:12:03Z","file_size":16302436,"access_level":"open_access","creator":"dernst","checksum":"fb5e59be145b95f9851d3d7c9dbb85e6","content_type":"application/pdf","relation":"main_file"}],"PlanS_conform":"1","isi":1,"year":"2025","corr_author":"1","title":"Mechanochemical bistability of intestinal organoids enables robust morphogenesis","publisher":"Springer Nature","doi":"10.1038/s41567-025-02792-1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"02","status":"public","OA_place":"publisher","author":[{"last_name":"Xue","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","first_name":"Shi-lei"},{"full_name":"Yang, Qiutan","first_name":"Qiutan","last_name":"Yang"},{"last_name":"Liberali","first_name":"Prisca","full_name":"Liberali, Prisca"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561"}],"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"}],"publication_status":"published","quality_controlled":"1","_id":"19373","file_date_updated":"2025-08-05T12:12:03Z","article_type":"original","article_processing_charge":"Yes (via OA deal)","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).","article_number":"078104","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.","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.","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","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.","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."},"oa":1,"arxiv":1,"date_updated":"2025-09-30T10:47:36Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2025-03-09T23:01:28Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"oa_version":"Published Version","scopus_import":"1","pmid":1,"ddc":["530"],"language":[{"iso":"eng"}],"volume":21,"department":[{"_id":"EdHa"}],"date_published":"2025-02-28T00:00:00Z","external_id":{"isi":["001434072800001"],"pmid":["40248571"],"arxiv":["2403.19900"]},"has_accepted_license":"1","publication":"Nature Physics","OA_type":"hybrid","intvolume":" 21","ec_funded":1,"day":"28"},{"article_processing_charge":"No","article_number":"100051","citation":{"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.","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.","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","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.","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).","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.","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"},"date_updated":"2025-03-10T06:53:16Z","date_created":"2025-03-09T23:01:29Z","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"}],"year":"2025","type":"journal_article","title":"The new PrNi6Si6 intermetallic: From crystal structure to thermal and electrical transport properties across a wide temperature range (2–900 K)","publication_identifier":{"eissn":["1573-4803"],"issn":["0022-2461"]},"publisher":"Springer Nature","scopus_import":"1","oa_version":"None","doi":"10.1007/s10853-024-10582-y","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":60,"department":[{"_id":"MaIb"}],"month":"02","status":"public","author":[{"last_name":"Singh","first_name":"Saurabh","full_name":"Singh, Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269"},{"last_name":"Provino","first_name":"A.","full_name":"Provino, A."},{"first_name":"I.","full_name":"Pallecchi, I.","last_name":"Pallecchi"},{"last_name":"Caglieris","full_name":"Caglieris, F.","first_name":"F."},{"first_name":"M.","full_name":"Mödlinger, M.","last_name":"Mödlinger"},{"first_name":"P.","full_name":"Mele, P.","last_name":"Mele"},{"last_name":"Latronico","first_name":"G.","full_name":"Latronico, G."},{"first_name":"T.","full_name":"Takeuchi, T.","last_name":"Takeuchi"},{"last_name":"Manfrinetti","first_name":"P.","full_name":"Manfrinetti, P."}],"date_published":"2025-02-08T00:00:00Z","publication_status":"published","quality_controlled":"1","OA_type":"closed access","publication":"Journal of Materials Science","_id":"19374","intvolume":" 60","article_type":"original","day":"08"},{"publication_status":"published","quality_controlled":"1","_id":"19375","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2410.18293","open_access":"1"}],"OA_place":"repository","status":"public","month":"01","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"author":[{"first_name":"Muqsit","full_name":"Azeem, Muqsit","last_name":"Azeem"},{"last_name":"Chakraborty","full_name":"Chakraborty, Debraj","first_name":"Debraj"},{"full_name":"Kanav, Sudeep","first_name":"Sudeep","last_name":"Kanav"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky"},{"last_name":"Mohagheghi","first_name":"Mohammadsadegh","full_name":"Mohagheghi, Mohammadsadegh"},{"full_name":"Mohr, Stefanie","first_name":"Stefanie","last_name":"Mohr"},{"last_name":"Weininger","full_name":"Weininger, Maximilian","id":"02ab0197-cc70-11ed-ab61-918e71f56881","first_name":"Maximilian"}],"doi":"10.1007/978-3-031-82703-7_5","publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"97-120","isi":1,"title":"1–2–3–Go! Policy synthesis for parameterized Markov decision processes via decision-tree learning and generalization","year":"2025","publication":"26th International Conference on Verification, Model Checking, and Abstract Interpretation","OA_type":"green","alternative_title":["LNCS"],"external_id":{"isi":["001446577100005"],"arxiv":["2410.18293"]},"day":"23","ec_funded":1,"intvolume":" 15530","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"volume":15530,"date_published":"2025-01-23T00:00:00Z","scopus_import":"1","oa_version":"Preprint","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031827020"]},"conference":{"name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","end_date":"2025-01-21","start_date":"2025-01-20","location":"Denver, CO, United States"},"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).","article_processing_charge":"No","type":"conference","abstract":[{"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.","lang":"eng"}],"date_created":"2025-03-09T23:01:29Z","date_updated":"2025-09-30T10:46:54Z","oa":1,"citation":{"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","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.","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.","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","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."},"arxiv":1},{"pmid":1,"scopus_import":"1","oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"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"}],"date_created":"2025-03-16T23:01:23Z","type":"journal_article","citation":{"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.","short":"A.A. Gu, M.C. Ucar, P. Tran, A. Prindle, N.P. Kamat, J. Steinkühler, Nature Communications 16 (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.","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.","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.","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"},"oa":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-09-30T10:59:30Z","article_number":"2026","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.","article_processing_charge":"Yes (via OA deal)","intvolume":" 16","day":"27","OA_type":"gold","publication":"Nature Communications","external_id":{"pmid":["40016255"],"isi":["001435269000002"]},"has_accepted_license":"1","DOAJ_listed":"1","date_published":"2025-02-27T00:00:00Z","department":[{"_id":"EdHa"}],"ddc":["570"],"language":[{"iso":"eng"}],"volume":16,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/s41467-025-57178-x","publisher":"Springer Nature","title":"Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles","isi":1,"year":"2025","file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"3bbae9b470c639005815342a39e96918","access_level":"open_access","file_size":2260791,"file_name":"2025_NatureComm_Gu.pdf","date_created":"2025-03-17T09:43:27Z","date_updated":"2025-03-17T09:43:27Z","success":1,"file_id":"19411"}],"file_date_updated":"2025-03-17T09:43:27Z","article_type":"original","_id":"19402","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Gu","first_name":"Andre A.","full_name":"Gu, Andre A."},{"orcid":"0000-0003-0506-4217","last_name":"Ucar","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"first_name":"Peter","full_name":"Tran, Peter","last_name":"Tran"},{"first_name":"Arthur","full_name":"Prindle, Arthur","last_name":"Prindle"},{"full_name":"Kamat, Neha P.","first_name":"Neha P.","last_name":"Kamat"},{"last_name":"Steinkühler","full_name":"Steinkühler, Jan","first_name":"Jan"}],"month":"02","status":"public","OA_place":"publisher"},{"project":[{"name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427"}],"author":[{"first_name":"Barbara","full_name":"Roos, Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","last_name":"Roos","orcid":"0000-0002-9071-5880"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"OA_place":"publisher","status":"public","month":"04","article_type":"original","file_date_updated":"2025-03-17T10:07:45Z","_id":"19403","publication_status":"published","quality_controlled":"1","title":"BCS critical temperature on half-spaces","year":"2025","corr_author":"1","isi":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"66803fb63a57987eb4f13ee2949bea77","creator":"dernst","file_size":1224282,"file_id":"19412","success":1,"date_updated":"2025-03-17T10:07:45Z","date_created":"2025-03-17T10:07:45Z","file_name":"2025_ArchiveRatMech_Roos.pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/s00205-025-02088-x","publisher":"Springer Nature","date_published":"2025-04-01T00:00:00Z","department":[{"_id":"RoSe"}],"volume":249,"language":[{"iso":"eng"}],"ddc":["510"],"day":"01","intvolume":" 249","OA_type":"hybrid","publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","external_id":{"isi":["001435380100001"],"pmid":["40041541"],"arxiv":["2306.05824"]},"type":"journal_article","date_created":"2025-03-16T23:01:24Z","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"}],"date_updated":"2025-09-30T11:01:08Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"B. Roos and R. Seiringer, “BCS critical temperature on half-spaces,” Archive for Rational Mechanics and Analysis, vol. 249. Springer Nature, 2025.","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.","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","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","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)."},"oa":1,"arxiv":1,"article_number":"20","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.","article_processing_charge":"Yes (via OA deal)","pmid":1,"scopus_import":"1","oa_version":"Published Version","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]}},{"publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"scopus_import":"1","oa_version":"Published Version","pmid":1,"article_processing_charge":"Yes","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).","article_number":"115387","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_updated":"2025-10-22T07:00:04Z","citation":{"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","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.","short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (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.","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","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.","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."},"oa":1,"type":"journal_article","date_created":"2025-03-16T23:01:24Z","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","external_id":{"pmid":["40057955"],"isi":["001443652700001"]},"publication":"Cell Reports","OA_type":"gold","day":"25","intvolume":" 44","volume":44,"language":[{"iso":"eng"}],"ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"date_published":"2025-03-25T00:00:00Z","DOAJ_listed":"1","publisher":"Elsevier","doi":"10.1016/j.celrep.2025.115387","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"57e05dd1598c807af0afdb32cec039d3","creator":"dernst","access_level":"open_access","file_size":9067797,"date_created":"2025-03-17T10:26:54Z","file_name":"2025_CellReports_Tavano.pdf","file_id":"19413","date_updated":"2025-03-17T10:26:54Z","success":1}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2025","isi":1,"corr_author":"1","title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","publication_status":"published","quality_controlled":"1","_id":"19404","article_type":"original","issue":"3","file_date_updated":"2025-03-17T10:26:54Z","OA_place":"publisher","status":"public","month":"03","author":[{"orcid":"0000-0001-9970-7804","last_name":"Tavano","first_name":"Ste","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","full_name":"Tavano, Ste"},{"orcid":"0000-0001-7205-2975","last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David"},{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X"},{"id":"50F65CDC-AA30-11E9-A72B-8A12E6697425","full_name":"Tong, Xin","first_name":"Xin","last_name":"Tong"},{"last_name":"Kardos","first_name":"Roland","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7659-9142","first_name":"Alexandra","full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer"},{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022"},{"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"}]},{"file":[{"file_size":4993506,"file_id":"19414","success":1,"date_updated":"2025-03-17T10:40:41Z","date_created":"2025-03-17T10:40:41Z","file_name":"2025_AstrophysicalJourSuppl_Pinsonneault.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"a01a6645c6cb0b5cc75490f3339a2244","creator":"dernst"}],"title":"APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields","year":"2025","isi":1,"doi":"10.3847/1538-4365/ad9fef","publisher":"IOP Publishing","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"02","status":"public","OA_place":"publisher","author":[{"last_name":"Pinsonneault","first_name":"Marc H.","full_name":"Pinsonneault, Marc H."},{"last_name":"Zinn","first_name":"Joel C.","full_name":"Zinn, Joel C."},{"last_name":"Tayar","full_name":"Tayar, Jamie","first_name":"Jamie"},{"last_name":"Serenelli","full_name":"Serenelli, Aldo","first_name":"Aldo"},{"first_name":"Rafael A.","full_name":"García, Rafael A.","last_name":"García"},{"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.","first_name":"Yvonne P.","last_name":"Elsworth"},{"last_name":"Mosser","first_name":"Benoit","full_name":"Mosser, Benoit"},{"last_name":"Stello","full_name":"Stello, Dennis","first_name":"Dennis"},{"last_name":"Bell","first_name":"Keaton J.","full_name":"Bell, Keaton J."},{"orcid":"0000-0003-0142-4000","last_name":"Bugnet","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"last_name":"Corsaro","first_name":"Enrico","full_name":"Corsaro, Enrico"},{"last_name":"Gaulme","full_name":"Gaulme, Patrick","first_name":"Patrick"},{"full_name":"Hekker, Saskia","first_name":"Saskia","last_name":"Hekker"},{"first_name":"Marc","full_name":"Hon, Marc","last_name":"Hon"},{"last_name":"Huber","first_name":"Daniel","full_name":"Huber, Daniel"},{"first_name":"Thomas","full_name":"Kallinger, Thomas","last_name":"Kallinger"},{"last_name":"Cao","first_name":"Kaili","full_name":"Cao, Kaili"},{"first_name":"Jennifer A.","full_name":"Johnson, Jennifer A.","last_name":"Johnson"},{"last_name":"Liagre","full_name":"Liagre, Bastien","first_name":"Bastien"},{"first_name":"Rachel A.","full_name":"Patton, Rachel A.","last_name":"Patton"},{"first_name":"Ângela R.G.","full_name":"Santos, Ângela R.G.","last_name":"Santos"},{"last_name":"Basu","first_name":"Sarbani","full_name":"Basu, Sarbani"},{"last_name":"Beck","full_name":"Beck, Paul G.","first_name":"Paul G."},{"full_name":"Beers, Timothy C.","first_name":"Timothy C.","last_name":"Beers"},{"first_name":"William J.","full_name":"Chaplin, William J.","last_name":"Chaplin"},{"first_name":"Katia","full_name":"Cunha, Katia","last_name":"Cunha"},{"full_name":"Frinchaboy, Peter M.","first_name":"Peter M.","last_name":"Frinchaboy"},{"full_name":"Girardi, Léo","first_name":"Léo","last_name":"Girardi"},{"last_name":"Godoy-Rivera","full_name":"Godoy-Rivera, Diego","first_name":"Diego"},{"last_name":"Holtzman","first_name":"Jon A.","full_name":"Holtzman, Jon A."},{"full_name":"Jönsson, Henrik","first_name":"Henrik","last_name":"Jönsson"},{"full_name":"Mészáros, Szabolcs","first_name":"Szabolcs","last_name":"Mészáros"},{"last_name":"Reyes","full_name":"Reyes, Claudia","first_name":"Claudia"},{"last_name":"Rix","full_name":"Rix, Hans Walter","first_name":"Hans Walter"},{"full_name":"Shetrone, Matthew","first_name":"Matthew","last_name":"Shetrone"},{"last_name":"Smith","first_name":"Verne V.","full_name":"Smith, Verne V."},{"full_name":"Spoo, Taylor","first_name":"Taylor","last_name":"Spoo"},{"full_name":"Stassun, Keivan G.","first_name":"Keivan G.","last_name":"Stassun"},{"last_name":"Wang","full_name":"Wang, Ji","first_name":"Ji"}],"quality_controlled":"1","publication_status":"published","file_date_updated":"2025-03-17T10:40:41Z","article_type":"original","issue":"2","_id":"19405","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.","article_number":"69","article_processing_charge":"Yes","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."}],"date_created":"2025-03-16T23:01:24Z","type":"journal_article","citation":{"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.","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).","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","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","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.","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.","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."},"oa":1,"arxiv":1,"date_updated":"2025-09-30T11:03:01Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa_version":"Published Version","publication_identifier":{"issn":["0067-0049"]},"department":[{"_id":"LiBu"}],"ddc":["520"],"volume":276,"language":[{"iso":"eng"}],"DOAJ_listed":"1","date_published":"2025-02-01T00:00:00Z","publication":"Astrophysical Journal, Supplement Series","OA_type":"gold","external_id":{"arxiv":["2410.00102"],"isi":["001414132600001"]},"has_accepted_license":"1","intvolume":" 276","day":"01"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Wiley","doi":"10.1111/nph.20428","year":"2025","isi":1,"title":"Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants","page":"176-191","_id":"19406","article_type":"original","issue":"1","publication_status":"published","quality_controlled":"1","author":[{"last_name":"Song","first_name":"Xin","full_name":"Song, Xin"},{"first_name":"Miao","full_name":"Zhang, Miao","last_name":"Zhang"},{"last_name":"Wang","first_name":"Ting Ting","full_name":"Wang, Ting Ting"},{"last_name":"Duan","full_name":"Duan, Yao Yuan","first_name":"Yao Yuan"},{"last_name":"Ren","first_name":"Jie","full_name":"Ren, Jie"},{"last_name":"Gao","full_name":"Gao, Hu","first_name":"Hu"},{"last_name":"Fan","full_name":"Fan, Yan Jie","first_name":"Yan Jie"},{"first_name":"Qiang Ming","full_name":"Xia, Qiang Ming","last_name":"Xia"},{"first_name":"Hui Xiang","full_name":"Cao, Hui Xiang","last_name":"Cao"},{"first_name":"Kai Dong","full_name":"Xie, Kai Dong","last_name":"Xie"},{"last_name":"Wu","first_name":"Xiao Meng","full_name":"Wu, Xiao Meng"},{"last_name":"Zhang","full_name":"Zhang, Fei","first_name":"Fei"},{"last_name":"Zhang","first_name":"Si Qi","full_name":"Zhang, Si Qi"},{"last_name":"Huang","first_name":"Ying","id":"11b5bbff-8b61-11ed-b69e-d8ddd6bce951","full_name":"Huang, Ying"},{"last_name":"Boualem","full_name":"Boualem, Adnane","first_name":"Adnane"},{"first_name":"Abdelhafid","full_name":"Bendahmane, Abdelhafid","last_name":"Bendahmane"},{"first_name":"Feng Quan","full_name":"Tan, Feng Quan","last_name":"Tan"},{"first_name":"Wen Wu","full_name":"Guo, Wen Wu","last_name":"Guo"}],"month":"04","status":"public","pmid":1,"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"oa_version":"None","scopus_import":"1","citation":{"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.","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","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.","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.","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.","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"},"date_updated":"2025-09-30T11:00:06Z","date_created":"2025-03-16T23:01:25Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","article_processing_charge":"No","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).","intvolume":" 246","day":"01","external_id":{"isi":["001424915600001"],"pmid":["39969116"]},"OA_type":"closed access","publication":"New Phytologist","date_published":"2025-04-01T00:00:00Z","language":[{"iso":"eng"}],"volume":246,"department":[{"_id":"XiFe"}]},{"citation":{"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.","short":"F. Ballini, D. Lombardo, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (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","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.","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.","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","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."},"oa":1,"date_updated":"2025-09-30T11:00:35Z","date_created":"2025-03-16T23:01:25Z","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."}],"type":"journal_article","article_processing_charge":"Yes (via OA deal)","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.","publication_identifier":{"eissn":["1473-7124"],"issn":["0308-2105"]},"scopus_import":"1","oa_version":"Published Version","date_published":"2025-02-06T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"TiBr"}],"day":"06","external_id":{"isi":["001414690400001"]},"publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","OA_type":"hybrid","isi":1,"title":"On the L-polynomials of curves over finite fields","year":"2025","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Cambridge University Press","doi":"10.1017/prm.2025.7","author":[{"full_name":"Ballini, Francesco","first_name":"Francesco","last_name":"Ballini"},{"full_name":"Lombardo, Davide","first_name":"Davide","last_name":"Lombardo"},{"last_name":"Verzobio","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo","first_name":"Matteo","orcid":"0000-0002-0854-0306"}],"month":"02","OA_place":"publisher","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/prm.2025.7"}],"_id":"19407","article_type":"original","quality_controlled":"1","publication_status":"epub_ahead"},{"file_date_updated":"2025-03-19T07:58:21Z","article_type":"original","issue":"3","_id":"19416","quality_controlled":"1","publication_status":"published","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","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","call_identifier":"H2020"}],"author":[{"last_name":"Casallas Garcia","first_name":"Alejandro","id":"92081129-2d75-11ef-a48d-b04dd7a2385a","full_name":"Casallas Garcia, Alejandro","orcid":"0000-0002-1988-5035"},{"last_name":"Tompkins","full_name":"Tompkins, A.M.","first_name":"A.M."},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350"},{"first_name":"G.","full_name":"Thompson, G.","last_name":"Thompson"}],"month":"03","status":"public","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1029/2024MS004791","publisher":"Wiley","corr_author":"1","title":"Sensitivity of self-aggregation and the key role of the free convection distance","year":"2025","isi":1,"file":[{"date_updated":"2025-03-19T07:58:21Z","file_id":"19417","file_name":"Casallas_et_al_2025_dclr.pdf","date_created":"2025-03-19T07:58:21Z","file_size":18285343,"access_level":"open_access","creator":"acasalla","checksum":"bc32677e63f8abb07b330f4a08da796d","relation":"main_file","content_type":"application/pdf"}],"intvolume":" 17","ec_funded":1,"day":"18","publication":"Journal of Advances in Modeling Earth Systems","OA_type":"gold","external_id":{"isi":["001447023900001"]},"has_accepted_license":"1","date_published":"2025-03-18T00:00:00Z","department":[{"_id":"CaMu"}],"ddc":["550"],"volume":17,"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","publication_identifier":{"eissn":["1942-2466"]},"abstract":[{"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 $d_{clr}$. ","lang":"eng"}],"date_created":"2025-03-19T07:58:38Z","type":"journal_article","oa":1,"citation":{"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","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.","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","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.","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.","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."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_updated":"2025-09-30T11:04:38Z","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).","article_number":"e2024MS004791","article_processing_charge":"Yes"},{"publisher":"Wiley","doi":"10.1112/jlms.70116","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"file_name":"2025_JournLondonMath_Draganic.pdf","date_created":"2025-03-20T09:46:20Z","date_updated":"2025-03-20T09:46:20Z","success":1,"file_id":"19427","file_size":625974,"creator":"dernst","checksum":"d8e0a03286a44c4f672709e3c829206e","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"isi":1,"title":"Size‐Ramsey numbers of graphs with maximum degree three","year":"2025","quality_controlled":"1","publication_status":"published","_id":"19418","file_date_updated":"2025-03-20T09:46:20Z","article_type":"original","issue":"3","month":"03","OA_place":"publisher","status":"public","author":[{"full_name":"Draganić, Nemanja","first_name":"Nemanja","last_name":"Draganić"},{"first_name":"Kalina H","id":"554ff4e4-f325-11ee-b0c4-a10dbd523381","full_name":"Petrova, Kalina H","last_name":"Petrova"}],"project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","article_number":"e70116","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.","citation":{"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","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.","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.","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.","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","short":"N. Draganić, K.H. Petrova, Journal of the London Mathematical Society 111 (2025).","ista":"Draganić N, Petrova KH. 2025. Size‐Ramsey numbers of graphs with maximum degree three. Journal of the London Mathematical Society. 111(3), e70116."},"arxiv":1,"oa":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-09-30T11:05:07Z","date_created":"2025-03-19T09:03:37Z","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."}],"type":"journal_article","external_id":{"isi":["001450645400019"],"arxiv":["2207.05048"]},"has_accepted_license":"1","OA_type":"hybrid","publication":"Journal of the London Mathematical Society","intvolume":" 111","ec_funded":1,"day":"01","ddc":["510"],"volume":111,"language":[{"iso":"eng"}],"department":[{"_id":"MaKw"}],"date_published":"2025-03-01T00:00:00Z"},{"doi":"10.1093/pcp/pcaf008","publisher":"Oxford University Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"title":"Auxin fluctuation and PIN polarization in moss leaf cell reprogramming.","year":"2025","corr_author":"1","quality_controlled":"1","publication_status":"published","article_type":"original","_id":"19420","month":"03","status":"public","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"}],"author":[{"orcid":"0000-0001-6152-6637","first_name":"Han","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","full_name":"Tang, Han","last_name":"Tang"},{"full_name":"Chen, L","first_name":"L","last_name":"Chen"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"scopus_import":"1","oa_version":"None","publication_identifier":{"issn":["0032-0781"],"eissn":["1471-9053"]},"pmid":1,"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.).","article_number":"pcaf008","article_processing_charge":"No","date_created":"2025-03-19T09:44:19Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","citation":{"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.","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.","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","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.","short":"H. Tang, L. Chen, J. Friml, Plant and Cell Physiology (2025).","ista":"Tang H, Chen L, Friml J. 2025. Auxin fluctuation and PIN polarization in moss leaf cell reprogramming. Plant and Cell Physiology., pcaf008.","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"},"date_updated":"2025-09-30T11:05:55Z","publication":"Plant and Cell Physiology","OA_type":"closed access","external_id":{"pmid":["39829340"],"isi":["001436802900001"]},"ec_funded":1,"day":"05","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"date_published":"2025-03-05T00:00:00Z"},{"year":"2025","isi":1,"title":"Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize","file":[{"file_name":"2025_NaturePlants_Jia_submitted.pdf","date_created":"2025-11-12T07:50:45Z","date_updated":"2025-11-12T07:50:45Z","success":1,"file_id":"20634","file_size":2714177,"creator":"dernst","checksum":"caeaf1a8bc3e1435e8c995d1d9df5390","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","doi":"10.1038/s41477-025-01934-w","author":[{"last_name":"Jia","first_name":"G","full_name":"Jia, G"},{"first_name":"G","full_name":"Chen, G","last_name":"Chen"},{"full_name":"Zhang, Z","first_name":"Z","last_name":"Zhang"},{"full_name":"Tian, C","first_name":"C","last_name":"Tian"},{"last_name":"Wang","full_name":"Wang, Y","first_name":"Y"},{"last_name":"Luo","first_name":"J","full_name":"Luo, J"},{"last_name":"Zhang","first_name":"K","full_name":"Zhang, K"},{"first_name":"X","full_name":"Zhao, X","last_name":"Zhao"},{"full_name":"Zhao, X","first_name":"X","last_name":"Zhao"},{"last_name":"Li","first_name":"Z","full_name":"Li, Z"},{"first_name":"L","full_name":"Sun, L","last_name":"Sun"},{"last_name":"Yang","full_name":"Yang, W","first_name":"W"},{"last_name":"Guo","first_name":"Y","full_name":"Guo, Y"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Z","full_name":"Gong, Z","last_name":"Gong"},{"last_name":"Zhang","first_name":"J","full_name":"Zhang, J"}],"status":"public","OA_place":"repository","month":"03","_id":"19422","article_type":"original","file_date_updated":"2025-11-12T07:50:45Z","quality_controlled":"1","publication_status":"published","date_updated":"2025-11-12T07:52:06Z","citation":{"ieee":"G. Jia et al., “Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize,” Nature Plants, vol. 11. Springer Nature, 2025.","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.","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.","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","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).","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.","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"},"oa":1,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_created":"2025-03-19T09:44:55Z","article_processing_charge":"No","article_number":"5207","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.).","pmid":1,"publication_identifier":{"issn":["2055-0278"]},"scopus_import":"1","oa_version":"Submitted Version","date_published":"2025-03-05T00:00:00Z","volume":11,"language":[{"iso":"eng"}],"ddc":["580"],"department":[{"_id":"JiFr"}],"day":"05","intvolume":" 11","has_accepted_license":"1","external_id":{"isi":["001437953800001"],"pmid":["40044942"]},"OA_type":"green","publication":"Nature Plants"},{"doi":"10.1111/nph.70019","publisher":"Wiley","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"1066-1083","file":[{"access_level":"open_access","checksum":"861c9bf47e7a7766ed03e6d85bd4f6dc","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_id":"19571","date_updated":"2025-04-16T08:03:36Z","success":1,"date_created":"2025-04-16T08:03:36Z","file_name":"2025_NewPhytologist_Kurtovic.pdf","file_size":12841729}],"title":"The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii","isi":1,"year":"2025","publication_status":"published","quality_controlled":"1","file_date_updated":"2025-04-16T08:03:36Z","issue":"3","article_type":"original","_id":"19423","month":"05","status":"public","OA_place":"publisher","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"}],"author":[{"last_name":"Kurtović","first_name":"K","full_name":"Kurtović, K"},{"last_name":"Vosolsobě","full_name":"Vosolsobě, S","first_name":"S"},{"first_name":"D","full_name":"Nedvěd, D","last_name":"Nedvěd"},{"last_name":"Müller","first_name":"K","full_name":"Müller, K"},{"last_name":"Dobrev","first_name":"PI","full_name":"Dobrev, PI"},{"first_name":"V","full_name":"Schmidt, V","last_name":"Schmidt"},{"full_name":"Piszczek, P","first_name":"P","last_name":"Piszczek"},{"last_name":"Kuhn","first_name":"A","full_name":"Kuhn, A"},{"last_name":"Smoljan","first_name":"Adrijana","full_name":"Smoljan, Adrijana","id":"cced8a85-223e-11ed-af04-b0596c55053b"},{"last_name":"Fisher","first_name":"TJ","full_name":"Fisher, TJ"},{"last_name":"Weijers","full_name":"Weijers, D","first_name":"D"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bowman, JL","first_name":"JL","last_name":"Bowman"},{"last_name":"Petrášek","first_name":"J","full_name":"Petrášek, J"}],"scopus_import":"1","oa_version":"Published Version","publication_identifier":{"issn":["1469-8137"]},"pmid":1,"acknowledgement":"This work was supported by funding from the Czech Science Foundation project no. 20-13587S to JP and SV, Charles University Grant Agency projects no. 289523 to KK and no. 393422 to VS, a DOC fellowship of the Austrian Academy of Sciences to AS, and the Austrian Science Fund (FWF): I 6123-B to JF. The authors acknowledge the Imaging Facility of the Institute of Experimental Botany AS CR supported by the MEYS CR (LM2023050 Czech-BioImaging), the Czech Academy of Sciences and IEB AS CR, and Viničná Microscopy Core Facility cofinanced by the Czech-BioImaging large RI project LM2023050. Computational resources were provided by the e-INFRA CZ project (ID:90254), supported by the MEYS CR. The authors would like to thank Ilse Foissner and Margit Höftberger for discussing details of immunostaining protocol, Katarzyna Retzer and Jan Martinek for help with western blots, Anna Kampová for help with phosphoproteome sampling, Anja Holzhausen and MadLAnd for providing Chara braunii strain S276, and Roman Skokan for valuable discussion. Open access publishing facilitated by Univerzita Karlova, as part of the Wiley - CzechELib agreement.","article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"Auxin, indole-3-acetic acid (IAA), is a key phytohormone with diverse morphogenic roles in land plants, but its function and transport mechanisms in algae remain poorly understood. We therefore aimed to explore the role of IAA in a complex, streptophyte algae Chara braunii.\r\nHere, we described novel responses of C. braunii to IAA and characterized two homologs of PIN auxin efflux carriers: CbPINa and CbPINc. We determined their localization in C. braunii using epitope-specific antibodies and tested their function in heterologous land plant models. Further, using phosphoproteomic analysis, we identified IAA-induced phosphorylation events.\r\nThe thallus regeneration assay showed that IAA promotes thallus elongation and side branch development. Immunolocalization of CbPINa and CbPINc confirmed their presence on the plasma membrane of vegetative and generative cells of C. braunii. However, functional assays in tobacco BY-2 cells demonstrated that CbPINa affects auxin transport, whereas CbPINc does not. The IAA is effective in the acceleration of cytoplasmic streaming and the phosphorylation of evolutionary conserved targets such as homolog of RAF-like kinase.\r\nThese findings suggest that, although canonical PIN-mediated auxin transport mechanisms might not be fully conserved in Chara, IAA is involved in morphogenesis and fast signaling processes.","lang":"eng"}],"date_created":"2025-03-19T09:45:11Z","type":"journal_article","oa":1,"citation":{"short":"K. Kurtović, S. Vosolsobě, D. Nedvěd, K. Müller, P. Dobrev, V. Schmidt, P. Piszczek, A. Kuhn, A. Smoljan, T. Fisher, D. Weijers, J. Friml, J. Bowman, J. Petrášek, New Phytologist 246 (2025) 1066–1083.","ista":"Kurtović K, Vosolsobě S, Nedvěd D, Müller K, Dobrev P, Schmidt V, Piszczek P, Kuhn A, Smoljan A, Fisher T, Weijers D, Friml J, Bowman J, Petrášek J. 2025. The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii. New Phytologist. 246(3), 1066–1083.","ama":"Kurtović K, Vosolsobě S, Nedvěd D, et al. The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii. New Phytologist. 2025;246(3):1066-1083. doi:10.1111/nph.70019","chicago":"Kurtović, K, S Vosolsobě, D Nedvěd, K Müller, PI Dobrev, V Schmidt, P Piszczek, et al. “The Role of Indole-3-Acetic Acid and Characterization of PIN Transporters in Complex Streptophyte Alga Chara Braunii.” New Phytologist. Wiley, 2025. https://doi.org/10.1111/nph.70019.","apa":"Kurtović, K., Vosolsobě, S., Nedvěd, D., Müller, K., Dobrev, P., Schmidt, V., … Petrášek, J. (2025). The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii. New Phytologist. Wiley. https://doi.org/10.1111/nph.70019","ieee":"K. Kurtović et al., “The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii,” New Phytologist, vol. 246, no. 3. Wiley, pp. 1066–1083, 2025.","mla":"Kurtović, K., et al. “The Role of Indole-3-Acetic Acid and Characterization of PIN Transporters in Complex Streptophyte Alga Chara Braunii.” New Phytologist, vol. 246, no. 3, Wiley, 2025, pp. 1066–83, doi:10.1111/nph.70019."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-09-30T11:11:18Z","publication":"New Phytologist","OA_type":"hybrid","external_id":{"isi":["001438711600001"],"pmid":["40047465"]},"has_accepted_license":"1","intvolume":" 246","day":"01","department":[{"_id":"JiFr"}],"ddc":["580"],"volume":246,"language":[{"iso":"eng"}],"date_published":"2025-05-01T00:00:00Z"},{"date_published":"2025-03-14T00:00:00Z","department":[{"_id":"MaKw"}],"volume":13,"language":[{"iso":"eng"}],"ddc":["510"],"day":"14","ec_funded":1,"intvolume":" 13","publication":"Forum of Mathematics, Sigma","OA_type":"gold","has_accepted_license":"1","external_id":{"arxiv":["2308.12268"],"isi":["001444429200001"]},"type":"journal_article","date_created":"2025-03-20T12:59:14Z","abstract":[{"lang":"eng","text":"An ordered r-matching is an r-uniform hypergraph matching equipped with an ordering on its vertices. These objects can be viewed as natural generalisations of r-dimensional orders. The theory of ordered 2-matchings is well developed and has connections and applications to extremal and enumerative combinatorics, probability and geometry. On the other hand, in the case r≥3 much less is known, largely due to a lack of powerful bijective tools. Recently, Dudek, Grytczuk and Ruciński made some first steps towards a general theory of ordered r-matchings, and in this paper we substantially improve several of their results and introduce some new directions of study. Many intriguing open questions remain."}],"date_updated":"2025-09-30T11:18:57Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"citation":{"apa":"Anastos, M., Jin, Z., Kwan, M. A., & Sudakov, B. (2025). Extremal, enumerative and probabilistic results on ordered hypergraph matchings. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2024.144","chicago":"Anastos, Michael, Zhihan Jin, Matthew Alan Kwan, and Benny Sudakov. “Extremal, Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” Forum of Mathematics, Sigma. Cambridge University Press, 2025. https://doi.org/10.1017/fms.2024.144.","mla":"Anastos, Michael, et al. “Extremal, Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” Forum of Mathematics, Sigma, vol. 13, e55, Cambridge University Press, 2025, doi:10.1017/fms.2024.144.","ieee":"M. Anastos, Z. Jin, M. A. Kwan, and B. Sudakov, “Extremal, enumerative and probabilistic results on ordered hypergraph matchings,” Forum of Mathematics, Sigma, vol. 13. Cambridge University Press, 2025.","ama":"Anastos M, Jin Z, Kwan MA, Sudakov B. Extremal, enumerative and probabilistic results on ordered hypergraph matchings. Forum of Mathematics, Sigma. 2025;13. doi:10.1017/fms.2024.144","ista":"Anastos M, Jin Z, Kwan MA, Sudakov B. 2025. Extremal, enumerative and probabilistic results on ordered hypergraph matchings. Forum of Mathematics, Sigma. 13, e55.","short":"M. Anastos, Z. Jin, M.A. Kwan, B. Sudakov, Forum of Mathematics, Sigma 13 (2025)."},"arxiv":1,"article_number":"e55","acknowledgement":"We would like to thank Timo Seppäläinen for some illuminating discussion about random high-dimensional orders and for bringing our attention to [59]. We would also like to thank the referees for helpful feedback. Michael Anastos is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101034413. Matthew Kwan is supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777, also funded by the European Union. Zhihan Jin and Benny Sudakov are supported by SNSF grant 200021-228014.","article_processing_charge":"Yes","oa_version":"Published Version","scopus_import":"1","publication_identifier":{"issn":["2050-5094"]},"project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"},{"grant_number":"101076777","_id":"bd95085b-d553-11ed-ba76-e55d3349be45","name":"Randomness and structure in combinatorics"}],"author":[{"first_name":"Michael","full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos"},{"last_name":"Jin","first_name":"Zhihan","full_name":"Jin, Zhihan"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"}],"status":"public","OA_place":"publisher","month":"03","article_type":"original","file_date_updated":"2025-04-03T11:24:35Z","_id":"19433","publication_status":"published","quality_controlled":"1","corr_author":"1","year":"2025","title":"Extremal, enumerative and probabilistic results on ordered hypergraph matchings","isi":1,"file":[{"creator":"dernst","checksum":"f396270ad78c1ed67095c8e5a66fca26","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2025_ForumMathSigma_Anastos.pdf","date_created":"2025-04-03T11:24:35Z","success":1,"date_updated":"2025-04-03T11:24:35Z","file_id":"19468","file_size":630297}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1017/fms.2024.144","publisher":"Cambridge University Press"},{"article_processing_charge":"Yes","acknowledgement":"We thank Prof. Ying Li of Nanjing Agricultural University for her help in providing seeds of K2 materials. This work was carried out with the support of National Natural Science Foundation of China (Grant No. 32070608).","article_number":"16","date_updated":"2025-09-30T11:17:08Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” Molecular Horticulture. Springer Nature, 2025. https://doi.org/10.1186/s43897-024-00137-9.","apa":"Zhang, J., Wu, D., Zhang, Y., Feng, X., & Gao, H. (2025). DNA methylation dynamics in male germline development in Brassica Rapa. Molecular Horticulture. Springer Nature. https://doi.org/10.1186/s43897-024-00137-9","ieee":"J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics in male germline development in Brassica Rapa,” Molecular Horticulture, vol. 5. Springer Nature, 2025.","mla":"Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” Molecular Horticulture, vol. 5, 16, Springer Nature, 2025, doi:10.1186/s43897-024-00137-9.","short":"J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).","ista":"Zhang J, Wu D, Zhang Y, Feng X, Gao H. 2025. DNA methylation dynamics in male germline development in Brassica Rapa. Molecular Horticulture. 5, 16.","ama":"Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline development in Brassica Rapa. Molecular Horticulture. 2025;5. doi:10.1186/s43897-024-00137-9"},"oa":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Dynamic DNA methylation represses transposable elements (TEs) and regulates gene activity, playing a pivotal role in plant development. Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana, whether similar mechanisms exist in other dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes, microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing (WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis, while distinct patterns were observed in the dynamics of global CG and CHG methylation in B. rapa. Differentially methylated region (DMR) analysis identified specifically methylated loci in the male sex cells of B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis. Additionally, we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline development. A subset of long terminal repeat (LTR) TEs were activated, possibly due to the dynamic regulation of DNA methylation during male sexual development in B. Rapa. These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants."}],"date_created":"2025-03-23T23:01:25Z","publication_identifier":{"eissn":["2730-9401"]},"oa_version":"Published Version","scopus_import":"1","pmid":1,"language":[{"iso":"eng"}],"volume":5,"ddc":["580"],"department":[{"_id":"XiFe"}],"date_published":"2025-03-04T00:00:00Z","DOAJ_listed":"1","has_accepted_license":"1","external_id":{"isi":["001436233900001"],"pmid":["40033451"]},"OA_type":"gold","publication":"Molecular Horticulture","day":"04","intvolume":" 5","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"6d1e0e9b0e1902e4a711f81c5c17a070","creator":"dernst","access_level":"open_access","file_size":3014980,"date_created":"2025-03-25T12:15:32Z","file_name":"2025_MolecularHorticulture_Zhang.pdf","file_id":"19460","date_updated":"2025-03-25T12:15:32Z","success":1}],"year":"2025","isi":1,"corr_author":"1","title":"DNA methylation dynamics in male germline development in Brassica Rapa","publisher":"Springer Nature","doi":"10.1186/s43897-024-00137-9","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","OA_place":"publisher","month":"03","author":[{"last_name":"Zhang","full_name":"Zhang, Jun","first_name":"Jun"},{"first_name":"Di","full_name":"Wu, Di","last_name":"Wu"},{"full_name":"Zhang, Yating","first_name":"Yating","last_name":"Zhang"},{"first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234"},{"last_name":"Gao","id":"77c2e73a-eabd-11ef-aee9-8093a2ba7a93","full_name":"Gao, Hongbo","first_name":"Hongbo"}],"quality_controlled":"1","publication_status":"published","_id":"19436","article_type":"original","file_date_updated":"2025-03-25T12:15:32Z"},{"author":[{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","full_name":"Kluibenschedl, Florian","first_name":"Florian","last_name":"Kluibenschedl"},{"id":"d7b23d3a-9e21-11ec-b482-f76739596b95","full_name":"Koutentakis, Georgios","first_name":"Georgios","last_name":"Koutentakis"},{"full_name":"Al Hyder, Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","last_name":"Al Hyder"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"},{"_id":"8fa7db46-16d5-11f0-9cad-917600954daf","grant_number":"12078","name":"Polarons in Lead Halide Perovskites"}],"OA_place":"publisher","status":"public","month":"03","_id":"19437","issue":"9","article_type":"original","file_date_updated":"2025-03-25T12:37:07Z","publication_status":"published","quality_controlled":"1","corr_author":"1","isi":1,"year":"2025","title":"Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model","file":[{"access_level":"open_access","creator":"dernst","checksum":"1901efd7f95e8fe70cac412f91ea4da3","relation":"main_file","content_type":"application/pdf","success":1,"date_updated":"2025-03-25T12:37:07Z","file_id":"19461","file_name":"2025_PhysReviewLetters_Kluibenschedl.pdf","date_created":"2025-03-25T12:37:07Z","file_size":708750}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Physical Society","doi":"10.1103/PhysRevLett.134.096302","date_published":"2025-03-07T00:00:00Z","language":[{"iso":"eng"}],"volume":134,"ddc":["530"],"department":[{"_id":"MiLe"}],"day":"07","intvolume":" 134","ec_funded":1,"has_accepted_license":"1","external_id":{"arxiv":["2407.19993"],"isi":["001492808800010"],"pmid":["40131090"]},"publication":"Physical Review Letters","OA_type":"hybrid","date_updated":"2025-09-30T11:17:58Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"citation":{"chicago":"Kluibenschedl, Florian, Georgios Koutentakis, Ragheed Al Hyder, and Mikhail Lemeshko. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice Model.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.096302.","apa":"Kluibenschedl, F., Koutentakis, G., Al Hyder, R., & Lemeshko, M. (2025). Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.134.096302","mla":"Kluibenschedl, Florian, et al. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice Model.” Physical Review Letters, vol. 134, no. 9, 096302, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.096302.","ieee":"F. Kluibenschedl, G. Koutentakis, R. Al Hyder, and M. Lemeshko, “Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model,” Physical Review Letters, vol. 134, no. 9. American Physical Society, 2025.","ama":"Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. Physical Review Letters. 2025;134(9). doi:10.1103/PhysRevLett.134.096302","ista":"Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. 2025. Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. Physical Review Letters. 134(9), 096302.","short":"F. Kluibenschedl, G. Koutentakis, R. Al Hyder, M. Lemeshko, Physical Review Letters 134 (2025)."},"oa":1,"type":"journal_article","date_created":"2025-03-23T23:01:25Z","abstract":[{"lang":"eng","text":"We demonstrate the formation of ferroelectric domain-wall polarons in a minimal two-dimensional lattice model of electrons interacting with rotating dipoles. Along the domain wall, the rotors polarize in opposite directions, causing the electron to localize along a particular lattice direction. The rotor-electron coupling is identified as the origin of a structural instability in the crystal that leads to the domain-wall formation via a symmetry-breaking process. Our results provide the first theoretical description of ferroelectric polarons, as discussed in the context of soft semiconductors."}],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank, in alphabetical order, Zhanybek Alpichshev, Cesare Franchini, Areg Ghazaryan, Sebastian Maehrlein, and Artem Volosniev for fruitful discussions and comments. G. M. K. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413. R. A. received funding from the Austrian Academy of Science ÖWA Grant No. PR1029OEAW03. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","article_number":"096302","pmid":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"oa_version":"Published Version","scopus_import":"1"},{"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"This work was supported by the Natural Environment Research Council (NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish Research Council VR (2018-03695) and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions. R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and the annotation. The bioinformatic analyses were performed on resources at the University of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous reviewers for helpful comments on a previous version.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"date_updated":"2025-09-30T11:19:56Z","citation":{"apa":"Perini, S., Johannesson, K., Butlin, R. K., & Westram, A. M. (2025). Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voaf002","chicago":"Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” Journal of Evolutionary Biology. Oxford University Press, 2025. https://doi.org/10.1093/jeb/voaf002.","mla":"Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” Journal of Evolutionary Biology, vol. 38, no. 3, Oxford University Press, 2025, pp. 367–78, doi:10.1093/jeb/voaf002.","ieee":"S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs and SNPs as markers of evolutionary processes in hybrid zones,” Journal of Evolutionary Biology, vol. 38, no. 3. Oxford University Press, pp. 367–378, 2025.","ama":"Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal of Evolutionary Biology. 2025;38(3):367-378. doi:10.1093/jeb/voaf002","ista":"Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal of Evolutionary Biology. 38(3), 367–378.","short":"S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary Biology 38 (2025) 367–378."},"oa":1,"type":"journal_article","abstract":[{"text":"Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evidence from model organisms shows INDELs to be more strongly influenced by purifying selection than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic processes or to detect divergent selection. Here, we compared INDELs and SNPs in the intertidal snail Littorina saxatilis, focussing on hybrid zones between ecotypes, in order to test the utility of INDELs in the detection of divergent selection. We computed INDEL and SNP site frequency spectra using capture sequencing data. We assessed the impact of divergent selection by analyzing allele frequency clines across habitat boundaries. We also examined the influence of GC-biased gene conversion because it may be confounded with signatures of selection. We show evidence that short INDELs are affected more by purifying selection than SNPs, but part of the observed site frequency spectra difference can be attributed to GC-biased gene conversion. We did not find a difference in the impact of divergent selection between short INDELs and SNPs. Short INDELs and SNPs were similarly distributed across the genome and so are likely to respond to indirect selection in the same way. A few regions likely affected by divergent selection were revealed by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers helping to identify genomic regions important for adaptation and population divergence.","lang":"eng"}],"date_created":"2025-03-23T23:01:25Z","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"scopus_import":"1","oa_version":"Published Version","pmid":1,"volume":38,"language":[{"iso":"eng"}],"ddc":["570"],"department":[{"_id":"NiBa"}],"date_published":"2025-03-01T00:00:00Z","has_accepted_license":"1","external_id":{"pmid":["39803902"],"isi":["001415267900001"]},"OA_type":"hybrid","publication":"Journal of Evolutionary Biology","day":"01","intvolume":" 38","file":[{"file_name":"2025_JourEvolBiology_Perini.pdf","date_created":"2025-04-03T11:53:06Z","date_updated":"2025-04-03T11:53:06Z","success":1,"file_id":"19469","file_size":12826085,"creator":"dernst","checksum":"01408e626a4131bfec5ffc70b0af9129","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"page":"367-378","license":"https://creativecommons.org/licenses/by-nc/4.0/","corr_author":"1","title":"Short INDELs and SNPs as markers of evolutionary processes in hybrid zones","year":"2025","isi":1,"publisher":"Oxford University Press","doi":"10.1093/jeb/voaf002","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","status":"public","month":"03","author":[{"last_name":"Perini","full_name":"Perini, Samuel","first_name":"Samuel"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."},{"last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"}],"publication_status":"published","quality_controlled":"1","_id":"19438","issue":"3","article_type":"original","file_date_updated":"2025-04-03T11:53:06Z"}]