[{"ddc":["570"],"publisher":"Institute of Science and Technology Austria","OA_place":"repository","related_material":{"record":[{"status":"public","id":"13314","relation":"used_in_publication"},{"relation":"used_in_publication","id":"21427","status":"public"},{"id":"21423","status":"public","relation":"used_in_publication"}]},"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"file":[{"file_id":"21440","success":1,"file_size":154465214,"content_type":"application/zip","date_created":"2026-03-11T20:41:28Z","relation":"main_file","checksum":"47809a9a31b748b16e21e92d11ddc87f","creator":"zdunajov","access_level":"open_access","file_name":"Supplementary_movies_Thesis_Dunajova.zip","date_updated":"2026-03-11T20:41:28Z"},{"access_level":"open_access","creator":"zdunajov","checksum":"a64a174bc6abf0a5e77631e4fd121f1f","file_name":"readme.txt","date_updated":"2026-03-11T20:52:39Z","date_created":"2026-03-11T20:52:39Z","relation":"main_file","file_size":2289,"content_type":"text/plain","file_id":"21441","success":1}],"contributor":[{"orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","last_name":"Tasciyan","contributor_type":"researcher"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","contributor_type":"researcher","last_name":"Radler","orcid":"0000-0001-9198-2182 "}],"corr_author":"1","type":"research_data","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"doi":"10.15479/AT-ISTA-21439","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"citation":{"ieee":"Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization of migrating cells and chiral filaments.’” Institute of Science and Technology Austria, 2026.","short":"Z. Dunajova, (2026).","mla":"Dunajova, Zuzana. <i>Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>.","ama":"Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>","apa":"Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">https://doi.org/10.15479/AT-ISTA-21439</a>","chicago":"Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">https://doi.org/10.15479/AT-ISTA-21439</a>.","ista":"Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>."},"day":"12","file_date_updated":"2026-03-11T20:52:39Z","abstract":[{"text":"These files contain supplementary movies accompanying the PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” by Zuzana Dunajova (2026). The videos provide additional visual material supporting the experiments and results described in the thesis.","lang":"eng"}],"oa_version":"None","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","OA_type":"free access","oa":1,"date_updated":"2026-03-18T14:11:36Z","project":[{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"author":[{"full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova","first_name":"Zuzana"}],"date_created":"2026-03-11T21:05:20Z","date_published":"2026-03-12T00:00:00Z","title":"Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”","month":"03","year":"2026","_id":"21439","article_processing_charge":"No","status":"public"},{"year":"2026","_id":"21370","intvolume":"         8","title":"Roadmap on deep learning for microscopy","month":"03","scopus_import":"1","date_published":"2026-03-01T00:00:00Z","DOAJ_listed":"1","PlanS_conform":"1","status":"public","article_type":"original","article_processing_charge":"Yes","language":[{"iso":"eng"}],"OA_type":"gold","volume":8,"oa":1,"external_id":{"arxiv":["2303.03793"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa_version":"Published Version","abstract":[{"text":"Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning (ML) are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap encompasses key aspects of how ML is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of ML for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.","lang":"eng"}],"author":[{"first_name":"Giovanni","last_name":"Volpe","full_name":"Volpe, Giovanni"},{"full_name":"Wählby, Carolina","first_name":"Carolina","last_name":"Wählby"},{"full_name":"Tian, Lei","first_name":"Lei","last_name":"Tian"},{"first_name":"Michael","last_name":"Hecht","full_name":"Hecht, Michael"},{"full_name":"Yakimovich, Artur","first_name":"Artur","last_name":"Yakimovich"},{"last_name":"Monakhova","first_name":"Kristina","full_name":"Monakhova, Kristina"},{"full_name":"Waller, Laura","first_name":"Laura","last_name":"Waller"},{"last_name":"Sbalzarini","first_name":"Ivo F.","full_name":"Sbalzarini, Ivo F."},{"first_name":"Christopher A.","last_name":"Metzler","full_name":"Metzler, Christopher A."},{"full_name":"Xie, Mingyang","last_name":"Xie","first_name":"Mingyang"},{"first_name":"Kevin","last_name":"Zhang","full_name":"Zhang, Kevin"},{"full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","last_name":"Lenton","first_name":"Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb"},{"first_name":"Halina","last_name":"Rubinsztein-Dunlop","full_name":"Rubinsztein-Dunlop, Halina"},{"full_name":"Brunner, Daniel","last_name":"Brunner","first_name":"Daniel"},{"full_name":"Bai, Bijie","first_name":"Bijie","last_name":"Bai"},{"first_name":"Aydogan","last_name":"Ozcan","full_name":"Ozcan, Aydogan"},{"full_name":"Midtvedt, Daniel","first_name":"Daniel","last_name":"Midtvedt"},{"last_name":"Wang","first_name":"Hao","full_name":"Wang, Hao"},{"full_name":"Li, Tongyu","last_name":"Li","first_name":"Tongyu"},{"first_name":"Nataša","last_name":"Sladoje","full_name":"Sladoje, Nataša"},{"full_name":"Lindblad, Joakim","last_name":"Lindblad","first_name":"Joakim"},{"full_name":"Smith, Jason T.","first_name":"Jason T.","last_name":"Smith"},{"full_name":"Ochoa, Marien","last_name":"Ochoa","first_name":"Marien"},{"full_name":"Barroso, Margarida","first_name":"Margarida","last_name":"Barroso"},{"last_name":"Intes","first_name":"Xavier","full_name":"Intes, Xavier"},{"full_name":"Qiu, Tong","last_name":"Qiu","first_name":"Tong"},{"full_name":"Yu, Li Yu","last_name":"Yu","first_name":"Li Yu"},{"first_name":"Sixian","last_name":"You","full_name":"You, Sixian"},{"last_name":"Liu","first_name":"Yongtao","full_name":"Liu, Yongtao"},{"full_name":"Ziatdinov, Maxim A.","last_name":"Ziatdinov","first_name":"Maxim A."},{"first_name":"Sergei V.","last_name":"Kalinin","full_name":"Kalinin, Sergei V."},{"full_name":"Sheridan, Arlo","first_name":"Arlo","last_name":"Sheridan"},{"last_name":"Manor","first_name":"Uri","full_name":"Manor, Uri"},{"first_name":"Elias","last_name":"Nehme","full_name":"Nehme, Elias"},{"full_name":"Goldenberg, Ofri","last_name":"Goldenberg","first_name":"Ofri"},{"full_name":"Shechtman, Yoav","first_name":"Yoav","last_name":"Shechtman"},{"full_name":"Moberg, Henrik K.","first_name":"Henrik K.","last_name":"Moberg"},{"last_name":"Langhammer","first_name":"Christoph","full_name":"Langhammer, Christoph"},{"last_name":"Špačková","first_name":"Barbora","full_name":"Špačková, Barbora"},{"last_name":"Helgadottir","first_name":"Saga","full_name":"Helgadottir, Saga"},{"full_name":"Midtvedt, Benjamin","first_name":"Benjamin","last_name":"Midtvedt"},{"last_name":"Argun","first_name":"Aykut","full_name":"Argun, Aykut"},{"full_name":"Thalheim, Tobias","first_name":"Tobias","last_name":"Thalheim"},{"full_name":"Cichos, Frank","last_name":"Cichos","first_name":"Frank"},{"last_name":"Bo","first_name":"Stefano","full_name":"Bo, Stefano"},{"first_name":"Lars","last_name":"Hubatsch","full_name":"Hubatsch, Lars"},{"full_name":"Pineda, Jesus","first_name":"Jesus","last_name":"Pineda"},{"full_name":"Manzo, Carlo","first_name":"Carlo","last_name":"Manzo"},{"full_name":"Bachimanchi, Harshith","last_name":"Bachimanchi","first_name":"Harshith"},{"full_name":"Selander, Erik","first_name":"Erik","last_name":"Selander"},{"last_name":"Homs-Corbera","first_name":"Antoni","full_name":"Homs-Corbera, Antoni"},{"first_name":"Martin","last_name":"Fränzl","full_name":"Fränzl, Martin"},{"full_name":"De Haan, Kevin","first_name":"Kevin","last_name":"De Haan"},{"full_name":"Rivenson, Yair","first_name":"Yair","last_name":"Rivenson"},{"last_name":"Korczak","first_name":"Zofia","full_name":"Korczak, Zofia"},{"full_name":"Adiels, Caroline Beck","first_name":"Caroline Beck","last_name":"Adiels"},{"last_name":"Mijalkov","first_name":"Mite","full_name":"Mijalkov, Mite"},{"first_name":"Dániel","last_name":"Veréb","full_name":"Veréb, Dániel"},{"full_name":"Chang, Yu Wei","first_name":"Yu Wei","last_name":"Chang"},{"first_name":"Joana B.","last_name":"Pereira","full_name":"Pereira, Joana B."},{"full_name":"Matuszewski, Damian","last_name":"Matuszewski","first_name":"Damian"},{"full_name":"Kylberg, Gustaf","last_name":"Kylberg","first_name":"Gustaf"},{"full_name":"Sintorn, Ida Maria","first_name":"Ida Maria","last_name":"Sintorn"},{"first_name":"Juan C.","last_name":"Caicedo","full_name":"Caicedo, Juan C."},{"full_name":"Cimini, Beth A.","first_name":"Beth A.","last_name":"Cimini"},{"first_name":"Muyinatu A.","last_name":"Lediju Bell","full_name":"Lediju Bell, Muyinatu A."},{"full_name":"Saraiva, Bruno M.","first_name":"Bruno M.","last_name":"Saraiva"},{"first_name":"Guillaume","last_name":"Jacquemet","full_name":"Jacquemet, Guillaume"},{"first_name":"Ricardo","last_name":"Henriques","full_name":"Henriques, Ricardo"},{"full_name":"Ouyang, Wei","last_name":"Ouyang","first_name":"Wei"},{"first_name":"Trang","last_name":"Le","full_name":"Le, Trang"},{"full_name":"Gómez-De-Mariscal, Estibaliz","last_name":"Gómez-De-Mariscal","first_name":"Estibaliz"},{"first_name":"Daniel","last_name":"Sage","full_name":"Sage, Daniel"},{"last_name":"Muñoz-Barrutia","first_name":"Arrate","full_name":"Muñoz-Barrutia, Arrate"},{"full_name":"Lindqvist, Ebba Josefson","first_name":"Ebba Josefson","last_name":"Lindqvist"},{"first_name":"Johanna","last_name":"Bergman","full_name":"Bergman, Johanna"}],"date_created":"2026-03-01T23:01:39Z","date_updated":"2026-03-23T13:18:11Z","publication_identifier":{"eissn":["2515-7647"]},"citation":{"ieee":"G. Volpe <i>et al.</i>, “Roadmap on deep learning for microscopy,” <i>Journal of Physics: Photonics</i>, vol. 8, no. 1. IOP Publishing, 2026.","short":"G. Volpe, C. Wählby, L. Tian, M. Hecht, A. Yakimovich, K. Monakhova, L. Waller, I.F. Sbalzarini, C.A. Metzler, M. Xie, K. Zhang, I.C. Lenton, H. Rubinsztein-Dunlop, D. Brunner, B. Bai, A. Ozcan, D. Midtvedt, H. Wang, T. Li, N. Sladoje, J. Lindblad, J.T. Smith, M. Ochoa, M. Barroso, X. Intes, T. Qiu, L.Y. Yu, S. You, Y. Liu, M.A. Ziatdinov, S.V. Kalinin, A. Sheridan, U. Manor, E. Nehme, O. Goldenberg, Y. Shechtman, H.K. Moberg, C. Langhammer, B. Špačková, S. Helgadottir, B. Midtvedt, A. Argun, T. Thalheim, F. Cichos, S. Bo, L. Hubatsch, J. Pineda, C. Manzo, H. Bachimanchi, E. Selander, A. Homs-Corbera, M. Fränzl, K. De Haan, Y. Rivenson, Z. Korczak, C.B. Adiels, M. Mijalkov, D. Veréb, Y.W. Chang, J.B. Pereira, D. Matuszewski, G. Kylberg, I.M. Sintorn, J.C. Caicedo, B.A. Cimini, M.A. Lediju Bell, B.M. Saraiva, G. Jacquemet, R. Henriques, W. Ouyang, T. Le, E. Gómez-De-Mariscal, D. Sage, A. Muñoz-Barrutia, E.J. Lindqvist, J. Bergman, Journal of Physics: Photonics 8 (2026).","ama":"Volpe G, Wählby C, Tian L, et al. Roadmap on deep learning for microscopy. <i>Journal of Physics: Photonics</i>. 2026;8(1). doi:<a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">10.1088/2515-7647/ae0fd1</a>","apa":"Volpe, G., Wählby, C., Tian, L., Hecht, M., Yakimovich, A., Monakhova, K., … Bergman, J. (2026). Roadmap on deep learning for microscopy. <i>Journal of Physics: Photonics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">https://doi.org/10.1088/2515-7647/ae0fd1</a>","ista":"Volpe G, Wählby C, Tian L, Hecht M, Yakimovich A, Monakhova K, Waller L, Sbalzarini IF, Metzler CA, Xie M, Zhang K, Lenton IC, Rubinsztein-Dunlop H, Brunner D, Bai B, Ozcan A, Midtvedt D, Wang H, Li T, Sladoje N, Lindblad J, Smith JT, Ochoa M, Barroso M, Intes X, Qiu T, Yu LY, You S, Liu Y, Ziatdinov MA, Kalinin SV, Sheridan A, Manor U, Nehme E, Goldenberg O, Shechtman Y, Moberg HK, Langhammer C, Špačková B, Helgadottir S, Midtvedt B, Argun A, Thalheim T, Cichos F, Bo S, Hubatsch L, Pineda J, Manzo C, Bachimanchi H, Selander E, Homs-Corbera A, Fränzl M, De Haan K, Rivenson Y, Korczak Z, Adiels CB, Mijalkov M, Veréb D, Chang YW, Pereira JB, Matuszewski D, Kylberg G, Sintorn IM, Caicedo JC, Cimini BA, Lediju Bell MA, Saraiva BM, Jacquemet G, Henriques R, Ouyang W, Le T, Gómez-De-Mariscal E, Sage D, Muñoz-Barrutia A, Lindqvist EJ, Bergman J. 2026. Roadmap on deep learning for microscopy. Journal of Physics: Photonics. 8(1), 012501.","chicago":"Volpe, Giovanni, Carolina Wählby, Lei Tian, Michael Hecht, Artur Yakimovich, Kristina Monakhova, Laura Waller, et al. “Roadmap on Deep Learning for Microscopy.” <i>Journal of Physics: Photonics</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">https://doi.org/10.1088/2515-7647/ae0fd1</a>.","mla":"Volpe, Giovanni, et al. “Roadmap on Deep Learning for Microscopy.” <i>Journal of Physics: Photonics</i>, vol. 8, no. 1, 012501, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.1088/2515-7647/ae0fd1\">10.1088/2515-7647/ae0fd1</a>."},"day":"01","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"1","doi":"10.1088/2515-7647/ae0fd1","article_number":"012501","file_date_updated":"2026-03-02T09:05:53Z","has_accepted_license":"1","OA_place":"publisher","publisher":"IOP Publishing","publication":"Journal of Physics: Photonics","ddc":["530"],"quality_controlled":"1","type":"journal_article","publication_status":"published","file":[{"creator":"dernst","access_level":"open_access","checksum":"172720f1f0c5c9d06a282e52023a0030","file_name":"2026_JPhysPhotonics_Volpe.pdf","date_updated":"2026-03-02T09:05:53Z","date_created":"2026-03-02T09:05:53Z","relation":"main_file","content_type":"application/pdf","file_size":16789781,"file_id":"21375","success":1}],"department":[{"_id":"ScWa"}]},{"file_date_updated":"2026-03-23T13:24:01Z","day":"10","citation":{"short":"M. Bahl, G. Koutentakis, M. Maslov, T. Jungnickel, T. Gaßen, M. Lemeshko, O.H. Heckl, Journal of Physics: Photonics 8 (2026).","ieee":"M. Bahl <i>et al.</i>, “The R-index: A universal metric for evaluating OAM content and mode purity in optical fields,” <i>Journal of Physics: Photonics</i>, vol. 8, no. 1. IOP Publishing, 2026.","chicago":"Bahl, Monika, Georgios Koutentakis, Mikhail Maslov, Tom Jungnickel, Timo Gaßen, Mikhail Lemeshko, and Oliver H. Heckl. “The R-Index: A Universal Metric for Evaluating OAM Content and Mode Purity in Optical Fields.” <i>Journal of Physics: Photonics</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.1088/2515-7647/ae3506\">https://doi.org/10.1088/2515-7647/ae3506</a>.","ista":"Bahl M, Koutentakis G, Maslov M, Jungnickel T, Gaßen T, Lemeshko M, Heckl OH. 2026. The R-index: A universal metric for evaluating OAM content and mode purity in optical fields. Journal of Physics: Photonics. 8(1), 015071.","ama":"Bahl M, Koutentakis G, Maslov M, et al. The R-index: A universal metric for evaluating OAM content and mode purity in optical fields. <i>Journal of Physics: Photonics</i>. 2026;8(1). doi:<a href=\"https://doi.org/10.1088/2515-7647/ae3506\">10.1088/2515-7647/ae3506</a>","apa":"Bahl, M., Koutentakis, G., Maslov, M., Jungnickel, T., Gaßen, T., Lemeshko, M., &#38; Heckl, O. H. (2026). The R-index: A universal metric for evaluating OAM content and mode purity in optical fields. <i>Journal of Physics: Photonics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2515-7647/ae3506\">https://doi.org/10.1088/2515-7647/ae3506</a>","mla":"Bahl, Monika, et al. “The R-Index: A Universal Metric for Evaluating OAM Content and Mode Purity in Optical Fields.” <i>Journal of Physics: Photonics</i>, vol. 8, no. 1, 015071, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.1088/2515-7647/ae3506\">10.1088/2515-7647/ae3506</a>."},"doi":"10.1088/2515-7647/ae3506","issue":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/F1004]. For open access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission.","article_number":"015071","quality_controlled":"1","publication_status":"published","type":"journal_article","file":[{"file_size":1150404,"content_type":"application/pdf","file_id":"21476","success":1,"date_updated":"2026-03-23T13:24:01Z","file_name":"2026_JPhysPhotonics_Bahl.pdf","creator":"dernst","checksum":"0ec8a2d3f9efa704203a41f068344974","access_level":"open_access","relation":"main_file","date_created":"2026-03-23T13:24:01Z"}],"corr_author":"1","department":[{"_id":"MiLe"}],"OA_place":"publisher","has_accepted_license":"1","publisher":"IOP Publishing","ddc":["530"],"publication":"Journal of Physics: Photonics","status":"public","article_processing_charge":"Yes (in subscription journal)","article_type":"original","language":[{"iso":"eng"}],"year":"2026","_id":"21470","intvolume":"         8","scopus_import":"1","month":"03","title":"The R-index: A universal metric for evaluating OAM content and mode purity in optical fields","date_published":"2026-03-10T00:00:00Z","date_created":"2026-03-22T23:04:32Z","author":[{"last_name":"Bahl","first_name":"Monika","full_name":"Bahl, Monika"},{"full_name":"Koutentakis, Georgios","last_name":"Koutentakis","first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95"},{"first_name":"Mikhail","last_name":"Maslov","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail"},{"last_name":"Jungnickel","first_name":"Tom","full_name":"Jungnickel, Tom"},{"first_name":"Timo","last_name":"Gaßen","full_name":"Gaßen, Timo"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oliver H.","last_name":"Heckl","full_name":"Heckl, Oliver H."}],"project":[{"grant_number":"F100403","name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3"}],"date_updated":"2026-03-23T13:26:26Z","publication_identifier":{"eissn":["2515-7647"]},"oa":1,"OA_type":"hybrid","volume":8,"external_id":{"arxiv":["2508.12973"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","arxiv":1,"abstract":[{"lang":"eng","text":"Despite its pivotal role in optical manipulation, high capacity communications, and quantum information, a general measure of orbital angular momentum (OAM) in structured light remains elusive. In optical fields, where multiple vortices coexist, the local nature of vortex OAM and the absence of a common rotation axis make the total OAM of the field difficult to quantify. Here, we introduce the R index—a metric that captures the intrinsic OAM content of any structured optical field, from pure Laguerre–Gaussian modes to arbitrary multi vortex superpositions. Not only does this metric quantify the total OAM, it also assesses field purity, providing insight into the fidelity and robustness of the OAM generation. By unifying OAM characterization into a single figure of merit, the R index enables direct comparison across diverse beam profiles and facilitates the identification of optimal configurations for both foundational studies and applied technologies."}]},{"month":"03","scopus_import":"1","title":"Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response","date_published":"2026-03-13T00:00:00Z","year":"2026","_id":"21469","intvolume":"       136","article_processing_charge":"Yes (via OA deal)","article_type":"original","language":[{"iso":"eng"}],"status":"public","PlanS_conform":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Terahertz (THz) spectroscopy is a powerful probe of low-energy excitations in complex materials. Extending it into the nonlinear regime broadens its scope and can provide valuable insight into interactions among these modes. However, interpreting nonlinear spectra is challenging because resonant features in this case do not always reflect intrinsic material dynamics. Here, we study nonlinear THz-induced Kerr effect in a generic material LaAlO3. After detailed analysis of temporal oscillations of the Kerr signal, we identify an 𝐸𝑔 Raman mode at 1.1 THz excited through a two-photon process, while two additional peaks (0.86 and 0.36 THz) arise from phase matching of the near-infrared probe beam with co- and counterpropagating THz pump fields, mediated by off-resonant electronic hyperpolarizability. These results demonstrate the crucial role of kinematic effects in shaping THz-induced Kerr response and establish a framework for interpreting nonlinear spectroscopies in complex materials."}],"volume":136,"oa":1,"OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-03-23T13:11:09Z","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"date_created":"2026-03-22T23:04:31Z","author":[{"id":"f84c083e-dc8d-11ea-abe3-aaf3d822a8bb","first_name":"Chao","last_name":"Shen","full_name":"Shen, Chao"},{"full_name":"Frenzel, Maximilian","first_name":"Maximilian","last_name":"Frenzel"},{"full_name":"Maehrlein, Sebastian F.","last_name":"Maehrlein","first_name":"Sebastian F."},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek"}],"project":[{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Nonlinear THz spectroscopy of quantum critical materials","grant_number":"F8602","_id":"34a97cc6-11ca-11ed-8bc3-9acbba792f33"}],"doi":"10.1103/1c5k-9z82","issue":"10","acknowledgement":"Z. A. acknowledges support from the collaborative research project SFB Q-M&S funded by the Austrian Science Fund (FWF, Grant No. PR1050F8602). S. F. M. acknowledges support and funding from the Deutsche Forschungsgemeinschaft (DFG, Grant No. 469405347).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"106901","day":"13","citation":{"mla":"Shen, Chao, et al. “Disentangling Electronic and Ionic Nonlinear Polarization Effects in Bulk THz Kerr Response.” <i>Physical Review Letters</i>, vol. 136, no. 10, 106901, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/1c5k-9z82\">10.1103/1c5k-9z82</a>.","apa":"Shen, C., Frenzel, M., Maehrlein, S. F., &#38; Alpichshev, Z. (2026). Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/1c5k-9z82\">https://doi.org/10.1103/1c5k-9z82</a>","ama":"Shen C, Frenzel M, Maehrlein SF, Alpichshev Z. Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response. <i>Physical Review Letters</i>. 2026;136(10). doi:<a href=\"https://doi.org/10.1103/1c5k-9z82\">10.1103/1c5k-9z82</a>","chicago":"Shen, Chao, Maximilian Frenzel, Sebastian F. Maehrlein, and Zhanybek Alpichshev. “Disentangling Electronic and Ionic Nonlinear Polarization Effects in Bulk THz Kerr Response.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/1c5k-9z82\">https://doi.org/10.1103/1c5k-9z82</a>.","ista":"Shen C, Frenzel M, Maehrlein SF, Alpichshev Z. 2026. Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response. Physical Review Letters. 136(10), 106901.","ieee":"C. Shen, M. Frenzel, S. F. Maehrlein, and Z. Alpichshev, “Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response,” <i>Physical Review Letters</i>, vol. 136, no. 10. American Physical Society, 2026.","short":"C. Shen, M. Frenzel, S.F. Maehrlein, Z. Alpichshev, Physical Review Letters 136 (2026)."},"file_date_updated":"2026-03-23T13:08:06Z","publication":"Physical Review Letters","ddc":["530"],"has_accepted_license":"1","OA_place":"publisher","publisher":"American Physical Society","file":[{"file_id":"21475","success":1,"content_type":"application/pdf","file_size":1375532,"relation":"main_file","date_created":"2026-03-23T13:08:06Z","file_name":"2026_PhysicalReviewLetters_Shen.pdf","date_updated":"2026-03-23T13:08:06Z","creator":"dernst","access_level":"open_access","checksum":"712b05b4b0e0fbe9fd426a8c9d41ce20"}],"corr_author":"1","department":[{"_id":"ZhAl"},{"_id":"GradSch"}],"quality_controlled":"1","publication_status":"published","type":"journal_article"},{"author":[{"last_name":"Giacomelli","first_name":"Emanuela L.","full_name":"Giacomelli, Emanuela L."},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"first_name":"Phan Thành","last_name":"Nam","full_name":"Nam, Phan Thành"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"}],"date_created":"2026-03-22T23:04:33Z","date_updated":"2026-03-23T13:32:14Z","publication_identifier":{"issn":["0010-3640"],"eissn":["1097-0312"]},"oa":1,"OA_type":"hybrid","external_id":{"arxiv":["2409.17914"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa_version":"Published Version","abstract":[{"text":"We study the ground state energy of a gas of spin 1/2 fermions with repulsive short-range interactions. We derive an upper bound that agrees, at low density e, with the Huang–Yang conjecture. The latter captures the first three terms in an asymptotic low-density expansion, and in particular the Huang–Yang correction term of order e^7/3. Our trial state is constructed using an adaptation of the bosonic Bogoliubov theory to the Fermi system, where the correlation structure of fermionic particles is incorporated by quasi-bosonic Bogoliubov transformations. In the latter, it is important to consider a modified zero-energy scattering equation that takes into account the presence of the Fermi sea, in the spirit of the Bethe–Goldstone equation.","lang":"eng"}],"status":"public","article_type":"original","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"_id":"21472","year":"2026","title":"The Huang–Yang formula for the low-density Fermi gas: Upper bound","scopus_import":"1","month":"03","date_published":"2026-03-13T00:00:00Z","quality_controlled":"1","type":"journal_article","publication_status":"epub_ahead","department":[{"_id":"RoSe"}],"OA_place":"publisher","publisher":"Wiley","publication":"Communications on Pure and Applied Mathematics","citation":{"short":"E.L. Giacomelli, C. Hainzl, P.T. Nam, R. Seiringer, Communications on Pure and Applied Mathematics (2026).","ieee":"E. L. Giacomelli, C. Hainzl, P. T. Nam, and R. Seiringer, “The Huang–Yang formula for the low-density Fermi gas: Upper bound,” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2026.","mla":"Giacomelli, Emanuela L., et al. “The Huang–Yang Formula for the Low-Density Fermi Gas: Upper Bound.” <i>Communications on Pure and Applied Mathematics</i>, Wiley, 2026, doi:<a href=\"https://doi.org/10.1002/cpa.70040\">10.1002/cpa.70040</a>.","ista":"Giacomelli EL, Hainzl C, Nam PT, Seiringer R. 2026. The Huang–Yang formula for the low-density Fermi gas: Upper bound. Communications on Pure and Applied Mathematics.","chicago":"Giacomelli, Emanuela L., Christian Hainzl, Phan Thành Nam, and Robert Seiringer. “The Huang–Yang Formula for the Low-Density Fermi Gas: Upper Bound.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2026. <a href=\"https://doi.org/10.1002/cpa.70040\">https://doi.org/10.1002/cpa.70040</a>.","apa":"Giacomelli, E. L., Hainzl, C., Nam, P. T., &#38; Seiringer, R. (2026). The Huang–Yang formula for the low-density Fermi gas: Upper bound. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.70040\">https://doi.org/10.1002/cpa.70040</a>","ama":"Giacomelli EL, Hainzl C, Nam PT, Seiringer R. The Huang–Yang formula for the low-density Fermi gas: Upper bound. <i>Communications on Pure and Applied Mathematics</i>. 2026. doi:<a href=\"https://doi.org/10.1002/cpa.70040\">10.1002/cpa.70040</a>"},"main_file_link":[{"url":"https://doi.org/10.1002/cpa.70040","open_access":"1"}],"day":"13","acknowledgement":"We thank the referees for valuable remarks. This work was partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via the TRR 352 – Project-ID 470903074. PTN was partially supported by the European Research Council via the ERC Consolidator Grant RAMBAS – Project-Nr. 10104424.\r\nOpen access publishing facilitated by Università degli Studi di Milano, as part of the Wiley - CRUI-CARE agreement.","doi":"10.1002/cpa.70040"},{"date_published":"2026-03-09T00:00:00Z","title":"Exercise enhances hippocampal-cortical ripple interactions in the human brain","month":"03","scopus_import":"1","intvolume":"         8","year":"2026","_id":"21473","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes","DOAJ_listed":"1","PlanS_conform":"1","status":"public","abstract":[{"lang":"eng","text":"Physical exercise acutely improves hippocampus-dependent memory. Whereas animal studies have offered cellular- and synaptic-level accounts of these effects, human neuroimaging studies show that exercise improves hippocampal-cortical connectivity at the macroscale level. However, the neurophysiological basis of exercise-induced effects on hippocampal-cortical circuits remains unknown. Experimental evidence supports the idea that hippocampal sharp wave-ripples (SWR) play a critical role in learning and memory. Coupling between SWRs in the hippocampus and neocortex may reflect modulations in inter-regional connectivity required by mnemonic processes. Here, we examine the hypothesis that exercise modulates hippocampal-cortical ripple dynamics in the human brain. We performed intracranial recordings in epilepsy patients undergoing pre-surgical evaluation, during awake resting state, before and after an exercise session. Exercise increased ripple rate in the hippocampus. Exercise also enhanced the coupling and phase-synchrony between cortical ripples in the limbic and the default mode (DM) cortical networks and hippocampal SWRs. Further, a higher heart rate during exercise, reflecting exercise intensity, was related to a subsequent increase in resting state ripples across specific cortical networks, including the DM network. These results offer the first direct evidence that a single exercise session elicits changes in ripple events, a well-established neurophysiological marker of mnemonic processing. The characterisation and anatomical distribution of the described modulation points to hippocampal ripples as a potential mechanism by which exercise elicits its reported short-term effects in cognition."}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8,"OA_type":"gold","oa":1,"publication_identifier":{"eissn":["2632-1297"]},"date_updated":"2026-03-23T14:30:47Z","author":[{"last_name":"Cardenas","first_name":"Araceli R.","full_name":"Cardenas, Araceli R."},{"full_name":"Ramirez Villegas, Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F","last_name":"Ramirez Villegas"},{"first_name":"Christopher K.","last_name":"Kovach","full_name":"Kovach, Christopher K."},{"first_name":"Phillip E.","last_name":"Gander","full_name":"Gander, Phillip E."},{"last_name":"Cole","first_name":"Rachel C.","full_name":"Cole, Rachel C."},{"full_name":"Grossbach, Andrew J.","last_name":"Grossbach","first_name":"Andrew J."},{"first_name":"Hiroto","last_name":"Kawasaki","full_name":"Kawasaki, Hiroto"},{"full_name":"Greenlee, Jeremy D.W.","first_name":"Jeremy D.W.","last_name":"Greenlee"},{"full_name":"Howard, Matthew A.","last_name":"Howard","first_name":"Matthew A."},{"full_name":"Nourski, Kirill V.","last_name":"Nourski","first_name":"Kirill V."},{"first_name":"Matthew I.","last_name":"Banks","full_name":"Banks, Matthew I."},{"full_name":"Voss, Michelle W.","last_name":"Voss","first_name":"Michelle W."}],"date_created":"2026-03-22T23:04:34Z","article_number":"fcag041","acknowledgement":"We acknowledge the generosity of the patients, who contributed time and effort to take part in this study.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"2","doi":"10.1093/braincomms/fcag041","citation":{"short":"A.R. Cardenas, J.F. Ramirez Villegas, C.K. Kovach, P.E. Gander, R.C. Cole, A.J. Grossbach, H. Kawasaki, J.D.W. Greenlee, M.A. Howard, K.V. Nourski, M.I. Banks, M.W. Voss, Brain Communications 8 (2026).","ieee":"A. R. Cardenas <i>et al.</i>, “Exercise enhances hippocampal-cortical ripple interactions in the human brain,” <i>Brain Communications</i>, vol. 8, no. 2. Oxford University Press, 2026.","mla":"Cardenas, Araceli R., et al. “Exercise Enhances Hippocampal-Cortical Ripple Interactions in the Human Brain.” <i>Brain Communications</i>, vol. 8, no. 2, fcag041, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/braincomms/fcag041\">10.1093/braincomms/fcag041</a>.","chicago":"Cardenas, Araceli R., Juan F Ramirez Villegas, Christopher K. Kovach, Phillip E. Gander, Rachel C. Cole, Andrew J. Grossbach, Hiroto Kawasaki, et al. “Exercise Enhances Hippocampal-Cortical Ripple Interactions in the Human Brain.” <i>Brain Communications</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/braincomms/fcag041\">https://doi.org/10.1093/braincomms/fcag041</a>.","ista":"Cardenas AR, Ramirez Villegas JF, Kovach CK, Gander PE, Cole RC, Grossbach AJ, Kawasaki H, Greenlee JDW, Howard MA, Nourski KV, Banks MI, Voss MW. 2026. Exercise enhances hippocampal-cortical ripple interactions in the human brain. Brain Communications. 8(2), fcag041.","ama":"Cardenas AR, Ramirez Villegas JF, Kovach CK, et al. Exercise enhances hippocampal-cortical ripple interactions in the human brain. <i>Brain Communications</i>. 2026;8(2). doi:<a href=\"https://doi.org/10.1093/braincomms/fcag041\">10.1093/braincomms/fcag041</a>","apa":"Cardenas, A. R., Ramirez Villegas, J. F., Kovach, C. K., Gander, P. E., Cole, R. C., Grossbach, A. J., … Voss, M. W. (2026). Exercise enhances hippocampal-cortical ripple interactions in the human brain. <i>Brain Communications</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/braincomms/fcag041\">https://doi.org/10.1093/braincomms/fcag041</a>"},"day":"09","file_date_updated":"2026-03-23T14:27:39Z","publication":"Brain Communications","ddc":["570"],"publisher":"Oxford University Press","has_accepted_license":"1","OA_place":"publisher","department":[{"_id":"JoCs"}],"file":[{"file_size":33974419,"content_type":"application/pdf","file_id":"21478","success":1,"checksum":"b5b45c16defeaf88056fc3b939bd0350","creator":"dernst","access_level":"open_access","file_name":"2026_BrainCommunications_Cardenas.pdf","date_updated":"2026-03-23T14:27:39Z","date_created":"2026-03-23T14:27:39Z","relation":"main_file"}],"corr_author":"1","type":"journal_article","publication_status":"published","quality_controlled":"1"},{"file":[{"content_type":"application/pdf","file_size":495080,"success":1,"file_id":"21477","creator":"dernst","access_level":"open_access","checksum":"6116108a12c4a5cc91fc653d67885309","date_updated":"2026-03-23T14:01:44Z","file_name":"2026_AmericanJourBotany_Backlund.pdf","date_created":"2026-03-23T14:01:44Z","relation":"main_file"}],"corr_author":"1","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","ddc":["580","570"],"publication":"American Journal of Botany","has_accepted_license":"1","OA_place":"publisher","publisher":"Wiley","file_date_updated":"2026-03-23T14:01:44Z","acknowledgement":"We thank the Barton group at the Institute of Scienceand Technology Austria for many fruitful conversationsthat triggered the germination of the ideas and questions discussed here. N. H. Barton, P. Surendranadh, A. Pal,Z. Mérai, and two anonymous reviewers provided useful comments on the manuscript.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"3","doi":"10.1002/ajb2.70175","article_number":"e70175","citation":{"mla":"Backlund, Sofia Maria, et al. “Seeds as Space-Time Travelers: How Does Evolution Balance the Joint Benefits and Trade-Offs of Dormancy and Dispersal?” <i>American Journal of Botany</i>, vol. 113, no. 3, e70175, Wiley, 2026, doi:<a href=\"https://doi.org/10.1002/ajb2.70175\">10.1002/ajb2.70175</a>.","ista":"Backlund SM, Stankowski S, Soler Schaller RM. 2026. Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal? American Journal of Botany. 113(3), e70175.","chicago":"Backlund, Sofia Maria, Sean Stankowski, and Rosina Matilde Soler Schaller. “Seeds as Space-Time Travelers: How Does Evolution Balance the Joint Benefits and Trade-Offs of Dormancy and Dispersal?” <i>American Journal of Botany</i>. Wiley, 2026. <a href=\"https://doi.org/10.1002/ajb2.70175\">https://doi.org/10.1002/ajb2.70175</a>.","ama":"Backlund SM, Stankowski S, Soler Schaller RM. Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal? <i>American Journal of Botany</i>. 2026;113(3). doi:<a href=\"https://doi.org/10.1002/ajb2.70175\">10.1002/ajb2.70175</a>","apa":"Backlund, S. M., Stankowski, S., &#38; Soler Schaller, R. M. (2026). Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal? <i>American Journal of Botany</i>. Wiley. <a href=\"https://doi.org/10.1002/ajb2.70175\">https://doi.org/10.1002/ajb2.70175</a>","short":"S.M. Backlund, S. Stankowski, R.M. Soler Schaller, American Journal of Botany 113 (2026).","ieee":"S. M. Backlund, S. Stankowski, and R. M. Soler Schaller, “Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal?,” <i>American Journal of Botany</i>, vol. 113, no. 3. Wiley, 2026."},"day":"11","date_updated":"2026-03-23T14:47:52Z","publication_identifier":{"eissn":["1537-2197"],"issn":["0002-9122"]},"author":[{"full_name":"Backlund, Sofia Maria","first_name":"Sofia Maria","last_name":"Backlund","id":"a19ed178-1337-11ed-9389-c30ab879a82a"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Soler Schaller, Rosina Matilde","first_name":"Rosina Matilde","last_name":"Soler Schaller","id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803"}],"date_created":"2026-03-22T23:04:33Z","oa_version":"Published Version","volume":113,"oa":1,"OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["41814642"]},"article_type":"letter_note","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal?","scopus_import":"1","month":"03","date_published":"2026-03-11T00:00:00Z","_id":"21471","year":"2026","intvolume":"       113"},{"article_number":"A184","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank the anonymous referee for the insightful comments that helped improve the manuscript. We also thank Thibault Garel, Pascal Oesch, Irene Shivaei, Charlotte Simmonds, Andrew Hopkins, Daniel Schaerer, and Rashmi Gottumukkala for useful comments and productive discussions. We gratefully acknowledge support from the CBPsmn (PSMN, Pôle Scientifique de Modélisation Numérique) of the ENS de Lyon for the computing resources.\r\nFunded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. This work made extensive use of several open-source software packages, and we gratefully acknowledge the efforts of their authors: numpy (Harris et al. 2020), astropy (Astropy Collaboration 2022), matplotlib (Hunter 2007), ipython (Perez & Granger 2007), and scikit-learn (Pedregosa et al. 2011).","doi":"10.1051/0004-6361/202557114","citation":{"short":"I. Kramarenko, J. Rosdahl, J. Blaizot, J.J. Matthee, H. Katz, C. Di Cesare, Astronomy &#38; Astrophysics 707 (2026).","ieee":"I. Kramarenko, J. Rosdahl, J. Blaizot, J. J. Matthee, H. Katz, and C. Di Cesare, “H α as a tracer of star formation in the SPHINX cosmological simulations,” <i>Astronomy &#38; Astrophysics</i>, vol. 707. EDP Sciences, 2026.","mla":"Kramarenko, Ivan, et al. “H α as a Tracer of Star Formation in the SPHINX Cosmological Simulations.” <i>Astronomy &#38; Astrophysics</i>, vol. 707, A184, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202557114\">10.1051/0004-6361/202557114</a>.","chicago":"Kramarenko, Ivan, J. Rosdahl, J. Blaizot, Jorryt J Matthee, H. Katz, and Claudia Di Cesare. “H α as a Tracer of Star Formation in the SPHINX Cosmological Simulations.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202557114\">https://doi.org/10.1051/0004-6361/202557114</a>.","ista":"Kramarenko I, Rosdahl J, Blaizot J, Matthee JJ, Katz H, Di Cesare C. 2026. H α as a tracer of star formation in the SPHINX cosmological simulations. Astronomy &#38; Astrophysics. 707, A184.","apa":"Kramarenko, I., Rosdahl, J., Blaizot, J., Matthee, J. J., Katz, H., &#38; Di Cesare, C. (2026). H α as a tracer of star formation in the SPHINX cosmological simulations. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202557114\">https://doi.org/10.1051/0004-6361/202557114</a>","ama":"Kramarenko I, Rosdahl J, Blaizot J, Matthee JJ, Katz H, Di Cesare C. H α as a tracer of star formation in the SPHINX cosmological simulations. <i>Astronomy &#38; Astrophysics</i>. 2026;707. doi:<a href=\"https://doi.org/10.1051/0004-6361/202557114\">10.1051/0004-6361/202557114</a>"},"day":"05","file_date_updated":"2026-03-23T15:44:09Z","publication":"Astronomy & Astrophysics","ddc":["520"],"publisher":"EDP Sciences","OA_place":"publisher","has_accepted_license":"1","department":[{"_id":"JoMa"}],"corr_author":"1","file":[{"date_created":"2026-03-23T15:44:09Z","relation":"main_file","access_level":"open_access","checksum":"7429076b381dd498084f40ffd199e714","creator":"dernst","date_updated":"2026-03-23T15:44:09Z","file_name":"2026_AstronomyAstrophysics_Kramarenko.pdf","success":1,"file_id":"21492","content_type":"application/pdf","file_size":904565}],"type":"journal_article","publication_status":"published","quality_controlled":"1","date_published":"2026-03-05T00:00:00Z","title":"H α as a tracer of star formation in the SPHINX cosmological simulations","month":"03","intvolume":"       707","_id":"21481","year":"2026","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","DOAJ_listed":"1","PlanS_conform":"1","status":"public","abstract":[{"lang":"eng","text":"The Hα emission line in galaxies is a powerful tracer of their recent star formation activity. With the advent of JWST, we are now able to routinely observe Hα in galaxies at high redshift (z ≳ 3) and thus measure their star formation rates (SFRs). However, using classical SFR(Hα) calibrations to derive the SFRs leads to biased results because high-redshift galaxies are commonly characterized by low metallicities and bursty star formation histories, affecting the conversion factor between the Hα luminosity (LHα) and the SFR. We developed a set of new SFR(Hα) calibrations that allowed us to predict the SFRs of Hα-emitters at z ≳ 3 with very little error. We used the SPHINX cosmological simulations to select a sample of star-forming galaxies representative of the Hα-emitter population observed with JWST. We then derived linear corrections to the classical SFR(Hα) calibrations that took variations in the physical properties (e.g., stellar metallicities) among individual galaxies into account. We obtained two new SFR(Hα) calibrations that compared to the classical calibrations reduce the root mean squared error (RMSE) in the predicted SFRs by ΔRMSE ≈ 0.04 dex and ΔRMSE ≈ 0.06 dex, respectively. Using the recent JWST NIRCam/grism observations of Hα-emitters at z ∼ 6, we show that the new calibrations affect the high-redshift galaxy population statistics: (i) the estimated cosmic SFR density decreases by ΔρSFR ≈ 12%, and (ii) the observed slope of the star formation main sequence increases by Δ∂logSFR/∂logM★ = 0.08 ± 0.02."}],"oa_version":"Published Version","arxiv":1,"external_id":{"arxiv":["2509.05403"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":707,"oa":1,"OA_type":"diamond","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"date_updated":"2026-03-23T15:46:31Z","project":[{"name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224","_id":"bd9b2118-d553-11ed-ba76-db24564edfea"}],"author":[{"id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4","first_name":"Ivan","last_name":"Kramarenko","orcid":"0000-0001-5346-6048","full_name":"Kramarenko, Ivan"},{"full_name":"Rosdahl, J.","last_name":"Rosdahl","first_name":"J."},{"last_name":"Blaizot","first_name":"J.","full_name":"Blaizot, J."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X"},{"last_name":"Katz","first_name":"H.","full_name":"Katz, H."},{"full_name":"Di Cesare, Claudia","id":"2d002343-372f-11ef-98ec-a164d20427cb","first_name":"Claudia","last_name":"Di Cesare"}],"date_created":"2026-03-23T14:58:03Z"},{"file_date_updated":"2026-03-23T15:35:27Z","article_number":"090801","doi":"10.1103/rbg2-f61m","issue":"9","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We acknowledge insightful discussions with Antoine Browaeys, Mari Carmen Bañuls, Soonwon Choi, Thierry Lahaye, Daniel Stilck-França, Georgios Styliaris, and Xavier Waintal. The experimental data have been collected using the Qiskit library [103], and have been postprocessed using the RandomMeas [104] and ITensor [105] libraries. The work of M. V. and B. V. was funded by the French National Research Agency via the JCJC project QRand (No. ANR-20-CE47-0005), and via the research programs Plan France 2030 EPIQ (No. ANR-22-\r\nPETQ-0007), QUBITAF (No. ANR-22-PETQ-0004), and HQI (No. ANR-22-PNCQ-0002). We acknowledge the use of IBM Quantum Credits for this work. M. L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868. The work of C. L. was funded by the French National Research Agency via the PRC project ESQuisses (No. ANR-20-CE47-0014-01). J. I. C.\r\nacknowledges funding from the Federal Ministry of Education and Research Germany (BMBF) via the project FermiQP (No. 13N15889). Work at MPQ is part of the Munich Quantum Valley, which is supported by the Bavarian state government with funds from the Hightech Agenda\r\nBayern Plus. P. Z. acknowledges support by the European Union’s Horizon Europe research and innovation program under Grant Agreement No. 101113690 (PASQANS2). The work of L. P. was funded by the European Union (ERC, QUANTHEM, No. 101114881). We acknowledge support\r\nby the Erwin Schrödinger International Institute for Mathematics and Physics (ESI).","day":"04","citation":{"mla":"Votto, Matteo, et al. “Learning Mixed Quantum States in Large-Scale Experiments.” <i>Physical Review Letters</i>, vol. 136, no. 9, 090801, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/rbg2-f61m\">10.1103/rbg2-f61m</a>.","apa":"Votto, M., Ljubotina, M., Lancien, C., Cirac, J. I., Zoller, P., Serbyn, M., … Vermersch, B. (2026). Learning mixed quantum states in large-scale experiments. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/rbg2-f61m\">https://doi.org/10.1103/rbg2-f61m</a>","ama":"Votto M, Ljubotina M, Lancien C, et al. Learning mixed quantum states in large-scale experiments. <i>Physical Review Letters</i>. 2026;136(9). doi:<a href=\"https://doi.org/10.1103/rbg2-f61m\">10.1103/rbg2-f61m</a>","ista":"Votto M, Ljubotina M, Lancien C, Cirac JI, Zoller P, Serbyn M, Piroli L, Vermersch B. 2026. Learning mixed quantum states in large-scale experiments. Physical Review Letters. 136(9), 090801.","chicago":"Votto, Matteo, Marko Ljubotina, Cécilia Lancien, J. Ignacio Cirac, Peter Zoller, Maksym Serbyn, Lorenzo Piroli, and Benoît Vermersch. “Learning Mixed Quantum States in Large-Scale Experiments.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/rbg2-f61m\">https://doi.org/10.1103/rbg2-f61m</a>.","ieee":"M. Votto <i>et al.</i>, “Learning mixed quantum states in large-scale experiments,” <i>Physical Review Letters</i>, vol. 136, no. 9. American Physical Society, 2026.","short":"M. Votto, M. Ljubotina, C. Lancien, J.I. Cirac, P. Zoller, M. Serbyn, L. Piroli, B. Vermersch, Physical Review Letters 136 (2026)."},"department":[{"_id":"MaSe"}],"file":[{"content_type":"application/pdf","file_size":500041,"file_id":"21491","success":1,"creator":"dernst","access_level":"open_access","checksum":"12b16ce2d49c62b2909da95121bfaadb","file_name":"2026_PhysicalReviewLetters_Votto.pdf","date_updated":"2026-03-23T15:35:27Z","date_created":"2026-03-23T15:35:27Z","relation":"main_file"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","publication":"Physical Review Letters","ddc":["530"],"publisher":"American Physical Society","OA_place":"publisher","has_accepted_license":"1","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","status":"public","PlanS_conform":"1","date_published":"2026-03-04T00:00:00Z","month":"03","title":"Learning mixed quantum states in large-scale experiments","intvolume":"       136","year":"2026","_id":"21480","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_updated":"2026-03-23T15:39:34Z","date_created":"2026-03-23T14:56:32Z","author":[{"full_name":"Votto, Matteo","last_name":"Votto","first_name":"Matteo"},{"orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","first_name":"Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"full_name":"Lancien, Cécilia","last_name":"Lancien","first_name":"Cécilia"},{"full_name":"Cirac, J. Ignacio","first_name":"J. Ignacio","last_name":"Cirac"},{"first_name":"Peter","last_name":"Zoller","full_name":"Zoller, Peter"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Lorenzo","last_name":"Piroli","full_name":"Piroli, Lorenzo"},{"full_name":"Vermersch, Benoît","first_name":"Benoît","last_name":"Vermersch"}],"abstract":[{"text":"We present and test a protocol to learn the matrix-product operator (MPO) representation of an experimentally prepared quantum state. The protocol takes as input classical shadows corresponding to local randomized measurements, and outputs the tensors of an MPO maximizing a suitably defined fidelity with the experimental state. The tensor optimization is carried out sequentially, similarly to the well-known density matrix renormalization group algorithm. Our approach is provably efficient under certain technical conditions expected to be met in short-range correlated states and in typical noisy experimental settings. Under the same conditions, we also provide an efficient scheme to estimate fidelities between the learned and the experimental states. We experimentally demonstrate our protocol by learning entangled quantum states of up to N = 96 qubits in a superconducting quantum processor. Our method upgrades classical shadows to large-scale quantum computation and simulation experiments.","lang":"eng"}],"arxiv":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2507.12550"]},"volume":136,"oa":1,"OA_type":"hybrid"},{"ddc":["530"],"publication":"Physical Review Research","publisher":"American Physical Society","OA_place":"publisher","has_accepted_license":"1","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"file":[{"file_name":"2026_PhysicalReviewResearch_Huebl.pdf","date_updated":"2026-03-23T15:53:29Z","checksum":"6d8a68e4a19f8dad5abdf75f72316f3d","access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2026-03-23T15:53:29Z","content_type":"application/pdf","file_size":2680924,"success":1,"file_id":"21493"}],"corr_author":"1","publication_status":"published","type":"journal_article","quality_controlled":"1","article_number":"L012054","doi":"10.1103/68rs-3qgn","acknowledgement":"We thank Maitane Muñoz-Basagoiti for helpful discussions. The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"05","citation":{"apa":"Hübl, M., &#38; Goodrich, C. P. (2026). Entropic size control of self-assembled filaments. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/68rs-3qgn\">https://doi.org/10.1103/68rs-3qgn</a>","ama":"Hübl M, Goodrich CP. Entropic size control of self-assembled filaments. <i>Physical Review Research</i>. 2026;8. doi:<a href=\"https://doi.org/10.1103/68rs-3qgn\">10.1103/68rs-3qgn</a>","ista":"Hübl M, Goodrich CP. 2026. Entropic size control of self-assembled filaments. Physical Review Research. 8, L012054.","chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” <i>Physical Review Research</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/68rs-3qgn\">https://doi.org/10.1103/68rs-3qgn</a>.","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” <i>Physical Review Research</i>, vol. 8, L012054, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/68rs-3qgn\">10.1103/68rs-3qgn</a>.","ieee":"M. Hübl and C. P. Goodrich, “Entropic size control of self-assembled filaments,” <i>Physical Review Research</i>, vol. 8. American Physical Society, 2026.","short":"M. Hübl, C.P. Goodrich, Physical Review Research 8 (2026)."},"file_date_updated":"2026-03-23T15:53:29Z","abstract":[{"text":"Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly and is highly relevant in material design and biology. Here, we show that specific but promiscuous short-range binding interactions make it possible to economically assemble linear filaments of user-defined length. Our approach leads to independent control over the mean and width of the filament size distribution and allows us to smoothly explore design trade-offs between assembly quality (spread in size) and cost (number of particle species). We employ a simple hierarchical assembly protocol to minimize assembly times and show that multiple stages of hierarchy make it possible to extend our approach to the assembly of higher-dimensional structures. Our work provides a conceptually simple solution to size control that is applicable to a broad range of systems, from DNA nanoparticles to supramolecular polymers and beyond.","lang":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8,"OA_type":"gold","oa":1,"publication_identifier":{"eissn":["2643-1564"]},"date_updated":"2026-03-23T15:59:11Z","project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"date_created":"2026-03-23T14:58:31Z","author":[{"full_name":"Hübl, Maximilian","last_name":"Hübl","first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"date_published":"2026-03-05T00:00:00Z","month":"03","title":"Entropic size control of self-assembled filaments","intvolume":"         8","_id":"21482","year":"2026","language":[{"iso":"eng"}],"article_processing_charge":"Yes","article_type":"original","status":"public","DOAJ_listed":"1"},{"project":[{"grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"},{"_id":"bd906599-d553-11ed-ba76-abf8547645d7","name":"Identification of a novel regulator in auxin canalization","grant_number":"E271"}],"date_created":"2026-03-23T15:11:16Z","author":[{"full_name":"Li, Mingyue","last_name":"Li","first_name":"Mingyue","id":"01f96916-0235-11eb-9379-a323192643b7"},{"full_name":"Rydza, Nikola","first_name":"Nikola","last_name":"Rydza"},{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"publication_identifier":{"issn":["0960-9822"]},"date_updated":"2026-03-24T08:36:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["41831441"]},"OA_type":"hybrid","oa":1,"volume":36,"abstract":[{"text":"Auxin canalization is a self-organizing process that governs the flexible formation of vasculature by reinforcing the formation of auxin transport channels. A key prerequisite is the feedback between auxin signaling and directional auxin transport, mediated by PIN transporters. Despite the developmental importance of canalization, the molecular components linking auxin perception to the regulation of PIN auxin transporters remain poorly understood. Here, we identify TOW, a novel and essential component of auxin canalization that links intracellular auxin signaling with cell surface auxin perception. TOW is regulated downstream of TIR1/AFB-Aux/IAA-WRKY23 transcriptional auxin signaling. tow mutants exhibit defects in regeneration and de novo vasculature formation, along with impaired formation of polarized, PIN-expressing auxin channels. At the subcellular level, these mutants display disrupted auxin-induced PIN polarization and altered PIN endocytic trafficking dynamics. TOW localizes predominantly to the plasma membrane, where it interacts with receptor-like kinases involved in auxin canalization, including the TMK1 auxin co-receptor and the CAMEL-CANAR complex. TOW promotes PIN interaction with these kinases and stabilizes PINs at the cell surface. Together, our findings identify TOW as a molecular link between intracellular and cell surface auxin signaling mechanisms that converge on PIN trafficking and polarity, providing new insights into how auxin signaling regulates directional auxin transport for the self-organizing formation of vasculature during flexible plant development.","lang":"eng"}],"oa_version":"Published Version","status":"public","PlanS_conform":"1","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","article_type":"original","intvolume":"        36","year":"2026","_id":"21490","date_published":"2026-03-23T00:00:00Z","month":"03","title":"Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization","publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"JiFr"}],"file":[{"file_id":"21496","success":1,"content_type":"application/pdf","file_size":12986894,"relation":"main_file","date_created":"2026-03-24T08:34:37Z","date_updated":"2026-03-24T08:34:37Z","file_name":"2026_CurrentBiology_Li.pdf","access_level":"open_access","creator":"dernst","checksum":"fe6c41fdab58a55df5f2a5860c02acdc"}],"corr_author":"1","publisher":"Elsevier","has_accepted_license":"1","OA_place":"publisher","ddc":["580"],"publication":"Current Biology","page":"1468-1480.e6","file_date_updated":"2026-03-24T08:34:37Z","day":"23","citation":{"ama":"Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. <i>Current Biology</i>. 2026;36(6):1468-1480.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">10.1016/j.cub.2026.02.023</a>","apa":"Li, M., Rydza, N., Mazur, E., Molnar, G., Nodzyński, T., &#38; Friml, J. (2026). Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">https://doi.org/10.1016/j.cub.2026.02.023</a>","ista":"Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. 2026. Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. Current Biology. 36(6), 1468–1480.e6.","chicago":"Li, Mingyue, Nikola Rydza, Ewa Mazur, Gergely Molnar, Tomasz Nodzyński, and Jiří Friml. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes PIN Transporters for Auxin Canalization.” <i>Current Biology</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">https://doi.org/10.1016/j.cub.2026.02.023</a>.","mla":"Li, Mingyue, et al. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes PIN Transporters for Auxin Canalization.” <i>Current Biology</i>, vol. 36, no. 6, Elsevier, 2026, p. 1468–1480.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">10.1016/j.cub.2026.02.023</a>.","ieee":"M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, and J. Friml, “Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization,” <i>Current Biology</i>, vol. 36, no. 6. Elsevier, p. 1468–1480.e6, 2026.","short":"M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, J. Friml, Current Biology 36 (2026) 1468–1480.e6."},"issue":"6","acknowledged_ssus":[{"_id":"MassSpec"},{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1016/j.cub.2026.02.023","acknowledgement":"We thank Dr. Z. Ge (ISTA) for providing vectors for the CRISPR-Cas9 system, Dr. Armel Nicolas and Dr. Bella Bruszel for phosphoproteomic analysis, Prof. Michael Wrzaczek (Czech Academy of Sciences, Czechia) for valuable suggestions, and Prof. Maciek Adamowski (University of Gdańsk) for technical assistance. We also acknowledge the support of the Mass Spectrometry and Proteomics Facility, the Imaging & Optics Facility, and the Lab Support Facility at the Institute of Science and Technology Austria. This research was supported by the Scientific Service Units (SSU) of ISTA, utilizing resources provided by the Imaging & Optics Facility (IOF) and the Lab Support Facility (LSF). The work conducted by the Friml group was funded by the European Research Council (ERC) under grant agreement no. 101142681 (CYNIPS) and by the Austrian Science Fund (FWF) under project ESP271. We acknowledge the core facility CELLIM supported by MEYS CR (LM2023050 Czech-BioImaging) and the Plant Sciences Core Facility of CEITEC Masaryk University. E.M. received support from the National Science Centre (NCN), Poland, through the OPUS call within the Weave programme (grant no. 2021/43/I/NZ1/01835). T.N. received support from TowArds Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the ERDF Programme Johannes Amos Comenius.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"abstract":[{"text":"An individual's phenotype reflects a complex interplay of the direct effects of their DNA, epigenetic modifications of their DNA induced by their parents, and indirect effects of their parents' DNA. Here, we derive how the genetic variance within a population is changed under the influence of indirect maternal, paternal and parent-of-origin effects under random mating. We also consider indirect effects of a sibling, in particular how the genetic variance is altered when looking at the phenotypic difference between two siblings. The calculations are then extended to include assortative mating (AM), which alters the variance by inducing increased homozygosity and correlations within and across loci. AM likely leads to covariance of parental genetic effects, a measure of the similarity of parents in the indirect effects they have on their children. We propose that this assortment for parental characteristics, where biological parents create similar environments for their children, can create shared parental effects across traits and the appearance of cross-trait AM. Our theory shows how the resemblance among relatives increases under both AM, indirect and parent-of-origin effects. When our model is used to predict correlations among relatives in human height, we find that explaining the patterns observed in real data requires both indirect genetic effects and assortative mating. The degree to which direct, indirect and epigenetic effects shape the phenotypic variance of complex traits remains an open question that requires large-scale family data to be resolved.","lang":"eng"}],"oa_version":"Published Version","external_id":{"pmid":["41677404"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","oa":1,"publication_identifier":{"issn":["1943-2631"]},"date_updated":"2026-03-24T06:48:10Z","author":[{"last_name":"Krätschmer","first_name":"Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73","full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259"},{"last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"}],"date_created":"2026-03-23T15:02:54Z","date_published":"2026-02-12T00:00:00Z","title":"A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating","month":"02","year":"2026","_id":"21484","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","status":"public","publication":"Genetics","publisher":"Oxford University Press","has_accepted_license":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/medical-genomics-group/familyMC"}]},"OA_place":"publisher","department":[{"_id":"MaRo"}],"corr_author":"1","type":"journal_article","publication_status":"epub_ahead","quality_controlled":"1","article_number":"iyag042","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank members of the Medical Genomics group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria.","doi":"10.1093/genetics/iyag042","citation":{"short":"I. Krätschmer, M.R. Robinson, Genetics (2026).","ieee":"I. Krätschmer and M. R. Robinson, “A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating,” <i>Genetics</i>. Oxford University Press, 2026.","chicago":"Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic Model for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative Mating.” <i>Genetics</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/genetics/iyag042\">https://doi.org/10.1093/genetics/iyag042</a>.","ista":"Krätschmer I, Robinson MR. 2026. A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. Genetics., iyag042.","apa":"Krätschmer, I., &#38; Robinson, M. R. (2026). A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyag042\">https://doi.org/10.1093/genetics/iyag042</a>","ama":"Krätschmer I, Robinson MR. A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. <i>Genetics</i>. 2026. doi:<a href=\"https://doi.org/10.1093/genetics/iyag042\">10.1093/genetics/iyag042</a>","mla":"Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic Model for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative Mating.” <i>Genetics</i>, iyag042, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/genetics/iyag042\">10.1093/genetics/iyag042</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyag042"}],"day":"12"},{"_id":"21486","year":"2026","date_published":"2026-03-12T00:00:00Z","month":"03","title":"Causes and consequences of sex-chromosome turnovers in Diptera","status":"public","DOAJ_listed":"1","language":[{"iso":"eng"}],"article_processing_charge":"Yes","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","oa":1,"abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analyzed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find that the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on Muller element F (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}],"oa_version":"Published Version","project":[{"grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"}],"date_created":"2026-03-23T15:05:42Z","author":[{"orcid":"0000-0002-1253-6297","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","first_name":"Lorena Alexandra","last_name":"Layana Franco"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"eissn":["2056-3744"]},"date_updated":"2026-03-24T07:14:08Z","day":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evlett/qrag003"}],"citation":{"ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera,” <i>Evolution Letters</i>. Oxford University Press, 2026.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, Evolution Letters (2026).","mla":"Layana Franco, Lorena Alexandra, et al. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” <i>Evolution Letters</i>, qrag003, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/evlett/qrag003\">10.1093/evlett/qrag003</a>.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2026). Causes and consequences of sex-chromosome turnovers in Diptera. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrag003\">https://doi.org/10.1093/evlett/qrag003</a>","ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. <i>Evolution Letters</i>. 2026. doi:<a href=\"https://doi.org/10.1093/evlett/qrag003\">10.1093/evlett/qrag003</a>","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” <i>Evolution Letters</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/evlett/qrag003\">https://doi.org/10.1093/evlett/qrag003</a>.","ista":"Layana Franco LA, Toups MA, Vicoso B. 2026. Causes and consequences of sex-chromosome turnovers in Diptera. Evolution Letters., qrag003."},"article_number":"qrag003","doi":"10.1093/evlett/qrag003","acknowledgement":"This work was supported by a grant from the Austrian Science Fund (FWF, grant number PAT 8748323) to B.V. We thank the Vicoso group for their feedback on an early version of the manuscript. We are grateful to Kamil Jaron and Julia Gries for helpful discussions and for sharing their unpublished work. Computational resources and support were provided by the Scientific Computing Unit at ISTA.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Oxford University Press","has_accepted_license":"1","OA_place":"publisher","ddc":["570"],"publication":"Evolution Letters","publication_status":"epub_ahead","type":"journal_article","quality_controlled":"1","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"corr_author":"1"},{"has_accepted_license":"1","OA_place":"repository","publisher":"Institute of Science and Technology Austria","type":"research_data","file":[{"description":"Python3 library written in C++20 to integrate vertex models. Please read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed instructions for installation and usage of the code in this repository. 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Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","ista":"Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","chicago":"Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>.","ama":"Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>","apa":"Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>","short":"S. Naik, (2026).","ieee":"S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026."},"day":"24","acknowledgement":"We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"doi":"10.15479/AT-ISTA-21137","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","file_date_updated":"2026-03-24T07:21:43Z","OA_type":"free access","oa":1,"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","oa_version":"None","author":[{"id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","first_name":"Suyash","last_name":"Naik","orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash"}],"date_created":"2026-02-04T16:38:02Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"8f060199-16d5-11f0-9cad-f3253b266c46","grant_number":"PAT 5044023","name":"Keratins in epithelial tissue spreading"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W1250-B20","_id":"252C3B08-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_updated":"2026-03-24T08:32:00Z","_id":"21137","year":"2026","title":"Data associated with Keratins coordinate tissue spreading ","month":"3","date_published":"2026-03-24T00:00:00Z","ec_funded":1,"status":"public","article_processing_charge":"No"},{"publisher":"Springer Nature","has_accepted_license":"1","publication":"Transformation Groups","ddc":["510"],"type":"journal_article","publication_status":"epub_ahead","quality_controlled":"1","department":[{"_id":"TaHa"}],"corr_author":"1","citation":{"mla":"Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced by Real Structures.” <i>Transformation Groups</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s00031-026-09958-y\">10.1007/s00031-026-09958-y</a>.","ista":"Elkner MM. 2026. On involutions of minuscule Kirillov algebras induced by real structures. Transformation Groups.","chicago":"Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced by Real Structures.” <i>Transformation Groups</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00031-026-09958-y\">https://doi.org/10.1007/s00031-026-09958-y</a>.","apa":"Elkner, M. M. (2026). On involutions of minuscule Kirillov algebras induced by real structures. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-026-09958-y\">https://doi.org/10.1007/s00031-026-09958-y</a>","ama":"Elkner MM. On involutions of minuscule Kirillov algebras induced by real structures. <i>Transformation Groups</i>. 2026. doi:<a href=\"https://doi.org/10.1007/s00031-026-09958-y\">10.1007/s00031-026-09958-y</a>","short":"M.M. Elkner, Transformation Groups (2026).","ieee":"M. M. Elkner, “On involutions of minuscule Kirillov algebras induced by real structures,” <i>Transformation Groups</i>. Springer Nature, 2026."},"main_file_link":[{"url":"https://doi.org/10.1007/s00031-026-09958-y","open_access":"1"}],"day":"14","acknowledgement":"I would like to thank Tamás Hausel for introducing me to this area of mathematics and for his constant guidance. I would also like to thank Jakub Löwit and Miguel González for fruitful discussions and many helpful comments on this paper. This work was done during the author’s PhD studies at the Institute of Science and Technology Austria (ISTA). It was funded by the Austrian Science Fund (FWF) 10.55776/P35847. Open access funding provided by Institute of Science and Technology (IST Austria). ","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00031-026-09958-y","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2411.16270"]},"oa":1,"abstract":[{"lang":"eng","text":"We study Kirillov algebras attached to minuscule highest weight representations of semisimple Lie algebras. They can be viewed as equivariant cohomology algebras of partial flag varieties. Real structures on the varieties then induce involutions of these algebras. We describe how these involutions act on the spectra of minuscule Kirillov algebras, and model the fixed points via the equivariant cohomology of real partial flag varieties. We then use this model to characterise freeness of the fixed point coordinate ring over the appropriate base. As an application, we recover a q = -1 phenomenon of Stembridge in the minuscule case by geometric means."}],"oa_version":"None","arxiv":1,"project":[{"_id":"34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3","name":"Geometry of the tip of the global nilpotent cone","grant_number":"P35847"}],"author":[{"last_name":"Elkner","first_name":"Mischa M","id":"477faa59-080d-11ed-979a-c693ab7638ab","full_name":"Elkner, Mischa M"}],"date_created":"2026-03-23T15:10:43Z","publication_identifier":{"issn":["1083-4362"],"eissn":["1531-586X"]},"date_updated":"2026-03-24T08:26:10Z","_id":"21489","year":"2026","date_published":"2026-03-14T00:00:00Z","title":"On involutions of minuscule Kirillov algebras induced by real structures","month":"03","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)"},{"doi":"10.15479/AT-ISTA-21393","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"supervisor":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"last_name":"Blanchette","first_name":"Jasmin","full_name":"Blanchette, Jasmin"}],"day":"04","citation":{"mla":"Dvorak, Martin. <i>Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21393\">10.15479/AT-ISTA-21393</a>.","ama":"Dvorak M. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21393\">10.15479/AT-ISTA-21393</a>","apa":"Dvorak, M. (2026). <i>Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21393\">https://doi.org/10.15479/AT-ISTA-21393</a>","ista":"Dvorak M. 2026. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria.","chicago":"Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21393\">https://doi.org/10.15479/AT-ISTA-21393</a>.","ieee":"M. Dvorak, “Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids,” Institute of Science and Technology Austria, 2026.","short":"M. Dvorak, Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids, Institute of Science and Technology Austria, 2026."},"file_date_updated":"2026-03-04T09:03:37Z","page":"160","ddc":["511","000"],"OA_place":"repository","related_material":{"link":[{"url":"https://github.com/madvorak/duality/tree/v3.5.0","relation":"software","description":"Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality)"},{"relation":"software","description":"Full version of all definitions, statements, and proofs for Chapter 3.2 (Valued Constraint Satisfaction Problems)","url":"https://github.com/madvorak/vcsp/tree/v8.2.0"},{"relation":"software","description":"Full version of all definitions, statements, and proofs for Chapter 4 (Seymour project)","url":"https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0"},{"description":"Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars)","relation":"software","url":"https://github.com/madvorak/chomsky/tree/v1.2.0"},{"description":"Old version (Lean 3) of the project about grammars","relation":"software","url":"https://github.com/madvorak/grammars"},{"description":"Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis","relation":"software","url":"https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean"}],"record":[{"relation":"part_of_dissertation","id":"13120","status":"public"},{"status":"public","id":"21398","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"20071","status":"public"}]},"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"success":1,"file_id":"21394","file_size":1771231,"content_type":"application/pdf","date_created":"2026-03-04T08:56:15Z","relation":"main_file","checksum":"cface6dc18152680962b5361575f6e4f","creator":"mdvorak","access_level":"open_access","date_updated":"2026-03-04T08:56:15Z","file_name":"2026_Dvorak_Martin_Thesis.pdf"},{"checksum":"290ddfacfb7e07fb07e6f0b334e67c90","access_level":"closed","creator":"mdvorak","date_updated":"2026-03-04T09:03:37Z","file_name":"2026_Dvorak_Martin_Thesis.docx","date_created":"2026-03-04T09:03:37Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":864585,"file_id":"21395"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publication_status":"published","type":"dissertation","month":"03","title":"Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids","date_published":"2026-03-04T00:00:00Z","_id":"21393","year":"2026","degree_awarded":"PhD","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion."}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-03-27T12:37:00Z","publication_identifier":{"isbn":["978-3-99078-074-9"],"issn":["2663-337X"]},"date_created":"2026-03-04T09:26:46Z","author":[{"full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X","last_name":"Dvorak","first_name":"Martin","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425"}]},{"file_date_updated":"2026-03-30T06:08:07Z","article_number":"010352","acknowledgement":"The authors acknowledge useful discussions with Berislav Buca. This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). M.L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111—390814868. This research was supported in part by grant NSF PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1103/sl79-1xgb","citation":{"mla":"Nicolau Jimenez, Eulalia, et al. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” <i>PRX Quantum</i>, vol. 7, 010352, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/sl79-1xgb\">10.1103/sl79-1xgb</a>.","ista":"Nicolau Jimenez E, Ljubotina M, Serbyn M. 2026. Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. 7, 010352.","chicago":"Nicolau Jimenez, Eulalia, Marko Ljubotina, and Maksym Serbyn. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” <i>PRX Quantum</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/sl79-1xgb\">https://doi.org/10.1103/sl79-1xgb</a>.","apa":"Nicolau Jimenez, E., Ljubotina, M., &#38; Serbyn, M. (2026). Fragmentation, zero modes, and collective bound states in constrained models. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/sl79-1xgb\">https://doi.org/10.1103/sl79-1xgb</a>","ama":"Nicolau Jimenez E, Ljubotina M, Serbyn M. Fragmentation, zero modes, and collective bound states in constrained models. <i>PRX Quantum</i>. 2026;7. doi:<a href=\"https://doi.org/10.1103/sl79-1xgb\">10.1103/sl79-1xgb</a>","short":"E. Nicolau Jimenez, M. Ljubotina, M. Serbyn, PRX Quantum 7 (2026).","ieee":"E. Nicolau Jimenez, M. Ljubotina, and M. Serbyn, “Fragmentation, zero modes, and collective bound states in constrained models,” <i>PRX Quantum</i>, vol. 7. American Physical Society, 2026."},"day":"13","department":[{"_id":"MaSe"}],"file":[{"content_type":"application/pdf","file_size":1848724,"file_id":"21505","success":1,"file_name":"2026_PRXQuantum_Nicolau.pdf","date_updated":"2026-03-30T06:08:07Z","access_level":"open_access","creator":"dernst","checksum":"d155ffa9e1a8275702149165f4bf963c","relation":"main_file","date_created":"2026-03-30T06:08:07Z"}],"corr_author":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","ddc":["530"],"publication":"PRX Quantum","publisher":"American Physical Society","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes","PlanS_conform":"1","ec_funded":1,"DOAJ_listed":"1","status":"public","date_published":"2026-03-13T00:00:00Z","title":"Fragmentation, zero modes, and collective bound states in constrained models","month":"03","scopus_import":"1","intvolume":"         7","year":"2026","_id":"21501","publication_identifier":{"eissn":["2691-3399"]},"date_updated":"2026-03-30T06:09:28Z","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"author":[{"full_name":"Nicolau Jimenez, Eulalia","id":"04b4791c-8fd7-11ee-a7df-be2fdc569c48","first_name":"Eulalia","last_name":"Nicolau Jimenez"},{"full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","first_name":"Marko"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2026-03-28T14:57:56Z","abstract":[{"lang":"eng","text":"Kinetically constrained models were originally introduced to capture slow relaxation in glassy systems, where dynamics are hindered by local constraints instead of energy barriers. Their quantum counterparts have recently drawn attention for exhibiting highly degenerate eigenstates at zero energy—known as zero modes—stemming from chiral symmetry. Yet, the structure and implications of these zero modes remain poorly understood. In this work, we focus on the properties of the zero mode subspace in quantum kinetically constrained models with a U(1) particle-conservation symmetry. We use the U(1) East, which lacks inversion symmetry, and the inversion-symmetric U(1) East-West models to illustrate our two main results. First, we observe that the simultaneous presence of constraints and chiral symmetry generally leads to a parametric increase in the number of zero modes due to the fragmentation of the many-body\r\nHilbert space into disconnected sectors. Second, we generalize the concept of compact localized states from single-particle physics and introduce the notion of collective bound states, a special kind of nonergodic eigenstates that are robust to enlarging the system size. We formulate sufficient criteria for their existence, arguing that the degenerate zero mode subspace plays a central role, and demonstrate bound states in both example models and in a two-dimensional model, the U(1) North-East, and in the pairflip model, a system without particle conservation. Our results motivate a systematic study of bound states and their relation to ergodicity breaking, transport, and other properties of quantum kinetically constrained\r\nmodels. "}],"arxiv":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2504.17627"]},"volume":7,"OA_type":"gold","oa":1},{"citation":{"ieee":"J. Hajto <i>et al.</i>, “Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants,” <i>Pharmacogenomics Journal</i>, vol. 26, no. 2. Springer Nature, 2026.","short":"J. Hajto, M. Piechota, I. Krätschmer, P. Konowalska, G.E. Boyle, D.M. Fowler, M. Borczyk, M. Korostynski, Pharmacogenomics Journal 26 (2026).","mla":"Hajto, Jacek, et al. “Computational Variant Predictors for Pharmacogenomics: From Evaluation of Single Alleles to Assessment of Adverse Drug Reactions to Antidepressants.” <i>Pharmacogenomics Journal</i>, vol. 26, no. 2, 8, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41397-026-00399-0\">10.1038/s41397-026-00399-0</a>.","ama":"Hajto J, Piechota M, Krätschmer I, et al. Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. <i>Pharmacogenomics Journal</i>. 2026;26(2). doi:<a href=\"https://doi.org/10.1038/s41397-026-00399-0\">10.1038/s41397-026-00399-0</a>","apa":"Hajto, J., Piechota, M., Krätschmer, I., Konowalska, P., Boyle, G. E., Fowler, D. M., … Korostynski, M. (2026). Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. <i>Pharmacogenomics Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41397-026-00399-0\">https://doi.org/10.1038/s41397-026-00399-0</a>","ista":"Hajto J, Piechota M, Krätschmer I, Konowalska P, Boyle GE, Fowler DM, Borczyk M, Korostynski M. 2026. Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. Pharmacogenomics Journal. 26(2), 8.","chicago":"Hajto, Jacek, Marcin Piechota, Ilse Krätschmer, Paula Konowalska, Gabriel E. Boyle, Douglas M. Fowler, Malgorzata Borczyk, and Michal Korostynski. “Computational Variant Predictors for Pharmacogenomics: From Evaluation of Single Alleles to Assessment of Adverse Drug Reactions to Antidepressants.” <i>Pharmacogenomics Journal</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41397-026-00399-0\">https://doi.org/10.1038/s41397-026-00399-0</a>."},"day":"09","acknowledgement":"This research has been conducted using the UK Biobank Resource under Application Number 62979. We are grateful to the UK Biobank and all its voluntary participants. This work used data provided by patients and collected by the NHS as part of their care and support.\r\n\r\nThis study was funded by the National Science Center, Poland: PRELUDIUM BIS-3 grant no. 2021/43/O/NZ7/01187 (development and benchmarking of variant scores) and SONATINA 5 grant 2021/40/C/NZ2/00218 (UKB analyses). Additional support came from the statutory funds of the Maj Institute of Pharmacology PAS. We gratefully acknowledge Poland’s high-performance Infrastructure PLGrid ACK Cyfronet AGH, for providing computer facilities and support within computational grant no PLG/2022/015861. DMF and GEB were funded by NIH grants NIH R35GM152106 and UM1HG011969.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1038/s41397-026-00399-0","issue":"2","article_number":"8","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2026-03-30T07:04:08Z","OA_place":"publisher","has_accepted_license":"1","publisher":"Springer Nature","ddc":["570"],"publication":"Pharmacogenomics Journal","quality_controlled":"1","type":"journal_article","publication_status":"published","file":[{"file_size":2618963,"content_type":"application/pdf","success":1,"file_id":"21506","checksum":"2fd3d7e48b779ac24245f6c35449b89a","creator":"dernst","access_level":"open_access","date_updated":"2026-03-30T07:04:08Z","file_name":"2026_PharmacogenomicsJour_Hajto.pdf","date_created":"2026-03-30T07:04:08Z","relation":"main_file"}],"department":[{"_id":"MaRo"}],"_id":"21503","year":"2026","intvolume":"        26","title":"Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants","month":"03","scopus_import":"1","date_published":"2026-03-09T00:00:00Z","status":"public","article_type":"original","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"oa":1,"volume":26,"OA_type":"hybrid","pmid":1,"external_id":{"pmid":["41803106"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"text":"Currently, pharmacogenetics relies on partially annotated star alleles, leaving novel variants and complex haplotypes uninterpretable. Computational scoring frameworks could overcome these limitations. Here, we comprehensively evaluated the ability of existing (CADD, FATHMM-XF, PROVEAN, MutationAssessor, SIFT, PhyloP100, APF, APF2) and novel (PharmGScore and PharmMLScore) variant effect predictors to assess pharmacogenetic alleles in multiple scenarios. Altogether we analyzed 541 PharmVar alleles, high‑throughput CYP2C9 and CYP2C19 mutational maps, and 200 642 UK Biobank exomes linked with health records containing antidepressant treatment outcomes. Many evaluated tools, especially ensemble frameworks, matched or exceeded star allele classifications (ROC‑AUC up to 0.85 for allele definitions, 0.95 in vitro; TPR up to 0.99 for exomes) and accurately predicted severe antidepressant adverse events for carriers of deleterious variants in CYP2C19 (OR 1.20–1.35). Our findings show that computational predictors deliver star allele accuracy while overcoming their limitations. With additional validation, computational tools could enhance clinical decision frameworks by enabling continuous scoring, incorporating previously unknown variants, and providing genome-wide applicability.","lang":"eng"}],"author":[{"first_name":"Jacek","last_name":"Hajto","full_name":"Hajto, Jacek"},{"last_name":"Piechota","first_name":"Marcin","full_name":"Piechota, Marcin"},{"full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259","last_name":"Krätschmer","first_name":"Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73"},{"last_name":"Konowalska","first_name":"Paula","full_name":"Konowalska, Paula"},{"full_name":"Boyle, Gabriel E.","last_name":"Boyle","first_name":"Gabriel E."},{"full_name":"Fowler, Douglas M.","last_name":"Fowler","first_name":"Douglas M."},{"first_name":"Malgorzata","last_name":"Borczyk","full_name":"Borczyk, Malgorzata"},{"last_name":"Korostynski","first_name":"Michal","full_name":"Korostynski, Michal"}],"date_created":"2026-03-29T22:07:08Z","date_updated":"2026-03-30T07:10:50Z","publication_identifier":{"issn":[" 1470-269X"],"eissn":["1473-1150"]}},{"doi":"10.1016/j.molcel.2026.01.021","issue":"4","acknowledgement":"We thank D. Hess, V. Iesmantavicius, and J. Seebacher (FMI Proteomics and Protein Analysis Facility) for mass spectrometry support; S. Smallwood, K. Shimada, D. Klein, and M. Schütz-Stoffregen for technical assistance; J. Côté and C. Lachance for critical discussions; and members of the Thomä lab for helpful feedback. Support for this work was provided to N.H.T. by the European Research Council under the European Union’s Horizon 2020 research program (NucEM, no. 884331), the Novartis Research Foundation, the Swiss National Science Foundation (SNF 31003A_179541, 310030_214852, and Sinergia CRSII5_186230), and the Swiss Cancer Research (KFS-4980-02-2020 and KFS-5933-08-2023). S.D. was supported by the European Research Council (DONUTS, no. 101092623), the Knut and Alice Wallenberg Foundation (2024.0012), the Cancerfonden (25 4453 Pj), and the Swedish Research Council (VR 03255). A.K.M. was supported by a Human Frontier Science Program Long-Term Fellowship, and L.V. was supported by an EMBO fellowship (ALTF 549-2021).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"19","citation":{"short":"J. Weiss, L. Vecchia, D. Domjan, S. Cavadini, A. Sabantsev, G. Kempf, G.R. Pathare, K. Brackmann, A.K. Michael, L. Kater, E. Hietter-Pfeiffer, M. Haddawi, U.P. Kuber, S. Mühlhäusser, R.S. Grand, M.B. Stadler, S. Deindl, N.H. Thomä, Molecular Cell 86 (2026) 625–639.e8.","ieee":"J. Weiss <i>et al.</i>, “The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2,” <i>Molecular Cell</i>, vol. 86, no. 4. Elsevier, p. 625–639.e8, 2026.","mla":"Weiss, Joscha, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” <i>Molecular Cell</i>, vol. 86, no. 4, Elsevier, 2026, p. 625–639.e8, doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">10.1016/j.molcel.2026.01.021</a>.","ista":"Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR, Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser S, Grand RS, Stadler MB, Deindl S, Thomä NH. 2026. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. 86(4), 625–639.e8.","chicago":"Weiss, Joscha, Luca Vecchia, David Domjan, Simone Cavadini, Anton Sabantsev, Georg Kempf, Ganesh R. Pathare, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” <i>Molecular Cell</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">https://doi.org/10.1016/j.molcel.2026.01.021</a>.","apa":"Weiss, J., Vecchia, L., Domjan, D., Cavadini, S., Sabantsev, A., Kempf, G., … Thomä, N. H. (2026). The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">https://doi.org/10.1016/j.molcel.2026.01.021</a>","ama":"Weiss J, Vecchia L, Domjan D, et al. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. <i>Molecular Cell</i>. 2026;86(4):625-639.e8. doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">10.1016/j.molcel.2026.01.021</a>"},"file_date_updated":"2026-03-30T12:04:38Z","page":"625-639.e8","publication":"Molecular Cell","ddc":["570"],"publisher":"Elsevier","OA_place":"publisher","has_accepted_license":"1","department":[{"_id":"AlMi"}],"file":[{"date_updated":"2026-03-30T12:04:38Z","file_name":"2026_MolecularCell_Weiss.pdf","creator":"dernst","access_level":"open_access","checksum":"e16a7315b64a706184b177ea1621523c","relation":"main_file","date_created":"2026-03-30T12:04:38Z","file_size":9786677,"content_type":"application/pdf","file_id":"21510","success":1}],"publication_status":"published","type":"journal_article","quality_controlled":"1","date_published":"2026-02-19T00:00:00Z","month":"02","scopus_import":"1","title":"The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2","intvolume":"        86","year":"2026","_id":"21509","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","status":"public","PlanS_conform":"1","abstract":[{"lang":"eng","text":"Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes."}],"oa_version":"Published Version","external_id":{"pmid":["41679301"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","volume":86,"oa":1,"publication_identifier":{"issn":["1097-2765"]},"date_updated":"2026-03-30T12:09:08Z","date_created":"2026-03-30T11:58:48Z","author":[{"full_name":"Weiss, Joscha","last_name":"Weiss","first_name":"Joscha"},{"first_name":"Luca","last_name":"Vecchia","full_name":"Vecchia, Luca"},{"first_name":"David","last_name":"Domjan","full_name":"Domjan, David"},{"full_name":"Cavadini, Simone","last_name":"Cavadini","first_name":"Simone"},{"full_name":"Sabantsev, Anton","last_name":"Sabantsev","first_name":"Anton"},{"first_name":"Georg","last_name":"Kempf","full_name":"Kempf, Georg"},{"last_name":"Pathare","first_name":"Ganesh R.","full_name":"Pathare, Ganesh R."},{"full_name":"Brackmann, Klaus","first_name":"Klaus","last_name":"Brackmann"},{"orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","last_name":"Michael"},{"full_name":"Kater, Lukas","first_name":"Lukas","last_name":"Kater"},{"last_name":"Hietter-Pfeiffer","first_name":"Eric","full_name":"Hietter-Pfeiffer, Eric"},{"last_name":"Haddawi","first_name":"Mina","full_name":"Haddawi, Mina"},{"full_name":"Kuber, Urja P.","last_name":"Kuber","first_name":"Urja P."},{"last_name":"Mühlhäusser","first_name":"Sandra","full_name":"Mühlhäusser, Sandra"},{"last_name":"Grand","first_name":"Ralph S.","full_name":"Grand, Ralph S."},{"full_name":"Stadler, Michael B.","last_name":"Stadler","first_name":"Michael B."},{"last_name":"Deindl","first_name":"Sebastian","full_name":"Deindl, Sebastian"},{"first_name":"Nicolas H.","last_name":"Thomä","full_name":"Thomä, Nicolas H."}]},{"day":"11","citation":{"ieee":"D. Babic, M. Zupunski, and J. Friml, “Imaging and genetic toolbox to study Arabidopsis embryogenesis,” <i>New Phytologist</i>. Wiley, 2026.","short":"D. Babic, M. Zupunski, J. Friml, New Phytologist (2026).","apa":"Babic, D., Zupunski, M., &#38; Friml, J. (2026). Imaging and genetic toolbox to study Arabidopsis embryogenesis. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.71072\">https://doi.org/10.1111/nph.71072</a>","ama":"Babic D, Zupunski M, Friml J. Imaging and genetic toolbox to study Arabidopsis embryogenesis. <i>New Phytologist</i>. 2026. doi:<a href=\"https://doi.org/10.1111/nph.71072\">10.1111/nph.71072</a>","chicago":"Babic, David, Milan Zupunski, and Jiří Friml. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” <i>New Phytologist</i>. Wiley, 2026. <a href=\"https://doi.org/10.1111/nph.71072\">https://doi.org/10.1111/nph.71072</a>.","ista":"Babic D, Zupunski M, Friml J. 2026. Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist., nph. 71072.","mla":"Babic, David, et al. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” <i>New Phytologist</i>, nph. 71072, Wiley, 2026, doi:<a href=\"https://doi.org/10.1111/nph.71072\">10.1111/nph.71072</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.71072"}],"doi":"10.1111/nph.71072","acknowledgement":"The authors would like to acknowledge the many colleagues whose valuable contributions to the field could not be included in this review due to space limitations and reference constraints. Open Access funding provided by Institute of Science and Technology Austria/KEMÖ.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"nph.71072","has_accepted_license":"1","OA_place":"publisher","publisher":"Wiley","publication":"New Phytologist","quality_controlled":"1","publication_status":"epub_ahead","type":"journal_article","corr_author":"1","department":[{"_id":"JiFr"},{"_id":"GradSch"}],"year":"2026","_id":"21483","month":"03","title":"Imaging and genetic toolbox to study Arabidopsis embryogenesis","date_published":"2026-03-11T00:00:00Z","status":"public","PlanS_conform":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","language":[{"iso":"eng"}],"oa":1,"OA_type":"hybrid","pmid":1,"external_id":{"pmid":["41808651"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"text":"Embryogenesis in the model plant Arabidopsis thaliana provides a framework for understanding how cell polarity and patterning coordinate with hormonal signalling to establish the plant body plan. Following fertilisation, the zygote divides asymmetrically to generate apical and basal lineages, establishing the apical–basal axis that defines future shoot and root poles. Genetic and molecular analyses of classical mutants including gnom, monopteros (mp), bodenlos (bdl) and topless revealed that localised auxin biosynthesis, directional transport and downstream transcriptional responses are central to apical–basal axis establishment and organ initiation. The main components of this regulation are polarly localised PIN auxin transporters and downstream modules involving MONOPTEROS and WUSCHEL-RELATED HOMEOBOX transcription factors. Advances in microscopy have transformed the study of Arabidopsis embryogenesis: fluorescence-compatible clearing reagents and three-dimensional reconstructions now permit quantitative analyses of cell geometry, division orientation, and cytoskeletal dynamics. Live ovule imaging setups with confocal laser scanning and multiphoton microscopes enable real-time observation of embryo development, while laser-assisted cell ablation can be used to probe cell-to-cell communication and fate plasticity. Together, these methodological breakthroughs position Arabidopsis embryos as a prime model for dissecting the chemical and biophysical cues that shape plant development.","lang":"eng"}],"date_created":"2026-03-23T14:59:06Z","author":[{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic","first_name":"David"},{"full_name":"Zupunski, Milan","last_name":"Zupunski","first_name":"Milan","id":"f6a21fce-573e-11f0-a150-a8d96aee2539"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"date_updated":"2026-03-30T05:58:35Z","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]}}]