[{"file_date_updated":"2025-03-17T10:26:54Z","publication_status":"published","doi":"10.1016/j.celrep.2025.115387","title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","volume":44,"year":"2025","OA_type":"gold","day":"25","oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation."}],"corr_author":"1","language":[{"iso":"eng"}],"article_number":"115387","article_type":"original","article_processing_charge":"Yes","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2025-10-22T07:00:04Z","type":"journal_article","publication":"Cell Reports","ddc":["570"],"scopus_import":"1","author":[{"first_name":"Ste","last_name":"Tavano","orcid":"0000-0001-9970-7804","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","full_name":"Tavano, Ste"},{"first_name":"David","last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","last_name":"Tasciyan","first_name":"Saren"},{"first_name":"Xin","last_name":"Tong","id":"50F65CDC-AA30-11E9-A72B-8A12E6697425","full_name":"Tong, Xin"},{"full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos","first_name":"Roland"},{"last_name":"Schauer","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra"},{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"pmid":1,"DOAJ_listed":"1","external_id":{"isi":["001443652700001"],"pmid":["40057955"]},"isi":1,"OA_place":"publisher","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","has_accepted_license":"1","file":[{"date_created":"2025-03-17T10:26:54Z","access_level":"open_access","relation":"main_file","file_name":"2025_CellReports_Tavano.pdf","success":1,"checksum":"57e05dd1598c807af0afdb32cec039d3","file_size":9067797,"file_id":"19413","date_updated":"2025-03-17T10:26:54Z","creator":"dernst","content_type":"application/pdf"}],"publisher":"Elsevier","citation":{"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.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>.","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.","mla":"Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>, vol. 44, no. 3, 115387, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>.","short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (2025).","ieee":"S. Tavano <i>et al.</i>, “BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation,” <i>Cell Reports</i>, vol. 44, no. 3. Elsevier, 2025.","apa":"Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A., … Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>","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. <i>Cell Reports</i>. 2025;44(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>"},"date_created":"2025-03-16T23:01:24Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"status":"public","month":"03","date_published":"2025-03-25T00:00:00Z","project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"},{"grant_number":"ALTF 1159-2018","_id":"269CD5C4-B435-11E9-9278-68D0E5697425","name":"Mechanosensation in cell migration: the role of friction forces in cell polarization and directed migration"}],"quality_controlled":"1","issue":"3","intvolume":"        44","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"_id":"19404"},{"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."}],"article_number":"69","language":[{"iso":"eng"}],"volume":276,"title":"APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields","year":"2025","OA_type":"gold","day":"01","oa":1,"publication_status":"published","doi":"10.3847/1538-4365/ad9fef","file_date_updated":"2025-03-17T10:40:41Z","ddc":["520"],"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2025-09-30T11:03:01Z","publication":"Astrophysical Journal, Supplement Series","type":"journal_article","article_type":"original","article_processing_charge":"Yes","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.","has_accepted_license":"1","file":[{"date_created":"2025-03-17T10:40:41Z","relation":"main_file","access_level":"open_access","checksum":"a01a6645c6cb0b5cc75490f3339a2244","success":1,"file_size":4993506,"file_name":"2025_AstrophysicalJourSuppl_Pinsonneault.pdf","date_updated":"2025-03-17T10:40:41Z","file_id":"19414","creator":"dernst","content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Pinsonneault, Marc H.","last_name":"Pinsonneault","first_name":"Marc H."},{"full_name":"Zinn, Joel C.","first_name":"Joel C.","last_name":"Zinn"},{"full_name":"Tayar, Jamie","first_name":"Jamie","last_name":"Tayar"},{"first_name":"Aldo","last_name":"Serenelli","full_name":"Serenelli, Aldo"},{"last_name":"García","first_name":"Rafael A.","full_name":"García, Rafael A."},{"full_name":"Mathur, Savita","first_name":"Savita","last_name":"Mathur"},{"full_name":"Vrard, Mathieu","last_name":"Vrard","first_name":"Mathieu"},{"first_name":"Yvonne P.","last_name":"Elsworth","full_name":"Elsworth, Yvonne P."},{"full_name":"Mosser, Benoit","first_name":"Benoit","last_name":"Mosser"},{"first_name":"Dennis","last_name":"Stello","full_name":"Stello, Dennis"},{"last_name":"Bell","first_name":"Keaton J.","full_name":"Bell, Keaton J."},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","last_name":"Bugnet"},{"first_name":"Enrico","last_name":"Corsaro","full_name":"Corsaro, Enrico"},{"full_name":"Gaulme, Patrick","last_name":"Gaulme","first_name":"Patrick"},{"first_name":"Saskia","last_name":"Hekker","full_name":"Hekker, Saskia"},{"full_name":"Hon, Marc","last_name":"Hon","first_name":"Marc"},{"first_name":"Daniel","last_name":"Huber","full_name":"Huber, Daniel"},{"full_name":"Kallinger, Thomas","first_name":"Thomas","last_name":"Kallinger"},{"first_name":"Kaili","last_name":"Cao","full_name":"Cao, Kaili"},{"first_name":"Jennifer A.","last_name":"Johnson","full_name":"Johnson, Jennifer A."},{"full_name":"Liagre, Bastien","last_name":"Liagre","first_name":"Bastien"},{"last_name":"Patton","first_name":"Rachel A.","full_name":"Patton, Rachel A."},{"last_name":"Santos","first_name":"Ângela R.G.","full_name":"Santos, Ângela R.G."},{"first_name":"Sarbani","last_name":"Basu","full_name":"Basu, Sarbani"},{"full_name":"Beck, Paul G.","first_name":"Paul G.","last_name":"Beck"},{"first_name":"Timothy C.","last_name":"Beers","full_name":"Beers, Timothy C."},{"last_name":"Chaplin","first_name":"William J.","full_name":"Chaplin, William J."},{"full_name":"Cunha, Katia","last_name":"Cunha","first_name":"Katia"},{"full_name":"Frinchaboy, Peter M.","first_name":"Peter M.","last_name":"Frinchaboy"},{"full_name":"Girardi, Léo","first_name":"Léo","last_name":"Girardi"},{"full_name":"Godoy-Rivera, Diego","last_name":"Godoy-Rivera","first_name":"Diego"},{"last_name":"Holtzman","first_name":"Jon A.","full_name":"Holtzman, Jon A."},{"full_name":"Jönsson, Henrik","last_name":"Jönsson","first_name":"Henrik"},{"last_name":"Mészáros","first_name":"Szabolcs","full_name":"Mészáros, Szabolcs"},{"full_name":"Reyes, Claudia","last_name":"Reyes","first_name":"Claudia"},{"full_name":"Rix, Hans Walter","last_name":"Rix","first_name":"Hans Walter"},{"full_name":"Shetrone, Matthew","last_name":"Shetrone","first_name":"Matthew"},{"full_name":"Smith, Verne V.","first_name":"Verne V.","last_name":"Smith"},{"full_name":"Spoo, Taylor","first_name":"Taylor","last_name":"Spoo"},{"full_name":"Stassun, Keivan G.","first_name":"Keivan G.","last_name":"Stassun"},{"first_name":"Ji","last_name":"Wang","full_name":"Wang, Ji"}],"DOAJ_listed":"1","external_id":{"arxiv":["2410.00102"],"isi":["001414132600001"]},"arxiv":1,"OA_place":"publisher","isi":1,"intvolume":"       276","publication_identifier":{"issn":["0067-0049"]},"issue":"2","_id":"19405","date_published":"2025-02-01T00:00:00Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","month":"02","publisher":"IOP Publishing","citation":{"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.” <i>Astrophysical Journal, Supplement Series</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.3847/1538-4365/ad9fef\">https://doi.org/10.3847/1538-4365/ad9fef</a>.","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).","mla":"Pinsonneault, Marc H., et al. “APOKASC-3: The Third Joint Spectroscopic and Asteroseismic Catalog for Evolved Stars in the Kepler Fields.” <i>Astrophysical Journal, Supplement Series</i>, vol. 276, no. 2, 69, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.3847/1538-4365/ad9fef\">10.3847/1538-4365/ad9fef</a>.","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. <i>Astrophysical Journal, Supplement Series</i>. 2025;276(2). doi:<a href=\"https://doi.org/10.3847/1538-4365/ad9fef\">10.3847/1538-4365/ad9fef</a>","ieee":"M. H. Pinsonneault <i>et al.</i>, “APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields,” <i>Astrophysical Journal, Supplement Series</i>, vol. 276, no. 2. IOP Publishing, 2025.","apa":"Pinsonneault, M. H., Zinn, J. C., Tayar, J., Serenelli, A., García, R. A., Mathur, S., … Wang, J. (2025). APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields. <i>Astrophysical Journal, Supplement Series</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4365/ad9fef\">https://doi.org/10.3847/1538-4365/ad9fef</a>"},"date_created":"2025-03-16T23:01:24Z","department":[{"_id":"LiBu"}]},{"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).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","external_id":{"pmid":["39969116"],"isi":["001424915600001"]},"pmid":1,"author":[{"full_name":"Song, Xin","first_name":"Xin","last_name":"Song"},{"full_name":"Zhang, Miao","last_name":"Zhang","first_name":"Miao"},{"last_name":"Wang","first_name":"Ting Ting","full_name":"Wang, Ting Ting"},{"full_name":"Duan, Yao Yuan","last_name":"Duan","first_name":"Yao Yuan"},{"full_name":"Ren, Jie","last_name":"Ren","first_name":"Jie"},{"full_name":"Gao, Hu","last_name":"Gao","first_name":"Hu"},{"full_name":"Fan, Yan Jie","last_name":"Fan","first_name":"Yan Jie"},{"first_name":"Qiang Ming","last_name":"Xia","full_name":"Xia, Qiang Ming"},{"full_name":"Cao, Hui Xiang","last_name":"Cao","first_name":"Hui Xiang"},{"full_name":"Xie, Kai Dong","first_name":"Kai Dong","last_name":"Xie"},{"full_name":"Wu, Xiao Meng","last_name":"Wu","first_name":"Xiao Meng"},{"first_name":"Fei","last_name":"Zhang","full_name":"Zhang, Fei"},{"last_name":"Zhang","first_name":"Si Qi","full_name":"Zhang, Si Qi"},{"full_name":"Huang, Ying","id":"11b5bbff-8b61-11ed-b69e-d8ddd6bce951","last_name":"Huang","first_name":"Ying"},{"full_name":"Boualem, Adnane","first_name":"Adnane","last_name":"Boualem"},{"full_name":"Bendahmane, Abdelhafid","last_name":"Bendahmane","first_name":"Abdelhafid"},{"full_name":"Tan, Feng Quan","first_name":"Feng Quan","last_name":"Tan"},{"full_name":"Guo, Wen Wu","first_name":"Wen Wu","last_name":"Guo"}],"isi":1,"_id":"19406","issue":"1","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"intvolume":"       246","date_published":"2025-04-01T00:00:00Z","quality_controlled":"1","page":"176-191","month":"04","status":"public","publisher":"Wiley","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.” <i>New Phytologist</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/nph.20428\">https://doi.org/10.1111/nph.20428</a>.","mla":"Song, Xin, et al. “Polyploidization Leads to Salt Stress Resilience via Ethylene Signaling in Citrus Plants.” <i>New Phytologist</i>, vol. 246, no. 1, Wiley, 2025, pp. 176–91, doi:<a href=\"https://doi.org/10.1111/nph.20428\">10.1111/nph.20428</a>.","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. <i>New Phytologist</i>. 2025;246(1):176-191. doi:<a href=\"https://doi.org/10.1111/nph.20428\">10.1111/nph.20428</a>","ieee":"X. Song <i>et al.</i>, “Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants,” <i>New Phytologist</i>, vol. 246, no. 1. Wiley, pp. 176–191, 2025.","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. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.20428\">https://doi.org/10.1111/nph.20428</a>"},"date_created":"2025-03-16T23:01:25Z","department":[{"_id":"XiFe"}],"abstract":[{"lang":"eng","text":"Polyploidization is a common occurrence in the evolutionary history of flowering plants, significantly contributing to their adaptability and diversity. However, the molecular mechanisms behind these adaptive advantages are not well understood.\r\nThrough comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus genera, we discovered that genome doubling significantly enhances salt stress resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene production in the roots of tetraploid plants was associated with hypomethylation and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene production activates the transcription of reactive oxygen species scavenging genes and stress-related hormone biosynthesis genes. Consequently, tetraploid plants exhibited superior root functionality under salt stress, maintaining improved cytosolic K+/Na+ homeostasis.\r\nTo genetically validate the link between salt stress resilience and ACO1 expression, we generated overexpression and knockout lines, confirming the central role of ACO1 expression regulation following genome doubling in salt stress resilience.\r\nOur work elucidates the molecular mechanisms underlying the role of genome doubling in stress resilience. We also highlight the importance of chromatin dynamics in fine-tuning ethylene gene expression and activating salt stress resilience pathways, offering valuable insights into plant adaptation and crop genome evolution."}],"language":[{"iso":"eng"}],"year":"2025","volume":246,"title":"Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants","OA_type":"closed access","day":"01","publication_status":"published","doi":"10.1111/nph.20428","scopus_import":"1","type":"journal_article","publication":"New Phytologist","date_updated":"2025-09-30T11:00:06Z","article_type":"original","article_processing_charge":"No"},{"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Ballini, Francesco","last_name":"Ballini","first_name":"Francesco"},{"last_name":"Lombardo","first_name":"Davide","full_name":"Lombardo, Davide"},{"last_name":"Verzobio","first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","orcid":"0000-0002-0854-0306","full_name":"Verzobio, Matteo"}],"external_id":{"isi":["001414690400001"]},"isi":1,"OA_place":"publisher","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.","status":"public","month":"02","citation":{"chicago":"Ballini, Francesco, Davide Lombardo, and Matteo Verzobio. “On the L-Polynomials of Curves over Finite Fields.” <i>Proceedings of the Royal Society of Edinburgh Section A: Mathematics</i>. Cambridge University Press, 2025. <a href=\"https://doi.org/10.1017/prm.2025.7\">https://doi.org/10.1017/prm.2025.7</a>.","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).","mla":"Ballini, Francesco, et al. “On the L-Polynomials of Curves over Finite Fields.” <i>Proceedings of the Royal Society of Edinburgh Section A: Mathematics</i>, Cambridge University Press, 2025, doi:<a href=\"https://doi.org/10.1017/prm.2025.7\">10.1017/prm.2025.7</a>.","ieee":"F. Ballini, D. Lombardo, and M. Verzobio, “On the L-polynomials of curves over finite fields,” <i>Proceedings of the Royal Society of Edinburgh Section A: Mathematics</i>. Cambridge University Press, 2025.","apa":"Ballini, F., Lombardo, D., &#38; Verzobio, M. (2025). On the L-polynomials of curves over finite fields. <i>Proceedings of the Royal Society of Edinburgh Section A: Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/prm.2025.7\">https://doi.org/10.1017/prm.2025.7</a>","ama":"Ballini F, Lombardo D, Verzobio M. On the L-polynomials of curves over finite fields. <i>Proceedings of the Royal Society of Edinburgh Section A: Mathematics</i>. 2025. doi:<a href=\"https://doi.org/10.1017/prm.2025.7\">10.1017/prm.2025.7</a>"},"publisher":"Cambridge University Press","department":[{"_id":"TiBr"}],"date_created":"2025-03-16T23:01:25Z","publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"_id":"19407","date_published":"2025-02-06T00:00:00Z","quality_controlled":"1","publication_status":"epub_ahead","doi":"10.1017/prm.2025.7","main_file_link":[{"url":"https://doi.org/10.1017/prm.2025.7","open_access":"1"}],"abstract":[{"lang":"eng","text":"We discuss, in a non-Archimedean setting, the distribution of the coefficients of L-polynomials of curves of genus g over  Fq . Among other results, this allows us to prove that the  Q-vector space spanned by such characteristic polynomials has dimension g + 1. We also state a conjecture about the Archimedean distribution of the number of rational points of curves over finite fields."}],"corr_author":"1","language":[{"iso":"eng"}],"title":"On the L-polynomials of curves over finite fields","year":"2025","day":"06","OA_type":"hybrid","oa":1,"article_type":"original","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_updated":"2025-09-30T11:00:35Z","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","type":"journal_article"},{"status":"public","month":"03","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_created":"2025-03-19T07:58:38Z","department":[{"_id":"CaMu"}],"citation":{"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,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 3. Wiley, 2025.","apa":"Casallas Garcia, A., Tompkins, A. M., Muller, C. J., &#38; Thompson, G. (2025). Sensitivity of self-aggregation and the key role of the free convection distance. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2024MS004791\">https://doi.org/10.1029/2024MS004791</a>","ama":"Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. Sensitivity of self-aggregation and the key role of the free convection distance. <i>Journal of Advances in Modeling Earth Systems</i>. 2025;17(3). doi:<a href=\"https://doi.org/10.1029/2024MS004791\">10.1029/2024MS004791</a>","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.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2025. <a href=\"https://doi.org/10.1029/2024MS004791\">https://doi.org/10.1029/2024MS004791</a>.","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).","mla":"Casallas Garcia, Alejandro, et al. “Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 3, e2024MS004791, Wiley, 2025, doi:<a href=\"https://doi.org/10.1029/2024MS004791\">10.1029/2024MS004791</a>."},"publisher":"Wiley","intvolume":"        17","publication_identifier":{"eissn":["1942-2466"]},"issue":"3","_id":"19416","quality_controlled":"1","project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"},{"call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041"}],"date_published":"2025-03-18T00:00:00Z","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","isi":1,"author":[{"last_name":"Casallas Garcia","first_name":"Alejandro","orcid":"0000-0002-1988-5035","id":"92081129-2d75-11ef-a48d-b04dd7a2385a","full_name":"Casallas Garcia, Alejandro"},{"first_name":"A.M.","last_name":"Tompkins","full_name":"Tompkins, A.M."},{"last_name":"Muller","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"full_name":"Thompson, G.","first_name":"G.","last_name":"Thompson"}],"external_id":{"isi":["001447023900001"]},"has_accepted_license":"1","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).","file":[{"content_type":"application/pdf","creator":"acasalla","date_updated":"2025-03-19T07:58:21Z","file_id":"19417","file_name":"Casallas_et_al_2025_dclr.pdf","checksum":"bc32677e63f8abb07b330f4a08da796d","file_size":18285343,"access_level":"open_access","relation":"main_file","date_created":"2025-03-19T07:58:21Z"}],"article_processing_charge":"Yes","article_type":"original","ddc":["550"],"scopus_import":"1","date_updated":"2025-09-30T11:04:38Z","publication":"Journal of Advances in Modeling Earth Systems","type":"journal_article","doi":"10.1029/2024MS004791","publication_status":"published","file_date_updated":"2025-03-19T07:58:21Z","ec_funded":1,"language":[{"iso":"eng"}],"article_number":"e2024MS004791","corr_author":"1","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"}],"day":"18","OA_type":"gold","oa":1,"volume":17,"title":"Sensitivity of self-aggregation and the key role of the free convection distance","year":"2025"},{"external_id":{"isi":["001450645400019"],"arxiv":["2207.05048"]},"arxiv":1,"author":[{"last_name":"Draganić","first_name":"Nemanja","full_name":"Draganić, Nemanja"},{"last_name":"Petrova","first_name":"Kalina H","full_name":"Petrova, Kalina H","id":"554ff4e4-f325-11ee-b0c4-a10dbd523381"}],"isi":1,"OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","file":[{"relation":"main_file","access_level":"open_access","date_created":"2025-03-20T09:46:20Z","file_size":625974,"checksum":"d8e0a03286a44c4f672709e3c829206e","success":1,"file_name":"2025_JournLondonMath_Draganic.pdf","file_id":"19427","date_updated":"2025-03-20T09:46:20Z","content_type":"application/pdf","creator":"dernst"}],"has_accepted_license":"1","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":{"ieee":"N. Draganić and K. H. Petrova, “Size‐Ramsey numbers of graphs with maximum degree three,” <i>Journal of the London Mathematical Society</i>, vol. 111, no. 3. Wiley, 2025.","ama":"Draganić N, Petrova KH. Size‐Ramsey numbers of graphs with maximum degree three. <i>Journal of the London Mathematical Society</i>. 2025;111(3). doi:<a href=\"https://doi.org/10.1112/jlms.70116\">10.1112/jlms.70116</a>","apa":"Draganić, N., &#38; Petrova, K. H. (2025). Size‐Ramsey numbers of graphs with maximum degree three. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.70116\">https://doi.org/10.1112/jlms.70116</a>","chicago":"Draganić, Nemanja, and Kalina H Petrova. “Size‐Ramsey Numbers of Graphs with Maximum Degree Three.” <i>Journal of the London Mathematical Society</i>. Wiley, 2025. <a href=\"https://doi.org/10.1112/jlms.70116\">https://doi.org/10.1112/jlms.70116</a>.","mla":"Draganić, Nemanja, and Kalina H. Petrova. “Size‐Ramsey Numbers of Graphs with Maximum Degree Three.” <i>Journal of the London Mathematical Society</i>, vol. 111, no. 3, e70116, Wiley, 2025, doi:<a href=\"https://doi.org/10.1112/jlms.70116\">10.1112/jlms.70116</a>.","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."},"publisher":"Wiley","date_created":"2025-03-19T09:03:37Z","department":[{"_id":"MaKw"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"month":"03","status":"public","date_published":"2025-03-01T00:00:00Z","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"quality_controlled":"1","_id":"19418","issue":"3","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"intvolume":"       111","ec_funded":1,"file_date_updated":"2025-03-20T09:46:20Z","publication_status":"published","doi":"10.1112/jlms.70116","year":"2025","volume":111,"title":"Size‐Ramsey numbers of graphs with maximum degree three","oa":1,"OA_type":"hybrid","day":"01","abstract":[{"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.","lang":"eng"}],"article_number":"e70116","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","type":"journal_article","publication":"Journal of the London Mathematical Society","date_updated":"2025-09-30T11:05:07Z","scopus_import":"1","ddc":["510"]},{"date_published":"2025-03-05T00:00:00Z","quality_controlled":"1","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publication_identifier":{"eissn":["1471-9053"],"issn":["0032-0781"]},"_id":"19420","citation":{"mla":"Tang, Han, et al. “Auxin Fluctuation and PIN Polarization in Moss Leaf Cell Reprogramming.” <i>Plant and Cell Physiology</i>, pcaf008, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/pcp/pcaf008\">10.1093/pcp/pcaf008</a>.","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.","chicago":"Tang, Han, L Chen, and Jiří Friml. “Auxin Fluctuation and PIN Polarization in Moss Leaf Cell Reprogramming.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/pcp/pcaf008\">https://doi.org/10.1093/pcp/pcaf008</a>.","ieee":"H. Tang, L. Chen, and J. Friml, “Auxin fluctuation and PIN polarization in moss leaf cell reprogramming.,” <i>Plant and Cell Physiology</i>. Oxford University Press, 2025.","apa":"Tang, H., Chen, L., &#38; Friml, J. (2025). Auxin fluctuation and PIN polarization in moss leaf cell reprogramming. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcaf008\">https://doi.org/10.1093/pcp/pcaf008</a>","ama":"Tang H, Chen L, Friml J. Auxin fluctuation and PIN polarization in moss leaf cell reprogramming. <i>Plant and Cell Physiology</i>. 2025. doi:<a href=\"https://doi.org/10.1093/pcp/pcaf008\">10.1093/pcp/pcaf008</a>"},"publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"date_created":"2025-03-19T09:44:19Z","status":"public","month":"03","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.).","pmid":1,"author":[{"first_name":"Han","last_name":"Tang","full_name":"Tang, Han","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","orcid":"0000-0001-6152-6637"},{"full_name":"Chen, L","first_name":"L","last_name":"Chen"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"external_id":{"isi":["001436802900001"],"pmid":["39829340"]},"isi":1,"oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T11:05:55Z","type":"journal_article","publication":"Plant and Cell Physiology","scopus_import":"1","article_type":"original","article_processing_charge":"No","title":"Auxin fluctuation and PIN polarization in moss leaf cell reprogramming.","year":"2025","day":"05","OA_type":"closed access","abstract":[{"lang":"eng","text":"Auxin and its PIN-FORMED (PIN) exporters are essential for tissue repair and regeneration in flowering plants. To gain insight into the evolution of this mechanism, we investigated their roles in leaves excised from Physcomitrium patens, a bryophyte known for its remarkable cell reprogramming capacity. We used various approaches to manipulate auxin levels, including exogenous application, pharmacological manipulations, and auxin biosynthesis mutants. We observed no significant effect on the rate of cell reprogramming. Rather, our analysis of auxin dynamics revealed a decrease in auxin levels upon excision, which was followed by a local increase before the reprogramming process began. Mutant analysis revealed that PpPINs are required for effective cell reprogramming, and endogenously expressed PpPINA-GFP accumulates polarly at sites that will develop into future filamentous stem cells. In addition, hyperpolarized PpPINA variants carrying mutated phosphorylation sites showed a marked delay in reprogramming, whereas endogenous or nonpolar versions do not have this effect. These results underscore that both the levels and the polarity of PpPINA are important for efficient cell reprogramming. Overall, these findings highlight the pivotal role of PIN polarity in plant regeneration. Furthermore, they suggest that understanding polarity mechanisms could have broader implications for improving regenerative processes across various plant species."}],"corr_author":"1","language":[{"iso":"eng"}],"article_number":"pcaf008","ec_funded":1,"publication_status":"published","doi":"10.1093/pcp/pcaf008"},{"citation":{"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. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-025-01934-w\">https://doi.org/10.1038/s41477-025-01934-w</a>","ieee":"G. Jia <i>et al.</i>, “Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize,” <i>Nature Plants</i>, vol. 11. Springer Nature, 2025.","ama":"Jia G, Chen G, Zhang Z, et al. Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize. <i>Nature Plants</i>. 2025;11. doi:<a href=\"https://doi.org/10.1038/s41477-025-01934-w\">10.1038/s41477-025-01934-w</a>","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.","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).","mla":"Jia, G., et al. “Ferredoxin-Mediated Mechanism for Efficient Nitrogen Utilization in Maize.” <i>Nature Plants</i>, vol. 11, 5207, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41477-025-01934-w\">10.1038/s41477-025-01934-w</a>.","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.” <i>Nature Plants</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41477-025-01934-w\">https://doi.org/10.1038/s41477-025-01934-w</a>."},"publisher":"Springer Nature","department":[{"_id":"JiFr"}],"date_created":"2025-03-19T09:44:55Z","status":"public","month":"03","date_published":"2025-03-05T00:00:00Z","quality_controlled":"1","publication_identifier":{"issn":["2055-0278"]},"intvolume":"        11","_id":"19422","author":[{"full_name":"Jia, G","last_name":"Jia","first_name":"G"},{"last_name":"Chen","first_name":"G","full_name":"Chen, G"},{"full_name":"Zhang, Z","last_name":"Zhang","first_name":"Z"},{"full_name":"Tian, C","last_name":"Tian","first_name":"C"},{"full_name":"Wang, Y","last_name":"Wang","first_name":"Y"},{"last_name":"Luo","first_name":"J","full_name":"Luo, J"},{"last_name":"Zhang","first_name":"K","full_name":"Zhang, K"},{"full_name":"Zhao, X","last_name":"Zhao","first_name":"X"},{"full_name":"Zhao, X","last_name":"Zhao","first_name":"X"},{"full_name":"Li, Z","last_name":"Li","first_name":"Z"},{"last_name":"Sun","first_name":"L","full_name":"Sun, L"},{"full_name":"Yang, W","last_name":"Yang","first_name":"W"},{"full_name":"Guo, Y","last_name":"Guo","first_name":"Y"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Z","last_name":"Gong","full_name":"Gong, Z"},{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"}],"pmid":1,"external_id":{"pmid":["40044942"],"isi":["001437953800001"]},"OA_place":"repository","isi":1,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.).","has_accepted_license":"1","file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2025-11-12T07:50:45Z","file_id":"20634","success":1,"file_size":2714177,"checksum":"caeaf1a8bc3e1435e8c995d1d9df5390","file_name":"2025_NaturePlants_Jia_submitted.pdf","date_created":"2025-11-12T07:50:45Z","relation":"main_file","access_level":"open_access"}],"article_type":"original","article_processing_charge":"No","date_updated":"2025-11-12T07:52:06Z","publication":"Nature Plants","type":"journal_article","ddc":["580"],"scopus_import":"1","file_date_updated":"2025-11-12T07:50:45Z","publication_status":"published","doi":"10.1038/s41477-025-01934-w","title":"Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize","volume":11,"year":"2025","day":"05","OA_type":"green","oa":1,"abstract":[{"lang":"eng","text":"Nitrogen (N) is an essential macronutrient for plant development and, ultimately, yield. Identifying the genetic components and mechanisms underlying N use efficiency in maize (Zea mays L.) is thus of great importance. Nitrate (NO3−) is the preferred inorganic N source in maize. Here we performed a genome-wide association study of shoot NO3− accumulation in maize seedlings grown under low-NO3− conditions, identifying the ferredoxin family gene ZmFd4 as a major contributor to this trait. ZmFd4 interacts and co-localizes with nitrite reductases (ZmNiRs) in chloroplasts to promote their enzymatic activity. Furthermore, ZmFd4 forms a high-affinity heterodimer with its closest paralogue, ZmFd9, in a NO3−-sensitive manner. Although ZmFd4 exerts similar biochemical functions as ZmFd9, ZmFd4 and ZmFd9 interaction limits their ability to associate with ZmNiRs and stimulate their activity. Knockout lines for ZmFd4 with decreased NO3− contents exhibit more efficient NO3− assimilation, and field experiments show consistently improved N utilization and grain yield under N-deficient conditions. Our work thus provides molecular and mechanistic insights into the natural variation in N utilization, instrumental for genetic improvement of yield in maize and, potentially, in other crops."}],"language":[{"iso":"eng"}],"article_number":"5207"},{"file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2025-04-16T08:03:36Z","file_id":"19571","success":1,"checksum":"861c9bf47e7a7766ed03e6d85bd4f6dc","file_size":12841729,"file_name":"2025_NewPhytologist_Kurtovic.pdf","date_created":"2025-04-16T08:03:36Z","relation":"main_file","access_level":"open_access"}],"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.","has_accepted_license":"1","OA_place":"publisher","isi":1,"external_id":{"pmid":["40047465"],"isi":["001438711600001"]},"pmid":1,"author":[{"full_name":"Kurtović, K","first_name":"K","last_name":"Kurtović"},{"first_name":"S","last_name":"Vosolsobě","full_name":"Vosolsobě, S"},{"full_name":"Nedvěd, D","first_name":"D","last_name":"Nedvěd"},{"full_name":"Müller, K","first_name":"K","last_name":"Müller"},{"full_name":"Dobrev, PI","last_name":"Dobrev","first_name":"PI"},{"full_name":"Schmidt, V","first_name":"V","last_name":"Schmidt"},{"last_name":"Piszczek","first_name":"P","full_name":"Piszczek, P"},{"full_name":"Kuhn, A","first_name":"A","last_name":"Kuhn"},{"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","first_name":"D","full_name":"Weijers, D"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Bowman, JL","first_name":"JL","last_name":"Bowman"},{"full_name":"Petrášek, J","last_name":"Petrášek","first_name":"J"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"}],"quality_controlled":"1","date_published":"2025-05-01T00:00:00Z","_id":"19423","issue":"3","intvolume":"       246","publication_identifier":{"issn":["1469-8137"]},"department":[{"_id":"JiFr"}],"date_created":"2025-03-19T09:45:11Z","publisher":"Wiley","citation":{"ieee":"K. Kurtović <i>et al.</i>, “The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii,” <i>New Phytologist</i>, vol. 246, no. 3. Wiley, pp. 1066–1083, 2025.","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. <i>New Phytologist</i>. 2025;246(3):1066-1083. doi:<a href=\"https://doi.org/10.1111/nph.70019\">10.1111/nph.70019</a>","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. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.70019\">https://doi.org/10.1111/nph.70019</a>","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.” <i>New Phytologist</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/nph.70019\">https://doi.org/10.1111/nph.70019</a>.","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.","mla":"Kurtović, K., et al. “The Role of Indole-3-Acetic Acid and Characterization of PIN Transporters in Complex Streptophyte Alga Chara Braunii.” <i>New Phytologist</i>, vol. 246, no. 3, Wiley, 2025, pp. 1066–83, doi:<a href=\"https://doi.org/10.1111/nph.70019\">10.1111/nph.70019</a>.","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."},"month":"05","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"1066-1083","oa":1,"day":"01","OA_type":"hybrid","year":"2025","volume":246,"title":"The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"file_date_updated":"2025-04-16T08:03:36Z","doi":"10.1111/nph.70019","publication_status":"published","type":"journal_article","publication":"New Phytologist","date_updated":"2025-09-30T11:11:18Z","scopus_import":"1","ddc":["580"],"article_processing_charge":"Yes (via OA deal)","article_type":"original"},{"file":[{"relation":"main_file","access_level":"open_access","date_created":"2025-04-03T11:24:35Z","success":1,"checksum":"f396270ad78c1ed67095c8e5a66fca26","file_size":630297,"file_name":"2025_ForumMathSigma_Anastos.pdf","file_id":"19468","date_updated":"2025-04-03T11:24:35Z","content_type":"application/pdf","creator":"dernst"}],"has_accepted_license":"1","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.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","arxiv":1,"external_id":{"arxiv":["2308.12268"],"isi":["001444429200001"]},"author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","full_name":"Anastos, Michael","last_name":"Anastos","first_name":"Michael"},{"first_name":"Zhihan","last_name":"Jin","full_name":"Jin, Zhihan"},{"first_name":"Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","first_name":"Benny","full_name":"Sudakov, Benny"}],"isi":1,"OA_place":"publisher","_id":"19433","intvolume":"        13","publication_identifier":{"issn":["2050-5094"]},"date_published":"2025-03-14T00:00:00Z","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"bd95085b-d553-11ed-ba76-e55d3349be45","name":"Randomness and structure in combinatorics","grant_number":"101076777"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"month":"03","status":"public","publisher":"Cambridge University Press","citation":{"ama":"Anastos M, Jin Z, Kwan MA, Sudakov B. Extremal, enumerative and probabilistic results on ordered hypergraph matchings. <i>Forum of Mathematics, Sigma</i>. 2025;13. doi:<a href=\"https://doi.org/10.1017/fms.2024.144\">10.1017/fms.2024.144</a>","apa":"Anastos, M., Jin, Z., Kwan, M. A., &#38; Sudakov, B. (2025). Extremal, enumerative and probabilistic results on ordered hypergraph matchings. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2024.144\">https://doi.org/10.1017/fms.2024.144</a>","ieee":"M. Anastos, Z. Jin, M. A. Kwan, and B. Sudakov, “Extremal, enumerative and probabilistic results on ordered hypergraph matchings,” <i>Forum of Mathematics, Sigma</i>, vol. 13. Cambridge University Press, 2025.","short":"M. Anastos, Z. Jin, M.A. Kwan, B. Sudakov, Forum of Mathematics, Sigma 13 (2025).","mla":"Anastos, Michael, et al. “Extremal, Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” <i>Forum of Mathematics, Sigma</i>, vol. 13, e55, Cambridge University Press, 2025, doi:<a href=\"https://doi.org/10.1017/fms.2024.144\">10.1017/fms.2024.144</a>.","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.","chicago":"Anastos, Michael, Zhihan Jin, Matthew Alan Kwan, and Benny Sudakov. “Extremal, Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2025. <a href=\"https://doi.org/10.1017/fms.2024.144\">https://doi.org/10.1017/fms.2024.144</a>."},"department":[{"_id":"MaKw"}],"date_created":"2025-03-20T12:59:14Z","corr_author":"1","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"article_number":"e55","year":"2025","title":"Extremal, enumerative and probabilistic results on ordered hypergraph matchings","volume":13,"oa":1,"day":"14","OA_type":"gold","publication_status":"published","doi":"10.1017/fms.2024.144","ec_funded":1,"file_date_updated":"2025-04-03T11:24:35Z","scopus_import":"1","ddc":["510"],"publication":"Forum of Mathematics, Sigma","type":"journal_article","date_updated":"2025-09-30T11:18:57Z","article_type":"original","article_processing_charge":"Yes"},{"has_accepted_license":"1","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).","file":[{"file_id":"19460","date_updated":"2025-03-25T12:15:32Z","creator":"dernst","content_type":"application/pdf","date_created":"2025-03-25T12:15:32Z","access_level":"open_access","relation":"main_file","file_name":"2025_MolecularHorticulture_Zhang.pdf","file_size":3014980,"checksum":"6d1e0e9b0e1902e4a711f81c5c17a070","success":1}],"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","isi":1,"author":[{"last_name":"Zhang","first_name":"Jun","full_name":"Zhang, Jun"},{"last_name":"Wu","first_name":"Di","full_name":"Wu, Di"},{"full_name":"Zhang, Yating","first_name":"Yating","last_name":"Zhang"},{"first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"},{"last_name":"Gao","first_name":"Hongbo","id":"77c2e73a-eabd-11ef-aee9-8093a2ba7a93","full_name":"Gao, Hongbo"}],"pmid":1,"DOAJ_listed":"1","external_id":{"isi":["001436233900001"],"pmid":["40033451"]},"publication_identifier":{"eissn":["2730-9401"]},"intvolume":"         5","_id":"19436","quality_controlled":"1","date_published":"2025-03-04T00:00:00Z","status":"public","month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"XiFe"}],"date_created":"2025-03-23T23:01:25Z","publisher":"Springer Nature","citation":{"chicago":"Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” <i>Molecular Horticulture</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1186/s43897-024-00137-9\">https://doi.org/10.1186/s43897-024-00137-9</a>.","short":"J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).","mla":"Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” <i>Molecular Horticulture</i>, vol. 5, 16, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1186/s43897-024-00137-9\">10.1186/s43897-024-00137-9</a>.","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.","ieee":"J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics in male germline development in Brassica Rapa,” <i>Molecular Horticulture</i>, vol. 5. Springer Nature, 2025.","ama":"Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline development in Brassica Rapa. <i>Molecular Horticulture</i>. 2025;5. doi:<a href=\"https://doi.org/10.1186/s43897-024-00137-9\">10.1186/s43897-024-00137-9</a>","apa":"Zhang, J., Wu, D., Zhang, Y., Feng, X., &#38; Gao, H. (2025). DNA methylation dynamics in male germline development in Brassica Rapa. <i>Molecular Horticulture</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s43897-024-00137-9\">https://doi.org/10.1186/s43897-024-00137-9</a>"},"language":[{"iso":"eng"}],"article_number":"16","abstract":[{"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.","lang":"eng"}],"corr_author":"1","day":"04","OA_type":"gold","oa":1,"volume":5,"title":"DNA methylation dynamics in male germline development in Brassica Rapa","year":"2025","doi":"10.1186/s43897-024-00137-9","publication_status":"published","file_date_updated":"2025-03-25T12:15:32Z","ddc":["580"],"scopus_import":"1","date_updated":"2025-09-30T11:17:08Z","publication":"Molecular Horticulture","type":"journal_article","article_processing_charge":"Yes","article_type":"original"},{"scopus_import":"1","ddc":["530"],"publication":"Physical Review Letters","type":"journal_article","date_updated":"2025-09-30T11:17:58Z","article_processing_charge":"Yes (via OA deal)","article_type":"original","article_number":"096302","language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"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.","lang":"eng"}],"oa":1,"day":"07","OA_type":"hybrid","year":"2025","title":"Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model","volume":134,"doi":"10.1103/PhysRevLett.134.096302","publication_status":"published","file_date_updated":"2025-03-25T12:37:07Z","ec_funded":1,"_id":"19437","issue":"9","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"intvolume":"       134","quality_controlled":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"},{"grant_number":"12078","_id":"8fa7db46-16d5-11f0-9cad-917600954daf","name":"Polarons in Lead Halide Perovskites"}],"date_published":"2025-03-07T00:00:00Z","month":"03","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_created":"2025-03-23T23:01:25Z","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","citation":{"chicago":"Kluibenschedl, Florian, Georgios Koutentakis, Ragheed Al Hyder, and Mikhail Lemeshko. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice Model.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">https://doi.org/10.1103/PhysRevLett.134.096302</a>.","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).","mla":"Kluibenschedl, Florian, et al. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice Model.” <i>Physical Review Letters</i>, vol. 134, no. 9, 096302, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">10.1103/PhysRevLett.134.096302</a>.","ieee":"F. Kluibenschedl, G. Koutentakis, R. Al Hyder, and M. Lemeshko, “Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model,” <i>Physical Review Letters</i>, 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. <i>Physical Review Letters</i>. 2025;134(9). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">10.1103/PhysRevLett.134.096302</a>","apa":"Kluibenschedl, F., Koutentakis, G., Al Hyder, R., &#38; Lemeshko, M. (2025). Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">https://doi.org/10.1103/PhysRevLett.134.096302</a>"},"file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2025-03-25T12:37:07Z","file_id":"19461","success":1,"file_size":708750,"checksum":"1901efd7f95e8fe70cac412f91ea4da3","file_name":"2025_PhysReviewLetters_Kluibenschedl.pdf","date_created":"2025-03-25T12:37:07Z","relation":"main_file","access_level":"open_access"}],"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).","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","OA_place":"publisher","isi":1,"external_id":{"arxiv":["2407.19993"],"pmid":["40131090"],"isi":["001492808800010"]},"arxiv":1,"pmid":1,"author":[{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl","first_name":"Florian"},{"first_name":"Georgios","last_name":"Koutentakis","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","full_name":"Koutentakis, Georgios"},{"full_name":"Al Hyder, Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","last_name":"Al Hyder"},{"last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}]},{"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.","has_accepted_license":"1","file":[{"file_name":"2025_JourEvolBiology_Perini.pdf","success":1,"checksum":"01408e626a4131bfec5ffc70b0af9129","file_size":12826085,"date_created":"2025-04-03T11:53:06Z","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2025-04-03T11:53:06Z","file_id":"19469"}],"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Perini","first_name":"Samuel","full_name":"Perini, Samuel"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram"}],"pmid":1,"external_id":{"pmid":["39803902"],"isi":["001415267900001"]},"isi":1,"OA_place":"publisher","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"intvolume":"        38","issue":"3","_id":"19438","date_published":"2025-03-01T00:00:00Z","quality_controlled":"1","page":"367-378","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"status":"public","month":"03","citation":{"apa":"Perini, S., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2025). Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>","ama":"Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. 2025;38(3):367-378. doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>","ieee":"S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs and SNPs as markers of evolutionary processes in hybrid zones,” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3. Oxford University Press, pp. 367–378, 2025.","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.","mla":"Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3, Oxford University Press, 2025, pp. 367–78, doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>.","short":"S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary Biology 38 (2025) 367–378.","chicago":"Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>."},"publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"date_created":"2025-03-23T23:01:25Z","corr_author":"1","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"title":"Short INDELs and SNPs as markers of evolutionary processes in hybrid zones","volume":38,"year":"2025","day":"01","OA_type":"hybrid","oa":1,"publication_status":"published","doi":"10.1093/jeb/voaf002","file_date_updated":"2025-04-03T11:53:06Z","ddc":["570"],"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2025-09-30T11:19:56Z","type":"journal_article","publication":"Journal of Evolutionary Biology","article_type":"original","article_processing_charge":"Yes (in subscription journal)"},{"quality_controlled":"1","date_published":"2025-02-01T00:00:00Z","_id":"19439","publication_identifier":{"issn":["0004-6280"]},"issue":"2","intvolume":"       137","department":[{"_id":"IlCa"}],"date_created":"2025-03-23T23:01:26Z","publisher":"IOP Publishing","citation":{"ieee":"A. C. Rodriguez <i>et al.</i>, “A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj,” <i>Publications of the Astronomical Society of the Pacific</i>, vol. 137, no. 2. IOP Publishing, 2025.","apa":"Rodriguez, A. C., El-Badry, K., Hakala, P., Rodríguez-Gil, P., Bao, T., Galiullin, I., … Smith, R. (2025). A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj. <i>Publications of the Astronomical Society of the Pacific</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">https://doi.org/10.1088/1538-3873/adb0f1</a>","ama":"Rodriguez AC, El-Badry K, Hakala P, et al. A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj. <i>Publications of the Astronomical Society of the Pacific</i>. 2025;137(2). doi:<a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">10.1088/1538-3873/adb0f1</a>","chicago":"Rodriguez, Antonio C., Kareem El-Badry, Pasi Hakala, Pablo Rodríguez-Gil, Tong Bao, Ilkham Galiullin, Jacob A. Kurlander, et al. “A Link between White Dwarf Pulsars and Polars: Multiwavelength Observations of the 9.36-Minute Period Variable Gaia22ayj.” <i>Publications of the Astronomical Society of the Pacific</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">https://doi.org/10.1088/1538-3873/adb0f1</a>.","short":"A.C. Rodriguez, K. El-Badry, P. Hakala, P. Rodríguez-Gil, T. Bao, I. Galiullin, J.A. Kurlander, C.J. Law, I. Pelisoli, M.R. Schreiber, K. Burdge, I. Caiazzo, J.V. Roestel, P. Szkody, A.J. Drake, D.A.H. Buckley, S.B. Potter, B. Gaensicke, K. Mori, E.C. Bellm, S.R. Kulkarni, T.A. Prince, M. Graham, M.M. Kasliwal, S. Rose, Y. Sharma, T. Ahumada, S. Anand, A. Viitanen, A. Wold, T.X. Chen, R. Riddle, R. Smith, Publications of the Astronomical Society of the Pacific 137 (2025).","mla":"Rodriguez, Antonio C., et al. “A Link between White Dwarf Pulsars and Polars: Multiwavelength Observations of the 9.36-Minute Period Variable Gaia22ayj.” <i>Publications of the Astronomical Society of the Pacific</i>, vol. 137, no. 2, 024202, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">10.1088/1538-3873/adb0f1</a>.","ista":"Rodriguez AC, El-Badry K, Hakala P, Rodríguez-Gil P, Bao T, Galiullin I, Kurlander JA, Law CJ, Pelisoli I, Schreiber MR, Burdge K, Caiazzo I, Roestel JV, Szkody P, Drake AJ, Buckley DAH, Potter SB, Gaensicke B, Mori K, Bellm EC, Kulkarni SR, Prince TA, Graham M, Kasliwal MM, Rose S, Sharma Y, Ahumada T, Anand S, Viitanen A, Wold A, Chen TX, Riddle R, Smith R. 2025. A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj. Publications of the Astronomical Society of the Pacific. 137(2), 024202."},"month":"02","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file":[{"date_updated":"2025-03-25T10:01:24Z","file_id":"19455","creator":"dernst","content_type":"application/pdf","date_created":"2025-03-25T10:01:24Z","relation":"main_file","access_level":"open_access","checksum":"42d5aa504479c3fdf2a10165a9e3319f","success":1,"file_size":3291933,"file_name":"2025_PubAstronomSocPacific_Rodriguez.pdf"}],"acknowledgement":"We wish to dedicate this work to the memory of our colleague and friend Tom Marsh. Tom's enthusiasm to work on this object and rapid efforts to facilitate data collection truly made this project possible.\r\n\r\nA.C.R. acknowledges support from an NSF Graduate Fellowship. A.C.R. thanks the LSST-DA Data Science Fellowship Program, which is funded by LSST-DA, the Brinson Foundation, and the Moore Foundation; his participation in the program has benefited this work. P.R.-G. acknowledges support by the Spanish Agencia Estatal de Investigación del Ministerio de Ciencia e Innovación (MCIN/AEI) and the European Regional Development Fund (ERDF) under grant PID2021–124879NB–I00. M.R.S. is supported by FONDECYT (grant No. 1221059) and eRO-STEP (SA 2131/15-2 project number 414059771). I.P. acknowledges support from a Royal Society University Research Fellowship (URF/R1/231496). We thank the referee for feedback that improved the clarity of this paper.\r\n\r\nBased on observations made with the Gran Telescopio Canarias (GTC), installed at the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofìsica de Canarias, on the island of La Palma. Based on observations obtained with the Samuel Oschin Telescope 48 inch and the 60 inch Telescope at the Palomar Observatory as part of the ZTF project. ZTF is supported by the National Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration including current partners Caltech, IPAC, the Weizmann Institute of Science, the Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan, the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern University and former partners the University of Washington, Los Alamos National Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted by COO, IPAC, and UW.\r\n\r\nSome of the data presented herein were obtained at Keck Observatory, which is a private 501(c)3 non-profit organization operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the Native Hawaiian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We are also grateful to the staff of Palomar Observatory for their assistance in carrying out observations used in this work.\r\n\r\nPartly based on observations made with the NOT, owned in collaboration by the University of Turku and Aarhus University, and operated jointly by Aarhus University, the University of Turku and the University of Oslo, representing Denmark, Finland and Norway, the University of Iceland and Stockholm University at the Observatorio del Roque de los Muchachos, La Palma, Spain, of the Instituto de Astrofisica de Canarias. The data presented here were obtained with ALFOSC, which is provided by the Instituto de Astrofisica de Andalucia (IAA) under a joint agreement with the University of Copenhagen and NOT. The observation with the SALT was obtained under program 2021-2-LSP-001 (PI: D. Buckley). Polish participation in SALT is funded by grant No. MEiN nr 2021/WK/01. D.A.H.B. acknowledges support from the National Research Foundation.\r\n\r\nThis work presents results from the European Space Agency (ESA) space mission Gaia. Gaia data are being processed by the Gaia Data Processing and Analysis Consortium (DPAC). Funding for the DPAC is provided by national institutions, in particular the institutions participating in the Gaia MultiLateral Agreement (MLA). The Gaia mission website is https://www.cosmos.esa.int/gaia. The Gaia archive website is https://archives.esac.esa.int/gaia. This work made use of data supplied by the UK Swift Science Data Centre at the University of Leicester\r\n\r\nE.C.B. and J.K. acknowledge support from the DIRAC Institute in the Department of Astronomy at the University of Washington. The DIRAC Institute is supported through generous gifts from the Charles and Lisa Simonyi Fund for Arts and Sciences, and the Washington Research Foundation.","has_accepted_license":"1","isi":1,"OA_place":"publisher","arxiv":1,"external_id":{"isi":["001427877700001"],"arxiv":["2501.01490"]},"author":[{"last_name":"Rodriguez","first_name":"Antonio C.","full_name":"Rodriguez, Antonio C."},{"full_name":"El-Badry, Kareem","last_name":"El-Badry","first_name":"Kareem"},{"first_name":"Pasi","last_name":"Hakala","full_name":"Hakala, Pasi"},{"full_name":"Rodríguez-Gil, Pablo","last_name":"Rodríguez-Gil","first_name":"Pablo"},{"full_name":"Bao, Tong","last_name":"Bao","first_name":"Tong"},{"full_name":"Galiullin, Ilkham","last_name":"Galiullin","first_name":"Ilkham"},{"first_name":"Jacob A.","last_name":"Kurlander","full_name":"Kurlander, Jacob A."},{"full_name":"Law, Casey J.","last_name":"Law","first_name":"Casey J."},{"full_name":"Pelisoli, Ingrid","last_name":"Pelisoli","first_name":"Ingrid"},{"last_name":"Schreiber","first_name":"Matthias R.","full_name":"Schreiber, Matthias R."},{"first_name":"Kevin","last_name":"Burdge","full_name":"Burdge, Kevin"},{"last_name":"Caiazzo","first_name":"Ilaria","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","full_name":"Caiazzo, Ilaria","orcid":"0000-0002-4770-5388"},{"first_name":"Jan Van","last_name":"Roestel","full_name":"Roestel, Jan Van"},{"full_name":"Szkody, Paula","last_name":"Szkody","first_name":"Paula"},{"first_name":"Andrew J.","last_name":"Drake","full_name":"Drake, Andrew J."},{"first_name":"David A.H.","last_name":"Buckley","full_name":"Buckley, David A.H."},{"full_name":"Potter, Stephen B.","first_name":"Stephen B.","last_name":"Potter"},{"full_name":"Gaensicke, Boris","last_name":"Gaensicke","first_name":"Boris"},{"first_name":"Kaya","last_name":"Mori","full_name":"Mori, Kaya"},{"full_name":"Bellm, Eric C.","last_name":"Bellm","first_name":"Eric C."},{"full_name":"Kulkarni, Shrinivas R.","first_name":"Shrinivas R.","last_name":"Kulkarni"},{"last_name":"Prince","first_name":"Thomas A.","full_name":"Prince, Thomas A."},{"last_name":"Graham","first_name":"Matthew","full_name":"Graham, Matthew"},{"full_name":"Kasliwal, Mansi M.","last_name":"Kasliwal","first_name":"Mansi M."},{"full_name":"Rose, Sam","first_name":"Sam","last_name":"Rose"},{"full_name":"Sharma, Yashvi","first_name":"Yashvi","last_name":"Sharma"},{"first_name":"Tomás","last_name":"Ahumada","full_name":"Ahumada, Tomás"},{"full_name":"Anand, Shreya","last_name":"Anand","first_name":"Shreya"},{"full_name":"Viitanen, Akke","last_name":"Viitanen","first_name":"Akke"},{"full_name":"Wold, Avery","last_name":"Wold","first_name":"Avery"},{"last_name":"Chen","first_name":"Tracy X.","full_name":"Chen, Tracy X."},{"last_name":"Riddle","first_name":"Reed","full_name":"Riddle, Reed"},{"last_name":"Smith","first_name":"Roger","full_name":"Smith, Roger"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","publication":"Publications of the Astronomical Society of the Pacific","type":"journal_article","date_updated":"2025-09-30T11:15:10Z","scopus_import":"1","ddc":["520"],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","oa":1,"day":"01","OA_type":"hybrid","year":"2025","title":"A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj","volume":137,"language":[{"iso":"eng"}],"article_number":"024202","abstract":[{"text":"White dwarfs (WDs) are the most abundant compact objects, and recent surveys have suggested that over a third of WDs in accreting binaries host a strong (B  ≳ 1 MG) magnetic field. However, the origin and evolution of WD magnetism remain under debate. Two WD pulsars, AR Sco and J191213.72–441045.1 (J1912), have been found, which are non-accreting binaries hosting rapidly spinning (1.97 minutes and 5.30 minutes, respectively) magnetic WDs. The WD in AR Sco is slowing down on a (math formular) yr timescale. It is believed they will eventually become polars, accreting systems in which a magnetic WD (B  ≈ 10−240 MG) accretes from a Roche lobe-filling donor spinning in sync with the orbit (≳78 minutes). Here, we present multiwavelength data and analysis of Gaia22ayj, which outbursted in 2022 March. We find that Gaia22ayj is a magnetic accreting WD that is rapidly spinning down (math formular\r\n yr) like WD pulsars, but shows clear evidence of accretion, like polars. Strong linear polarization (40%) is detected in Gaia22ayj; such high levels have only been seen in the WD pulsar AR Sco and demonstrate the WD is magnetic. High speed photometry reveals a 9.36 minutes period accompanying a high amplitude (∼2 mag) modulation. We associate this with a WD spin or spin–orbit beat period, not an orbital period as was previously suggested. Fast (60 s) optical spectroscopy reveals a broad \"hump,\" reminiscent of cyclotron emission in polars, between 4000 and 8000 Å. We find an X-ray luminosity of (math formular) in the 0.3–8 keV energy range, while two very large array radio campaigns resulted in a non-detection with a Fr < 15.8 μJy 3σ upper limit. The shared properties of both WD pulsars and polars suggest that Gaia22ayj is a missing link between the two classes of magnetic WD binaries.","lang":"eng"}],"file_date_updated":"2025-03-25T10:01:24Z","doi":"10.1088/1538-3873/adb0f1","publication_status":"published"},{"isi":1,"OA_place":"publisher","arxiv":1,"external_id":{"arxiv":["2304.03710"],"isi":["001420226800001"]},"author":[{"last_name":"Alon","first_name":"Yahav","full_name":"Alon, Yahav"},{"full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","first_name":"Michael"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2025-03-25T11:46:27Z","file_id":"19459","file_name":"2025_RandomStruc_Alon.pdf","success":1,"checksum":"6067747e805fa356d560dc45f2a89918","file_size":549236,"date_created":"2025-03-25T11:46:27Z","access_level":"open_access","relation":"main_file"}],"acknowledgement":"The authors would like to express their thanks to the referees of the article for their valuable input towards improving the presentation of our result. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","has_accepted_license":"1","department":[{"_id":"MaKw"}],"date_created":"2025-03-23T23:01:26Z","citation":{"apa":"Alon, Y., &#38; Anastos, M. (2025). The completion numbers of hamiltonicity and pancyclicity in random graphs. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.21286\">https://doi.org/10.1002/rsa.21286</a>","ieee":"Y. Alon and M. Anastos, “The completion numbers of hamiltonicity and pancyclicity in random graphs,” <i>Random Structures and Algorithms</i>, vol. 66, no. 2. Wiley, 2025.","ama":"Alon Y, Anastos M. The completion numbers of hamiltonicity and pancyclicity in random graphs. <i>Random Structures and Algorithms</i>. 2025;66(2). doi:<a href=\"https://doi.org/10.1002/rsa.21286\">10.1002/rsa.21286</a>","ista":"Alon Y, Anastos M. 2025. The completion numbers of hamiltonicity and pancyclicity in random graphs. Random Structures and Algorithms. 66(2), e21286.","short":"Y. Alon, M. Anastos, Random Structures and Algorithms 66 (2025).","mla":"Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity and Pancyclicity in Random Graphs.” <i>Random Structures and Algorithms</i>, vol. 66, no. 2, e21286, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/rsa.21286\">10.1002/rsa.21286</a>.","chicago":"Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity and Pancyclicity in Random Graphs.” <i>Random Structures and Algorithms</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/rsa.21286\">https://doi.org/10.1002/rsa.21286</a>."},"publisher":"Wiley","month":"03","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"quality_controlled":"1","date_published":"2025-03-01T00:00:00Z","_id":"19440","intvolume":"        66","issue":"2","publication_identifier":{"issn":["1042-9832"],"eissn":["1098-2418"]},"file_date_updated":"2025-03-25T11:46:27Z","ec_funded":1,"doi":"10.1002/rsa.21286","publication_status":"published","oa":1,"OA_type":"hybrid","day":"01","year":"2025","volume":66,"title":"The completion numbers of hamiltonicity and pancyclicity in random graphs","article_number":"e21286","language":[{"iso":"eng"}],"abstract":[{"text":"Let μ(G) denote the minimum number of edges whose addition to G results in a Hamiltonian graph, and let μ^(G) denote the minimum number of edges whose addition to G results in a pancyclic graph. We study the distributions of μ(G),μ^(G) in the context of binomial random graphs. Letting d=d(n):=n⋅p, we prove that there exists a function f:R+→[0,1] of order f(d)=12de−d+e−d+O(d6e−3d) such that, if G∼G(n,p) with 20≤d(n)≤0.4logn, then with high probability μ(G)=(1+o(1))⋅f(d)⋅n. Let ni(G) denote the number of degree i vertices in G. A trivial lower bound on μ(G) is given by the expression n0(G)+⌈12n1(G)⌉. In the denser regime of random graphs, we show that if np−13logn−2loglogn→∞ and G∼G(n,p) then, with high probability, μ(G)=n0(G)+⌈12n1(G)⌉. For completion to pancyclicity, we show that if G∼G(n,p) and np≥20 then, with high probability, μ^(G)=μ(G). Finally, we present a polynomial time algorithm such that, if G∼G(n,p) and np≥20, then, with high probability, the algorithm returns a set of edges of size μ(G) whose addition to G results in a pancyclic (and therefore also Hamiltonian) graph.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","type":"journal_article","publication":"Random Structures and Algorithms","date_updated":"2025-09-30T11:15:41Z","scopus_import":"1","ddc":["510"]},{"month":"03","status":"public","page":"11133-11145","department":[{"_id":"JePa"}],"date_created":"2025-03-23T23:01:26Z","citation":{"ieee":"C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J. A. Palacci, and A. Aubret, “Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers,” <i>ACS Nano</i>, vol. 19, no. 11. American Chemical Society, pp. 11133–11145, 2025.","apa":"Carrasco, C., Martinet, Q., Shen, Z., Lintuvuori, J., Palacci, J. A., &#38; Aubret, A. (2025). Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c18078\">https://doi.org/10.1021/acsnano.4c18078</a>","ama":"Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. <i>ACS Nano</i>. 2025;19(11):11133-11145. doi:<a href=\"https://doi.org/10.1021/acsnano.4c18078\">10.1021/acsnano.4c18078</a>","chicago":"Carrasco, Celso, Quentin Martinet, Zaiyi Shen, Juho Lintuvuori, Jérémie A Palacci, and Antoine Aubret. “Characterization of Nonequilibrium Interactions of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS Nano</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acsnano.4c18078\">https://doi.org/10.1021/acsnano.4c18078</a>.","ista":"Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. 2025. Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. ACS Nano. 19(11), 11133–11145.","short":"C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J.A. Palacci, A. Aubret, ACS Nano 19 (2025) 11133–11145.","mla":"Carrasco, Celso, et al. “Characterization of Nonequilibrium Interactions of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS Nano</i>, vol. 19, no. 11, American Chemical Society, 2025, pp. 11133–45, doi:<a href=\"https://doi.org/10.1021/acsnano.4c18078\">10.1021/acsnano.4c18078</a>."},"publisher":"American Chemical Society","_id":"19441","intvolume":"        19","issue":"11","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"project":[{"name":"Emergent Behavior in Spinning Active Matter","_id":"eb99c9bb-77a9-11ec-83b8-9f8cffa20a35","grant_number":"P35206"}],"quality_controlled":"1","date_published":"2025-03-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","isi":1,"OA_place":"repository","external_id":{"pmid":["40069094"],"isi":["001443359300001"]},"pmid":1,"author":[{"full_name":"Carrasco, Celso","last_name":"Carrasco","first_name":"Celso"},{"first_name":"Quentin","last_name":"Martinet","full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"full_name":"Shen, Zaiyi","last_name":"Shen","first_name":"Zaiyi"},{"full_name":"Lintuvuori, Juho","last_name":"Lintuvuori","first_name":"Juho"},{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"}],"acknowledgement":"The authors thank M. Perrin and A. Allard for enlightening discussions. This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/P35206]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No. 886024.","article_processing_charge":"No","article_type":"original","scopus_import":"1","type":"journal_article","publication":"ACS Nano","date_updated":"2025-10-16T10:26:59Z","doi":"10.1021/acsnano.4c18078","publication_status":"published","main_file_link":[{"url":"https://hal.science/hal-04682818v2","open_access":"1"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Catalytic microswimmers convert the chemical energy from fuel into motion. They sustain chemical gradients and fluid flows that propel them by phoresis. This leads to unconventional behavior and collective dynamics, such as self-organization into complex structures. Characterizing the nonequilibrium interactions of microswimmers is crucial for advancing our understanding of active systems. However, this remains a challenge owing to the importance of fluctuations at the microscale and the difficulty in disentangling the different contributions to the interactions. Here, we show a massive dependence of the nonequilibrium interactions on the shape of catalytic microswimmers. We perform tracking experiments at high throughput to map interactions between nanocolloidal tracers and dimeric microswimmers of various aspect ratios. Our method leverages dual tracers with differing phoretic mobilities to quantitatively disentangle phoretic motion from hydrodynamic advection. This approach is validated through experiments on single chemically active sites and on immobilized catalytic microswimmers. We further investigate the activity-driven interactions of free microswimmers and directly measure their phoretic interactions. When compared to standard models, our findings highlight the important role of osmotic flows for microswimmers near surfaces and reveal an enhanced contribution of hydrodynamic advection relative to phoretic motion as the size of the microswimmer increases. Our study provides robust measurements of the nonequilibrium interactions from catalytic microswimmers and lays the groundwork for a realistic description of active systems."}],"oa":1,"OA_type":"green","day":"11","year":"2025","title":"Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers","volume":19},{"file":[{"file_name":"2025_JournEcology_Heim.pdf","success":1,"file_size":2662766,"checksum":"e2785ae265e211b4dc7fc9c5b7744948","date_created":"2025-12-30T08:08:18Z","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_id":"20890","date_updated":"2025-12-30T08:08:18Z"}],"has_accepted_license":"1","acknowledgement":"We would like to express our sincere gratitude to all the data providers who carried out fieldwork in different regions of the Arctic and published their data, which we used for our meta-analysis. We recognise the hard work and dedication of these individuals, without whom this paper would not have been possible. We are grateful to the editor and the anonymous reviewer for their time and valuable feedback on this manuscript. We particularly appreciate the detailed and constructive comments provided by reviewer Mara Baudena, which significantly strengthened our work. We also acknowledge the Indigenous peoples and rural communities of the Arctic, whose traditional knowledge, rights, and interests are integral to the stewardship and study of these ecosystems. This work was funded in part by the U.S. National Aeronautics and Space Administration (NASA) grant 80NSSC22K1256 (GVF). Open Access funding enabled and organized by Projekt DEAL.","external_id":{"isi":["001443422900001"]},"author":[{"full_name":"Heim, Ramona Julia","last_name":"Heim","first_name":"Ramona Julia"},{"last_name":"Rocha","first_name":"Adrian V.","full_name":"Rocha, Adrian V."},{"last_name":"Zemlianskii","first_name":"Vitalii","full_name":"Zemlianskii, Vitalii"},{"full_name":"Barrett, Kirsten","last_name":"Barrett","first_name":"Kirsten"},{"first_name":"Helga","last_name":"Bültmann","full_name":"Bültmann, Helga"},{"last_name":"Breen","first_name":"Amy","full_name":"Breen, Amy"},{"full_name":"Frost, Gerald Verner","last_name":"Frost","first_name":"Gerald Verner"},{"full_name":"Hollingsworth, Teresa Nettleton","last_name":"Hollingsworth","first_name":"Teresa Nettleton"},{"first_name":"Randi","last_name":"Jandt","full_name":"Jandt, Randi"},{"first_name":"Maria","last_name":"Kozlova","full_name":"Kozlova, Maria"},{"first_name":"Anastasiya","last_name":"Kurka","full_name":"Kurka, Anastasiya"},{"full_name":"Jorgenson, Mark Torre","last_name":"Jorgenson","first_name":"Mark Torre"},{"first_name":"Simon M.","last_name":"Landhäusser","full_name":"Landhäusser, Simon M."},{"full_name":"Loranty, Michael Mark","first_name":"Michael Mark","last_name":"Loranty"},{"last_name":"Miller","first_name":"Eric A.","full_name":"Miller, Eric A."},{"first_name":"Kenji","last_name":"Narita","full_name":"Narita, Kenji"},{"id":"0b30719b-13f0-11ed-ab2a-94498bc6a278","full_name":"Pravdolyubova, Evgeniya","first_name":"Evgeniya","last_name":"Pravdolyubova"},{"full_name":"Hölzel, Norbert","first_name":"Norbert","last_name":"Hölzel"},{"full_name":"Schaepman-Strub, Gabriela","last_name":"Schaepman-Strub","first_name":"Gabriela"}],"isi":1,"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_published":"2025-05-01T00:00:00Z","quality_controlled":"1","_id":"19442","publication_identifier":{"issn":["0022-0477"],"eissn":["1365-2745"]},"issue":"5","intvolume":"       113","citation":{"chicago":"Heim, Ramona Julia, Adrian V. Rocha, Vitalii Zemlianskii, Kirsten Barrett, Helga Bültmann, Amy Breen, Gerald Verner Frost, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>.","short":"R.J. Heim, A.V. Rocha, V. Zemlianskii, K. Barrett, H. Bültmann, A. Breen, G.V. Frost, T.N. Hollingsworth, R. Jandt, M. Kozlova, A. Kurka, M.T. Jorgenson, S.M. Landhäusser, M.M. Loranty, E.A. Miller, K. Narita, E. Pravdolyubova, N. Hölzel, G. Schaepman-Strub, Journal of Ecology 113 (2025) 1042–1056.","mla":"Heim, Ramona Julia, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>, vol. 113, no. 5, Wiley, 2025, pp. 1042–56, doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>.","ista":"Heim RJ, Rocha AV, Zemlianskii V, Barrett K, Bültmann H, Breen A, Frost GV, Hollingsworth TN, Jandt R, Kozlova M, Kurka A, Jorgenson MT, Landhäusser SM, Loranty MM, Miller EA, Narita K, Pravdolyubova E, Hölzel N, Schaepman-Strub G. 2025. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? Journal of Ecology. 113(5), 1042–1056.","apa":"Heim, R. J., Rocha, A. V., Zemlianskii, V., Barrett, K., Bültmann, H., Breen, A., … Schaepman-Strub, G. (2025). Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>","ieee":"R. J. Heim <i>et al.</i>, “Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?,” <i>Journal of Ecology</i>, vol. 113, no. 5. Wiley, pp. 1042–1056, 2025.","ama":"Heim RJ, Rocha AV, Zemlianskii V, et al. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. 2025;113(5):1042-1056. doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>"},"publisher":"Wiley","date_created":"2025-03-23T23:01:27Z","department":[{"_id":"NiBa"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"1042-1056","month":"05","status":"public","year":"2025","volume":113,"title":"Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?","oa":1,"OA_type":"hybrid","day":"01","abstract":[{"text":"1. Climate change is expected to induce shifts in the composition, structure and functioning of Arctic tundra ecosystems. Increases in the frequency and severity of tundra fires have the potential to catalyse vegetation transitions with far-reaching local, regional and global consequences.\r\n2. We propose that post-fire tundra recovery, coupled with climate change, may not necessarily lead to pre-fire conditions. Our hypothesis, based on surveys and literature, suggests two climate–fire driven trajectories. One trajectory results in increased woody vegetation under low fire frequency; the other results in grass dominance under high frequency.\r\n3. Future research should address uncertainties regarding possible tundra ecosystem shifts linked to fires, using methods that encompass greater temporal and spatial scales than previously addressed. More case studies, especially in underrepresented regions and ecosystem types, are essential to broaden the empirical basis for forecasts and potential fire management strategies.\r\n4. Synthesis. Our review synthesises current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems, highlighting potential transitions and alternative ecosystem states and their implications. We discuss challenges in defining and predicting these trajectories as well as future directions.","lang":"eng"}],"language":[{"iso":"eng"}],"file_date_updated":"2025-12-30T08:08:18Z","publication_status":"published","doi":"10.1111/1365-2745.70022","type":"journal_article","publication":"Journal of Ecology","date_updated":"2025-12-30T08:09:47Z","PlanS_conform":"1","scopus_import":"1","ddc":["550","570"],"article_type":"review","article_processing_charge":"Yes (via OA deal)"},{"file_date_updated":"2025-08-05T12:15:13Z","doi":"10.1016/j.str.2025.01.020","publication_status":"published","oa":1,"day":"03","OA_type":"hybrid","year":"2025","title":"FakET: Simulating cryo-electron tomograms with neural style transfer","volume":33,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/."}],"corr_author":"1","article_processing_charge":"Yes (in subscription journal)","article_type":"original","publication":"Structure","type":"journal_article","PlanS_conform":"1","date_updated":"2025-09-30T11:13:02Z","scopus_import":"1","ddc":["570"],"OA_place":"publisher","isi":1,"external_id":{"pmid":["39947174"],"isi":["001463196100001"]},"author":[{"last_name":"Harar","first_name":"Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","orcid":"0000-0001-5206-1794","full_name":"Harar, Pavol"},{"full_name":"Herrmann, Lukas","first_name":"Lukas","last_name":"Herrmann"},{"last_name":"Grohs","first_name":"Philipp","full_name":"Grohs, Philipp"},{"last_name":"Haselbach","first_name":"David","full_name":"Haselbach, David"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","related_material":{"link":[{"url":"https://github.com/paloha/faket/","relation":"software"}]},"file":[{"content_type":"application/pdf","creator":"dernst","date_updated":"2025-08-05T12:15:13Z","file_id":"20130","file_size":4367530,"success":1,"checksum":"f346bc357a66a88cca3d0eb95793fb73","file_name":"2025_Structure_Harar.pdf","relation":"main_file","access_level":"open_access","date_created":"2025-08-05T12:15:13Z"}],"acknowledgement":"The IMP and D.H. are generously funded by Boehringer Ingelheim. We thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for helpful discussions.","has_accepted_license":"1","date_created":"2025-03-23T23:01:27Z","department":[{"_id":"AlMi"}],"publisher":"Elsevier","citation":{"ama":"Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. 2025;33(4):820-827.e4. doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>","apa":"Harar, P., Herrmann, L., Grohs, P., &#38; Haselbach, D. (2025). FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>","ieee":"P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” <i>Structure</i>, vol. 33, no. 4. Elsevier, p. 820–827.e4, 2025.","mla":"Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4, doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","ista":"Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 33(4), 820–827.e4.","chicago":"Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>."},"month":"04","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"820-827.e4","quality_controlled":"1","date_published":"2025-04-03T00:00:00Z","_id":"19443","intvolume":"        33","publication_identifier":{"eissn":["1878-4186"],"issn":["0969-2126"]},"issue":"4"},{"acknowledgement":"The authors thank members of their laboratories who provided feedback on earlier versions of this manuscript, including A. Jourdon, V. Mariano, T. L. Li, N. Caporale, E. Villa and M. Sutcliffe.","external_id":{"isi":["001437461900001"],"pmid":["39653126"]},"author":[{"first_name":"Sergiu P.","last_name":"Pașca","full_name":"Pașca, Sergiu P."},{"first_name":"Paola","last_name":"Arlotta","full_name":"Arlotta, Paola"},{"last_name":"Bateup","first_name":"Helen S.","full_name":"Bateup, Helen S."},{"last_name":"Camp","first_name":"J. Gray","full_name":"Camp, J. Gray"},{"last_name":"Cappello","first_name":"Silvia","full_name":"Cappello, Silvia"},{"first_name":"Fred H.","last_name":"Gage","full_name":"Gage, Fred H."},{"full_name":"Knoblich, Jürgen A.","last_name":"Knoblich","first_name":"Jürgen A."},{"last_name":"Kriegstein","first_name":"Arnold R.","full_name":"Kriegstein, Arnold R."},{"full_name":"Lancaster, Madeline A.","last_name":"Lancaster","first_name":"Madeline A."},{"full_name":"Ming, Guo Li","last_name":"Ming","first_name":"Guo Li"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"},{"last_name":"Okano","first_name":"Hideyuki","full_name":"Okano, Hideyuki"},{"first_name":"Malin","last_name":"Parmar","full_name":"Parmar, Malin"},{"full_name":"Park, In Hyun","first_name":"In Hyun","last_name":"Park"},{"full_name":"Reiner, Orly","last_name":"Reiner","first_name":"Orly"},{"first_name":"Hongjun","last_name":"Song","full_name":"Song, Hongjun"},{"full_name":"Studer, Lorenz","last_name":"Studer","first_name":"Lorenz"},{"last_name":"Takahashi","first_name":"Jun","full_name":"Takahashi, Jun"},{"last_name":"Temple","first_name":"Sally","full_name":"Temple, Sally"},{"last_name":"Testa","first_name":"Giuseppe","full_name":"Testa, Giuseppe"},{"full_name":"Treutlein, Barbara","last_name":"Treutlein","first_name":"Barbara"},{"last_name":"Vaccarino","first_name":"Flora M.","full_name":"Vaccarino, Flora M."},{"full_name":"Vanderhaeghen, Pierre","last_name":"Vanderhaeghen","first_name":"Pierre"},{"last_name":"Young-Pearse","first_name":"Tracy","full_name":"Young-Pearse, Tracy"}],"pmid":1,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","date_published":"2025-03-13T00:00:00Z","quality_controlled":"1","_id":"19444","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"intvolume":"       639","issue":"8054","citation":{"ista":"Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH, Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids and transplantation studies. Nature. 639(8054), 315–320.","mla":"Pașca, Sergiu P., et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>, vol. 639, no. 8054, Springer Nature, 2025, pp. 315–20, doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>.","short":"S.P. Pașca, P. Arlotta, H.S. Bateup, J.G. Camp, S. Cappello, F.H. Gage, J.A. Knoblich, A.R. Kriegstein, M.A. Lancaster, G.L. Ming, G. Novarino, H. Okano, M. Parmar, I.H. Park, O. Reiner, H. Song, L. Studer, J. Takahashi, S. Temple, G. Testa, B. Treutlein, F.M. Vaccarino, P. Vanderhaeghen, T. Young-Pearse, Nature 639 (2025) 315–320.","chicago":"Pașca, Sergiu P., Paola Arlotta, Helen S. Bateup, J. Gray Camp, Silvia Cappello, Fred H. Gage, Jürgen A. Knoblich, et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>.","ama":"Pașca SP, Arlotta P, Bateup HS, et al. A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. 2025;639(8054):315-320. doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>","ieee":"S. P. Pașca <i>et al.</i>, “A framework for neural organoids, assembloids and transplantation studies,” <i>Nature</i>, vol. 639, no. 8054. Springer Nature, pp. 315–320, 2025.","apa":"Pașca, S. P., Arlotta, P., Bateup, H. S., Camp, J. G., Cappello, S., Gage, F. H., … Young-Pearse, T. (2025). A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>"},"publisher":"Springer Nature","department":[{"_id":"GaNo"}],"date_created":"2025-03-23T23:01:27Z","page":"315-320","month":"03","status":"public","year":"2025","title":"A framework for neural organoids, assembloids and transplantation studies","volume":639,"OA_type":"closed access","day":"13","abstract":[{"text":"As the field of neural organoids and assembloids expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. In this Perspective, we present a framework for the experimental process that encompasses ensuring the quality and integrity of human pluripotent stem cells, characterizing and manipulating neural cells in vitro, transplantation techniques and considerations for modelling human development, evolution and disease. As with all scientific endeavours, we advocate for rigorous experimental designs tailored to explicit scientific questions as well as transparent methodologies and data sharing to provide useful knowledge for current research practices and for developing regulatory standards.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_status":"published","doi":"10.1038/s41586-024-08487-6","type":"journal_article","publication":"Nature","date_updated":"2025-09-30T11:13:47Z","scopus_import":"1","article_type":"original","article_processing_charge":"No"},{"acknowledgement":"J. M. Křišťan acknowledges the support of the Czech Science Foundation Grant No. 24-12046S. This work was supported by the Grant Agency of the Czech Technical University in Prague, grant No. SGS23/205/OHK3/3T/18. J. Svoboda acknowledges the support of the ERC CoG 863818 (ForM-SMArt) grant.","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","isi":1,"author":[{"first_name":"Jan Matyáš","last_name":"Křišťan","full_name":"Křišťan, Jan Matyáš"},{"orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub"}],"external_id":{"arxiv":["2411.12582"],"isi":["001537885900016"]},"arxiv":1,"publication_identifier":{"isbn":["9789819628445"],"eissn":["1611-3349"],"issn":["0302-9743"]},"intvolume":"     15411","_id":"19445","quality_controlled":"1","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"date_published":"2025-02-20T00:00:00Z","status":"public","month":"02","page":"244-265","date_created":"2025-03-23T23:01:27Z","department":[{"_id":"KrCh"}],"citation":{"ieee":"J. M. Křišťan and J. Svoboda, “Reconfiguration using generalized token jumping,” in <i>19th International Conference and Workshops on Algorithms and Computation</i>, Chengdu, China, 2025, vol. 15411, pp. 244–265.","apa":"Křišťan, J. M., &#38; Svoboda, J. (2025). Reconfiguration using generalized token jumping. In <i>19th International Conference and Workshops on Algorithms and Computation</i> (Vol. 15411, pp. 244–265). Chengdu, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">https://doi.org/10.1007/978-981-96-2845-2_16</a>","ama":"Křišťan JM, Svoboda J. Reconfiguration using generalized token jumping. In: <i>19th International Conference and Workshops on Algorithms and Computation</i>. Vol 15411. Springer Nature; 2025:244-265. doi:<a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">10.1007/978-981-96-2845-2_16</a>","chicago":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized Token Jumping.” In <i>19th International Conference and Workshops on Algorithms and Computation</i>, 15411:244–65. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">https://doi.org/10.1007/978-981-96-2845-2_16</a>.","mla":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized Token Jumping.” <i>19th International Conference and Workshops on Algorithms and Computation</i>, vol. 15411, Springer Nature, 2025, pp. 244–65, doi:<a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">10.1007/978-981-96-2845-2_16</a>.","short":"J.M. Křišťan, J. Svoboda, in:, 19th International Conference and Workshops on Algorithms and Computation, Springer Nature, 2025, pp. 244–265.","ista":"Křišťan JM, Svoboda J. 2025. Reconfiguration using generalized token jumping. 19th International Conference and Workshops on Algorithms and Computation. WALCOM: International Conference and Workshops on Algorithms and Computation, LNCS, vol. 15411, 244–265."},"publisher":"Springer Nature","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In reconfiguration, we are given two solutions to a graph problem, such as Vertex Cover or Dominating Set, with each solution represented by a placement of tokens on vertices of the graph. Our task is to reconfigure one into the other using small steps while ensuring the intermediate configurations of tokens are also valid solutions. The two commonly studied settings are Token Jumping and Token Sliding, which allows moving a single token to an arbitrary or an adjacent vertex, respectively.\r\n\r\nWe introduce new rules that generalize Token Jumping, parameterized by the number of tokens allowed to move at once and by the maximum distance of each move. Our main contribution is identifying minimal rules that allow reconfiguring any possible given solution into any other for Independent Set, Vertex Cover, and Dominating Set. For each minimal rule, we also provide an efficient algorithm that finds a corresponding reconfiguration sequence.\r\n\r\nWe further focus on the rule that allows each token to move to an adjacent vertex in a single step. This natural variant turns out to be the minimal rule that guarantees reconfigurability for Vertex Cover. We determine the computational complexity of deciding whether a (shortest) reconfiguration sequence exists under this rule for the three studied problems. While reachability for Vertex Cover is shown to be in P, finding a shortest sequence is shown to be NP-complete. For Independent Set and Dominating Set, even reachability is shown to be PSPACE-complete."}],"OA_type":"green","conference":{"start_date":"2025-02-28","location":"Chengdu, China","end_date":"2025-03-02","name":"WALCOM: International Conference and Workshops on Algorithms and Computation"},"day":"20","oa":1,"volume":15411,"title":"Reconfiguration using generalized token jumping","year":"2025","alternative_title":["LNCS"],"doi":"10.1007/978-981-96-2845-2_16","publication_status":"published","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2411.12582","open_access":"1"}],"scopus_import":"1","date_updated":"2025-09-30T11:14:33Z","type":"conference","publication":"19th International Conference and Workshops on Algorithms and Computation","article_processing_charge":"No"}]