[{"quality_controlled":"1","volume":121,"date_created":"2024-10-27T23:01:44Z","date_updated":"2025-09-08T14:31:58Z","_id":"18479","oa_version":"Published Version","month":"10","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"scopus_import":"1","doi":"10.1073/pnas.2406335121","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","date_published":"2024-10-29T00:00:00Z","citation":{"ama":"Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>","apa":"Mcdonough, Y., Ruzicka, F., &#38; Connallon, T. (2024). Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>","ieee":"Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","ista":"Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2406335121.","mla":"Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>.","chicago":"Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>.","short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"intvolume":"       121","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"status":"public","article_number":"e2406335121","department":[{"_id":"BeVi"}],"file_date_updated":"2024-11-04T10:29:43Z","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"The dominance of beneficial mutations is a key evolutionary parameter affecting the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate. A leading method to infer it is to compare the relative rates of adaptive substitution for X-linked and autosomal genes, which—according to a classic model by Charlesworth et al. (1987)—is a simple function of the dominance of new beneficial mutations. Recent evidence that rates of adaptive substitution are faster for X-linked genes implies, accordingly, that beneficial mutations are usually recessive. However, this conclusion is incompatible with leading theories of dominance, which predict that beneficial mutations tend to be dominant or overdominant with respect to fitness. To address this incompatibility, we use Fisher’s geometric model to predict the distribution of fitness effects of new mutations and the relative rates of positively selected substitution on the X and autosomes. Previous predictions of faster-X theory emerge as a special case of our model in which the phenotypic effects of mutations are small relative to the distance to the phenotypic optimum. But as mutational effects become large relative to the optimum, we observe an elevated tempo of positively selected substitutions on the X relative to the autosomes across a broader range of dominance conditions, including those predicted by theories of dominance. Our results imply that, contrary to previous models, dominant and overdominant beneficial mutations can plausibly generate patterns of faster-X adaptation. We discuss resulting implications for genomic studies of adaptation and inferences of dominance."}],"title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","publication_status":"published","acknowledgement":"This work was supported by funds from the Australian Research Council and The School of Biological Sciences at Monash University. F.R. was funded by a H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous reviewers for suggestions that substantially improved the paper and breadth of the analysis.","oa":1,"OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","issue":"44","day":"29","ddc":["570"],"author":[{"last_name":"Mcdonough","full_name":"Mcdonough, Yasmine","first_name":"Yasmine"},{"full_name":"Ruzicka, Filip","first_name":"Filip","last_name":"Ruzicka","id":"347955dd-57b0-11ee-9095-c28bdd368f4b"},{"full_name":"Connallon, Tim","first_name":"Tim","last_name":"Connallon"}],"language":[{"iso":"eng"}],"pmid":1,"external_id":{"isi":["001359216400017"],"pmid":["39436652"]},"article_type":"original","year":"2024","publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"eissn":["1091-6490"]},"isi":1,"file":[{"file_size":1299095,"date_updated":"2024-11-04T10:29:43Z","date_created":"2024-11-04T10:29:43Z","creator":"dernst","success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"18501","file_name":"2024_PNAS_McDonough.pdf","checksum":"73db3c87b35753e0f4324417f164a35e"}]},{"external_id":{"pmid":["39433757"],"isi":["001426270600023"]},"pmid":1,"language":[{"iso":"eng"}],"year":"2024","article_type":"original","publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"file":[{"checksum":"b936b1c047f41cd427f00e3dc79327d3","file_name":"2024_NatureComm_dosSantos.pdf","file_id":"18502","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2024-11-04T10:37:56Z","file_size":7358742,"date_created":"2024-11-04T10:37:56Z"}],"isi":1,"abstract":[{"lang":"eng","text":"Caloric restriction (CR) can extend the organism life- and health-span by improving glucose homeostasis. How CR affects the structure-function of pancreatic beta cells remains unknown. We used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis reveal that CR activates transcription factors important for beta cell identity and homeostasis, while imaging metabolomics demonstrates that beta cells upon CR are more energetically competent. In fact, high-resolution microscopy show that CR reduces beta cell mitophagy to increase mitochondria mass and the potential for ATP generation. However, CR beta cells have impaired adaptive proliferation in response to high fat diet feeding. Finally, we show that long-term CR delays the onset of beta cell aging hallmarks and promotes cell longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function during aging and diabetes."}],"title":"Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice","publication_status":"published","acknowledgement":"We are thankful to Michelle Reyzer from the Vanderbilt Mass Spectrometry Research Center for assistance with MALDI-MS imaging and analysis, to the outstanding team at the Vanderbilt Mouse Metabolic Phenotyping Center for all the assistance with in vivo glucose homeostasis tests (DK135073, 1S10RR028101-01). We also thank the University of Michigan Animal Phenotyping Core for conducting the bomb calorimetry experiments (1U2CDK110768, DK020575, and DK089503). This research was supported by recruitment funds from the Vanderbilt’s Department of Molecular Physiology and Biophysics and NIH grants 1R03DK127484, 5U24DK097771, and 1R01DK138141 to RAeD, by a grant from the Canadian Institutes of Health Research (CIHR; 487188) to PEM, by and NIH DK132669 to D.D. PEM holds the Canada Research Chair in Islet Biology.","oa":1,"OA_place":"publisher","OA_type":"gold","article_processing_charge":"Yes","author":[{"full_name":"Dos Santos, Cristiane","first_name":"Cristiane","last_name":"Dos Santos"},{"full_name":"Cambraia, Amanda","first_name":"Amanda","last_name":"Cambraia"},{"last_name":"Shrestha","full_name":"Shrestha, Shristi","first_name":"Shristi"},{"first_name":"Melanie","full_name":"Cutler, Melanie","last_name":"Cutler"},{"last_name":"Cottam","full_name":"Cottam, Matthew","first_name":"Matthew"},{"full_name":"Perkins, Guy","first_name":"Guy","last_name":"Perkins"},{"first_name":"Varda","full_name":"Lev-Ram, Varda","last_name":"Lev-Ram"},{"first_name":"Birbickram","full_name":"Roy, Birbickram","last_name":"Roy"},{"last_name":"Acree","first_name":"Christopher","full_name":"Acree, Christopher"},{"first_name":"Keun Young","full_name":"Kim, Keun Young","last_name":"Kim"},{"last_name":"Deerinck","first_name":"Thomas","full_name":"Deerinck, Thomas"},{"last_name":"Dean","full_name":"Dean, Danielle","first_name":"Danielle"},{"last_name":"Cartailler","first_name":"Jean Philippe","full_name":"Cartailler, Jean Philippe"},{"first_name":"Patrick E.","full_name":"Macdonald, Patrick E.","last_name":"Macdonald"},{"first_name":"Martin W","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"last_name":"Ellisman","full_name":"Ellisman, Mark","first_name":"Mark"},{"full_name":"Arrojo E Drigo, Rafael","first_name":"Rafael","last_name":"Arrojo E Drigo"}],"day":"21","ddc":["570"],"citation":{"apa":"Dos Santos, C., Cambraia, A., Shrestha, S., Cutler, M., Cottam, M., Perkins, G., … Arrojo E Drigo, R. (2024). Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53127-2\">https://doi.org/10.1038/s41467-024-53127-2</a>","ieee":"C. Dos Santos <i>et al.</i>, “Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Dos Santos C, Cambraia A, Shrestha S, et al. Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53127-2\">10.1038/s41467-024-53127-2</a>","mla":"Dos Santos, Cristiane, et al. “Calorie Restriction Increases Insulin Sensitivity to Promote Beta Cell Homeostasis and Longevity in Mice.” <i>Nature Communications</i>, vol. 15, 9063, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53127-2\">10.1038/s41467-024-53127-2</a>.","chicago":"Dos Santos, Cristiane, Amanda Cambraia, Shristi Shrestha, Melanie Cutler, Matthew Cottam, Guy Perkins, Varda Lev-Ram, et al. “Calorie Restriction Increases Insulin Sensitivity to Promote Beta Cell Homeostasis and Longevity in Mice.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53127-2\">https://doi.org/10.1038/s41467-024-53127-2</a>.","short":"C. Dos Santos, A. Cambraia, S. Shrestha, M. Cutler, M. Cottam, G. Perkins, V. Lev-Ram, B. Roy, C. Acree, K.Y. Kim, T. Deerinck, D. Dean, J.P. Cartailler, P.E. Macdonald, M. Hetzer, M. Ellisman, R. Arrojo E Drigo, Nature Communications 15 (2024).","ista":"Dos Santos C, Cambraia A, Shrestha S, Cutler M, Cottam M, Perkins G, Lev-Ram V, Roy B, Acree C, Kim KY, Deerinck T, Dean D, Cartailler JP, Macdonald PE, Hetzer M, Ellisman M, Arrojo E Drigo R. 2024. Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice. Nature Communications. 15, 9063."},"date_published":"2024-10-21T00:00:00Z","intvolume":"        15","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","DOAJ_listed":"1","status":"public","article_number":"9063","file_date_updated":"2024-11-04T10:37:56Z","department":[{"_id":"MaHe"}],"publisher":"Springer Nature","oa_version":"Published Version","_id":"18480","month":"10","quality_controlled":"1","date_updated":"2025-09-08T14:32:38Z","date_created":"2024-10-27T23:01:44Z","volume":15,"scopus_import":"1","doi":"10.1038/s41467-024-53127-2","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","type":"journal_article"},{"abstract":[{"lang":"eng","text":"A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues."}],"APC_amount":"3197,23 EUR","title":"Dynamics of morphogen source formation in a growing tissue","publication_status":"published","acknowledgement":"We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","oa":1,"OA_place":"publisher","article_processing_charge":"No","OA_type":"gold","ddc":["570"],"day":"14","author":[{"last_name":"Ho","first_name":"Richard D.J.G.","full_name":"Ho, Richard D.J.G."},{"full_name":"Kishi, Kasumi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","orcid":"0000-0001-6060-4795"},{"first_name":"Maciej","full_name":"Majka, Maciej","last_name":"Majka"},{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"full_name":"Zagórski, Marcin P","first_name":"Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"pmid":1,"external_id":{"isi":["001331700300003"],"pmid":["39401260"]},"article_type":"original","year":"2024","publication":"PLoS Computational Biology","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"isi":1,"file":[{"file_size":3732443,"date_created":"2024-10-29T11:59:09Z","date_updated":"2024-10-29T11:59:09Z","success":1,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_id":"18487","relation":"main_file","file_name":"2024_PloSComBio_Ho.pdf","checksum":"42fa714459943cb3961b40fab8fd82c8"}],"quality_controlled":"1","date_updated":"2026-04-07T12:31:58Z","date_created":"2024-10-27T23:01:45Z","volume":20,"_id":"18481","oa_version":"Published Version","month":"10","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"}],"scopus_import":"1","doi":"10.1371/journal.pcbi.1012508","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","type":"journal_article","related_material":{"record":[{"id":"20393","relation":"dissertation_contains","status":"public"}]},"citation":{"ista":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508.","mla":"Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>, vol. 20, e1012508, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>.","short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","chicago":"Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>.","ama":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. 2024;20. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>","apa":"Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., &#38; Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>","ieee":"R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” <i>PLoS Computational Biology</i>, vol. 20. Public Library of Science, 2024."},"date_published":"2024-10-14T00:00:00Z","DOAJ_listed":"1","intvolume":"        20","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","status":"public","article_number":"e1012508","department":[{"_id":"AnKi"}],"file_date_updated":"2024-10-29T11:59:09Z","publisher":"Public Library of Science"},{"department":[{"_id":"GradSch"}],"publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        85","date_published":"2024-06-01T00:00:00Z","citation":{"short":"P. Arkhipov, Automation and Remote Control 85 (2024) 522–532.","chicago":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” <i>Automation and Remote Control</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1134/S0005117924060031\">https://doi.org/10.1134/S0005117924060031</a>.","mla":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” <i>Automation and Remote Control</i>, vol. 85, no. 6, Springer Nature, 2024, pp. 522–32, doi:<a href=\"https://doi.org/10.1134/S0005117924060031\">10.1134/S0005117924060031</a>.","ista":"Arkhipov P. 2024. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 85(6), 522–532.","ieee":"P. Arkhipov, “An algorithm for finding the generalized Chebyshev center of sets defined via their support functions,” <i>Automation and Remote Control</i>, vol. 85, no. 6. Springer Nature, pp. 522–532, 2024.","apa":"Arkhipov, P. (2024). An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. <i>Automation and Remote Control</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0005117924060031\">https://doi.org/10.1134/S0005117924060031</a>","ama":"Arkhipov P. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. <i>Automation and Remote Control</i>. 2024;85(6):522-532. doi:<a href=\"https://doi.org/10.1134/S0005117924060031\">10.1134/S0005117924060031</a>"},"status":"public","corr_author":"1","type":"journal_article","scopus_import":"1","date_updated":"2025-09-08T14:27:08Z","volume":85,"quality_controlled":"1","date_created":"2024-10-27T23:01:45Z","_id":"18482","oa_version":"None","month":"06","doi":"10.1134/S0005117924060031","publication":"Automation and Remote Control","isi":1,"publication_identifier":{"issn":["0005-1179"],"eissn":["1608-3032"]},"language":[{"iso":"eng"}],"external_id":{"isi":["001338721700007"]},"article_type":"original","year":"2024","article_processing_charge":"No","OA_type":"closed access","day":"01","author":[{"id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","last_name":"Arkhipov","first_name":"Pavel","full_name":"Arkhipov, Pavel"}],"issue":"6","title":"An algorithm for finding the generalized Chebyshev center of sets defined via their support functions","abstract":[{"lang":"eng","text":"This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a shift to a vector x0 ∈ \r\nRn. The goal is to find t0 and x0. In the special case of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev center and the Chebyshev radius of A. This paper focuses on the case in which A and B are defined with their black-box support functions. An algorithm for solving such problems efficiently is suggested. The algorithm has a superlinear convergence rate, and it can solve hundred-dimensional test problems in a reasonable time, but some additional conditions on A and B are required to guarantee the presence of convergence. Additionally, the behavior of the algorithm for a simple special case is investigated, which leads to a number of theoretical results. Perturbations of this special case are also studied."}],"acknowledgement":"The author is grateful to Maxim Balashov for setting the problem, providing useful literature, important discussions and text review. Also, I thank Dmitry Tsarev and Kseniia Petukhova for meaningful talks and support.","page":"522-532","publication_status":"published"},{"author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"full_name":"Koudjinan, Edmond","first_name":"Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","last_name":"Koudjinan","orcid":"0000-0003-2640-4049"},{"full_name":"Zhang, Ke","first_name":"Ke","last_name":"Zhang"}],"day":"01","ddc":["510"],"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","oa":1,"acknowledgement":"We are grateful to the anonymous referee for their careful reading and valuable remarks and comments which helped to improve significantly the paper. Open access funding provided by Institute of Science and Technology (IST Austria). V.K. and C.E.K. gratefully acknowledge support from the European Research Council (ERC) through the Advanced Grant “SPERIG” (#885 707).","publication_status":"published","page":"1973-2007","title":"Birkhoff conjecture for nearly centrally symmetric domains","abstract":[{"text":"In this paper we prove a perturbative version of a remarkable Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) result. They prove non perturbative Birkhoff conjecture for centrally-symmetric convex domains, namely, a centrally-symmetric convex domain with integrable billiard is ellipse. We combine techniques from Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) with a local result by Kaloshin–Sorrentino (Ann. Math. 188(1):315–380, 2018) and show that a domain close enough to a centrally symmetric one with integrable billiard is ellipse. To combine these results we derive a slight extension of Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) by proving that a notion of rational integrability is equivalent to the C0-integrability condition used in their paper.","lang":"eng"}],"file":[{"checksum":"e7fcd9f78beb40408c7d858ac0625e27","relation":"main_file","file_id":"18833","file_name":"2024_GeometricFunctionalAnalysis_Kaloshin.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-13T09:14:24Z","file_size":2260980,"date_updated":"2025-01-13T09:14:24Z","success":1,"creator":"dernst"}],"isi":1,"publication_identifier":{"issn":["1016-443X"],"eissn":["1420-8970"]},"publication":"Geometric and Functional Analysis","year":"2024","article_type":"original","external_id":{"isi":["001329804200001"],"arxiv":["2306.12301"]},"language":[{"iso":"eng"}],"type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00039-024-00695-6","scopus_import":"1","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020","grant_number":"885707"}],"month":"12","_id":"18483","oa_version":"Published Version","date_created":"2024-10-27T23:01:45Z","date_updated":"2025-09-08T14:27:45Z","quality_controlled":"1","volume":34,"publisher":"Springer Nature","file_date_updated":"2025-01-13T09:14:24Z","department":[{"_id":"VaKa"}],"arxiv":1,"status":"public","corr_author":"1","ec_funded":1,"intvolume":"        34","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Kaloshin, V., Koudjinan, E., &#38; Zhang, K. (2024). Birkhoff conjecture for nearly centrally symmetric domains. <i>Geometric and Functional Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00039-024-00695-6\">https://doi.org/10.1007/s00039-024-00695-6</a>","ieee":"V. Kaloshin, E. Koudjinan, and K. Zhang, “Birkhoff conjecture for nearly centrally symmetric domains,” <i>Geometric and Functional Analysis</i>, vol. 34. Springer Nature, pp. 1973–2007, 2024.","ama":"Kaloshin V, Koudjinan E, Zhang K. Birkhoff conjecture for nearly centrally symmetric domains. <i>Geometric and Functional Analysis</i>. 2024;34:1973-2007. doi:<a href=\"https://doi.org/10.1007/s00039-024-00695-6\">10.1007/s00039-024-00695-6</a>","mla":"Kaloshin, Vadim, et al. “Birkhoff Conjecture for Nearly Centrally Symmetric Domains.” <i>Geometric and Functional Analysis</i>, vol. 34, Springer Nature, 2024, pp. 1973–2007, doi:<a href=\"https://doi.org/10.1007/s00039-024-00695-6\">10.1007/s00039-024-00695-6</a>.","short":"V. Kaloshin, E. Koudjinan, K. Zhang, Geometric and Functional Analysis 34 (2024) 1973–2007.","chicago":"Kaloshin, Vadim, Edmond Koudjinan, and Ke Zhang. “Birkhoff Conjecture for Nearly Centrally Symmetric Domains.” <i>Geometric and Functional Analysis</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00039-024-00695-6\">https://doi.org/10.1007/s00039-024-00695-6</a>.","ista":"Kaloshin V, Koudjinan E, Zhang K. 2024. Birkhoff conjecture for nearly centrally symmetric domains. Geometric and Functional Analysis. 34, 1973–2007."},"date_published":"2024-12-01T00:00:00Z"},{"publication":"PRX Quantum","isi":1,"file":[{"date_updated":"2024-10-30T08:59:09Z","file_size":1151431,"date_created":"2024-10-30T08:59:09Z","success":1,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"18489","file_name":"2024_PRXQuantum_Ljubotina.pdf","checksum":"2e057ba021744d0a74602517935326b3"}],"publication_identifier":{"eissn":["2691-3399"]},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2403.12325"],"isi":["001346198800001"]},"article_type":"original","year":"2024","article_processing_charge":"Yes","OA_type":"gold","OA_place":"publisher","oa":1,"day":"23","ddc":["530"],"author":[{"first_name":"Marko","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina"},{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","last_name":"Petrova","full_name":"Petrova, Elena","first_name":"Elena"},{"first_name":"Norbert","full_name":"Schuch, Norbert","last_name":"Schuch"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"issue":"4","title":"Tangent space generators of matrix product states and exact floquet quantum scars","APC_amount":"3711,01 EUR","abstract":[{"lang":"eng","text":"The advancement of quantum simulators motivates the development of a theoretical framework to assist with efficient state preparation in quantum many-body systems. Generally, preparing a target entangled state via unitary evolution with time-dependent couplings is a challenging task and very little is known about the existence of solutions and their properties. In this work we develop a constructive approach for preparing matrix product states (MPS) via continuous unitary evolution. We provide an explicit construction of the operator that exactly implements the evolution of a given MPS along a specified direction in its tangent space. This operator can be written as a sum of local terms of finite range, yet it is in general non-Hermitian. Relying on the explicit construction of the non-Hermitian generator of the dynamics, we demonstrate the existence of a Hermitian sequence of operators that implements the desired MPS evolution with an error that decreases exponentially with the operator range. The construction is benchmarked on an explicit periodic trajectory in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary generating the dynamics over one period of the trajectory features an approximate MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results show that our construction is not only useful for state preparation and control of many-body systems, but also provides a generic route towards Floquet scars—periodically driven models with quasilocal generators of dynamics that have exact MPS eigenstates in their spectrum."}],"acknowledgement":"We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions. This research was funded in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1, 10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This work was performed in part at the Aspen Center for Physics, which is supported by National Science Foundation Grant PHY-2210452. This research was supported in part by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).","publication_status":"published","department":[{"_id":"MaSe"}],"file_date_updated":"2024-10-30T08:59:09Z","publisher":"American Physical Society","DOAJ_listed":"1","intvolume":"         5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-23T00:00:00Z","citation":{"short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).","chicago":"Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>.","mla":"Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>, vol. 5, no. 4, 040311, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>.","ista":"Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.","ieee":"M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators of matrix product states and exact floquet quantum scars,” <i>PRX Quantum</i>, vol. 5, no. 4. American Physical Society, 2024.","apa":"Ljubotina, M., Petrova, E., Schuch, N., &#38; Serbyn, M. (2024). Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>","ama":"Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>"},"article_number":"040311","arxiv":1,"ec_funded":1,"corr_author":"1","status":"public","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","project":[{"call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"scopus_import":"1","quality_controlled":"1","volume":5,"date_updated":"2025-09-08T14:26:29Z","date_created":"2024-10-29T16:04:05Z","month":"10","_id":"18488","oa_version":"Published Version","doi":"10.1103/prxquantum.5.040311"},{"department":[{"_id":"JaMa"}],"file_date_updated":"2024-11-04T08:54:26Z","publisher":"London Mathematical Society","intvolume":"       110","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. <i>Journal of the London Mathematical Society</i>. 2024;110(5). doi:<a href=\"https://doi.org/10.1112/jlms.70003\">10.1112/jlms.70003</a>","ieee":"L. Dello Schiavo, R. Herry, E. Kopfer, and K. T. Sturm, “Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension,” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 5. London Mathematical Society, 2024.","apa":"Dello Schiavo, L., Herry, R., Kopfer, E., &#38; Sturm, K. T. (2024). Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. <i>Journal of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/jlms.70003\">https://doi.org/10.1112/jlms.70003</a>","ista":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. 2024. Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. Journal of the London Mathematical Society. 110(5), e70003.","short":"L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Journal of the London Mathematical Society 110 (2024).","chicago":"Dello Schiavo, Lorenzo, Ronan Herry, Eva Kopfer, and Karl Theodor Sturm. “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” <i>Journal of the London Mathematical Society</i>. London Mathematical Society, 2024. <a href=\"https://doi.org/10.1112/jlms.70003\">https://doi.org/10.1112/jlms.70003</a>.","mla":"Dello Schiavo, Lorenzo, et al. “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 5, e70003, London Mathematical Society, 2024, doi:<a href=\"https://doi.org/10.1112/jlms.70003\">10.1112/jlms.70003</a>."},"date_published":"2024-11-01T00:00:00Z","article_number":"e70003","ec_funded":1,"status":"public","type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"scopus_import":"1","volume":110,"date_updated":"2025-09-08T14:29:45Z","date_created":"2024-11-03T23:01:44Z","quality_controlled":"1","_id":"18490","month":"11","oa_version":"Published Version","doi":"10.1112/jlms.70003","publication":"Journal of the London Mathematical Society","isi":1,"file":[{"file_name":"2024_JourLondonMathSoc_Schiavo.pdf","relation":"main_file","file_id":"18497","checksum":"143816823b5f43bd3748da8e3e91cef5","success":1,"creator":"dernst","file_size":911476,"date_updated":"2024-11-04T08:54:26Z","date_created":"2024-11-04T08:54:26Z","access_level":"open_access","content_type":"application/pdf"}],"publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"language":[{"iso":"eng"}],"external_id":{"isi":["001351918100029"]},"article_type":"original","year":"2024","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","OA_place":"publisher","oa":1,"ddc":["510"],"day":"01","author":[{"orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo"},{"last_name":"Herry","full_name":"Herry, Ronan","first_name":"Ronan"},{"last_name":"Kopfer","full_name":"Kopfer, Eva","first_name":"Eva"},{"first_name":"Karl Theodor","full_name":"Sturm, Karl Theodor","last_name":"Sturm"}],"issue":"5","title":"Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension","abstract":[{"lang":"eng","text":"For large classes of even-dimensional Riemannian manifolds (Formula presented.), we construct and analyze conformally invariant random fields. These centered Gaussian fields (Formula presented.), called co-polyharmonic Gaussian fields, are characterized by their covariance kernels k which exhibit a precise logarithmic divergence: (Formula presented.). They share a fundamental quasi-invariance property under conformal transformations. In terms of the co-polyharmonic Gaussian field (Formula presented.), we define the Liouville Quantum Gravity measure, a random measure on (Formula presented.), heuristically given as (Formula presented.) and rigorously obtained as almost sure weak limit of the right-hand side with (Formula presented.) replaced by suitable regular approximations (Formula presented.). In terms on the Liouville Quantum Gravity measure, we define the Liouville Brownian motion on (Formula presented.) and the random GJMS operators. Finally, we present an approach to a conformal field theory in arbitrary even dimension with an ansatz based on Branson's (Formula presented.) -curvature: we give a rigorous meaning to the Polyakov–Liouville measure (Formula presented.) and we derive the corresponding conformal anomaly. The set of admissible manifolds is conformally invariant. It includes all compact 2-dimensional Riemannian manifolds, all compact non-negatively curved Einstein manifolds of even dimension, and large classes of compact hyperbolic manifolds of even dimension. However, not every compact even-dimensional Riemannian manifold is admissible. Our results concerning the logarithmic divergence of the kernel (Formula presented.) rely on new sharp estimates for heat kernels and higher order Green kernels on arbitrary closed manifolds. "}],"acknowledgement":"The authors are grateful to Masha Gordina for helpful references, and to Nathanaël Berestycki, Baptiste Cerclé, and Ewain Gwynne for valuable comments on the first circulated version of this paper. They also would like to thank Sebastian Andres, Peter Friz, and Yizheng Yuan for pointing out an erroneous formulation in the previous version of Theorem 5.7. Moreover, KTS would liketo express his thanks to Sebastian Andres, Matthias Erbar, Martin Huesmann, and Jan Mass for stimulating discussions on previous attempts to this project. LDS gratefully acknowledges financial support from the European Research Council (grant agreement No 716117, awarded to J. Maas), from the Austrian Science Fund (FWF) project 10.55776/ESP208, and from the Austrian Science Fund (FWF) project 10.55776/F65.RH, EK, and KTS gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through the project “Random Riemannian Geometry” within the SPP 2265 “Random Geomet-ric Systems,” through the Hausdorff Center for Mathematics (project ID 390685813), and through project B03 within the CRC 1060 (project ID 211504053). RH and KTS also gratefully acknowledge financial support from the European Research Council through the ERC AdG “RicciBounds”(grant agreement 694405).Data sharing not applicable to this article as no datasets were generated or analyzed during the current study. Open access funding enabled and organized by Projekt DEAL.","publication_status":"published"},{"file_date_updated":"2024-11-04T09:35:49Z","department":[{"_id":"NiBa"}],"publisher":"AAAS","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        10","DOAJ_listed":"1","citation":{"ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. Science Advances. 10(41), eadp2102.","mla":"Garcia Castillo, Diego Fernando, et al. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” <i>Science Advances</i>, vol. 10, no. 41, eadp2102, AAAS, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adp2102\">10.1126/sciadv.adp2102</a>.","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, Science Advances 10 (2024).","chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” <i>Science Advances</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/sciadv.adp2102\">https://doi.org/10.1126/sciadv.adp2102</a>.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. <i>Science Advances</i>. 2024;10(41). doi:<a href=\"https://doi.org/10.1126/sciadv.adp2102\">10.1126/sciadv.adp2102</a>","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adp2102\">https://doi.org/10.1126/sciadv.adp2102</a>","ieee":"D. F. Garcia Castillo <i>et al.</i>, “Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails,” <i>Science Advances</i>, vol. 10, no. 41. AAAS, 2024."},"date_published":"2024-10-11T00:00:00Z","article_number":"eadp2102","corr_author":"1","status":"public","type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","related_material":{"link":[{"url":"https://github.com/fernandoGarcia21/littorina_saxatilis_skerry","relation":"software"}],"record":[{"relation":"research_data","id":"18498","status":"public"},{"status":"public","id":"20991","relation":"dissertation_contains"}]},"scopus_import":"1","project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"},{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"month":"10","_id":"18491","oa_version":"Published Version","date_updated":"2026-04-07T11:42:09Z","quality_controlled":"1","date_created":"2024-11-03T23:01:44Z","volume":10,"doi":"10.1126/sciadv.adp2102","publication":"Science Advances","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"file_size":1154107,"date_created":"2024-11-04T09:35:49Z","date_updated":"2024-11-04T09:35:49Z","checksum":"96aa0d3640fa9401975138e59054f84e","file_name":"2024_ScienceAdv_Castillo.pdf","relation":"main_file","file_id":"18499"}],"isi":1,"publication_identifier":{"eissn":["2375-2548"]},"external_id":{"isi":["001354405400018"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"original","OA_type":"gold","article_processing_charge":"Yes","OA_place":"publisher","oa":1,"author":[{"full_name":"Garcia Castillo, Diego Fernando","first_name":"Diego Fernando","last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Jenny","full_name":"Larsson, Jenny","last_name":"Larsson"},{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"}],"ddc":["570"],"day":"11","issue":"41","title":"Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails","abstract":[{"text":"Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations.","lang":"eng"}],"APC_amount":"4569,23 EUR","acknowledgement":"This work was received funding from the following: Norwegian Research Council RCN project 315287 (A.M.W.), Swedish Research Council 2021-04191 (K.J.), European Research Council grant 101055327 HaplotypeStructure (N.B.), Austrian Science Fund FWF; P 32166-B32 Snapdragon Speciation (N.B.), European Research Council (R.B.), and Portuguese Foundation for Science and Technology FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021 (R.F.).","publication_status":"published"},{"type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","scopus_import":"1","project":[{"_id":"bd9b2118-d553-11ed-ba76-db24564edfea","name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224"}],"month":"10","_id":"18494","oa_version":"Published Version","quality_controlled":"1","volume":974,"date_created":"2024-11-03T23:01:45Z","date_updated":"2025-09-08T14:29:05Z","doi":"10.3847/1538-4357/ad778b","file_date_updated":"2024-11-04T08:42:23Z","department":[{"_id":"JoMa"}],"publisher":"IOP Publishing","intvolume":"       974","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","DOAJ_listed":"1","citation":{"short":"A.C. Eilers, R. Mackenzie, E. Pizzati, J.J. Matthee, J.F. Hennawi, H. Zhang, R. Bordoloi, D. Kashino, S.J. Lilly, R.P. Naidu, R.A. Simcoe, M. Yue, C.S. Frenk, J.C. Helly, M. Schaller, J. Schaye, Astrophysical Journal 974 (2024).","chicago":"Eilers, Anna Christina, Ruari Mackenzie, Elia Pizzati, Jorryt J Matthee, Joseph F. Hennawi, Haowen Zhang, Rongmon Bordoloi, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” <i>Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad778b\">https://doi.org/10.3847/1538-4357/ad778b</a>.","mla":"Eilers, Anna Christina, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” <i>Astrophysical Journal</i>, vol. 974, no. 2, 275, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778b\">10.3847/1538-4357/ad778b</a>.","ista":"Eilers AC, Mackenzie R, Pizzati E, Matthee JJ, Hennawi JF, Zhang H, Bordoloi R, Kashino D, Lilly SJ, Naidu RP, Simcoe RA, Yue M, Frenk CS, Helly JC, Schaller M, Schaye J. 2024. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. 974(2), 275.","ieee":"A. C. Eilers <i>et al.</i>, “EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6,” <i>Astrophysical Journal</i>, vol. 974, no. 2. IOP Publishing, 2024.","apa":"Eilers, A. C., Mackenzie, R., Pizzati, E., Matthee, J. J., Hennawi, J. F., Zhang, H., … Schaye, J. (2024). EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad778b\">https://doi.org/10.3847/1538-4357/ad778b</a>","ama":"Eilers AC, Mackenzie R, Pizzati E, et al. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. <i>Astrophysical Journal</i>. 2024;974(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778b\">10.3847/1538-4357/ad778b</a>"},"date_published":"2024-10-01T00:00:00Z","article_number":"275","status":"public","OA_type":"gold","article_processing_charge":"Yes","oa":1,"OA_place":"publisher","author":[{"first_name":"Anna Christina","full_name":"Eilers, Anna Christina","last_name":"Eilers"},{"last_name":"Mackenzie","first_name":"Ruari","full_name":"Mackenzie, Ruari"},{"first_name":"Elia","full_name":"Pizzati, Elia","last_name":"Pizzati"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"first_name":"Joseph F.","full_name":"Hennawi, Joseph F.","last_name":"Hennawi"},{"first_name":"Haowen","full_name":"Zhang, Haowen","last_name":"Zhang"},{"last_name":"Bordoloi","first_name":"Rongmon","full_name":"Bordoloi, Rongmon"},{"first_name":"Daichi","full_name":"Kashino, Daichi","last_name":"Kashino"},{"last_name":"Lilly","full_name":"Lilly, Simon J.","first_name":"Simon J."},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"last_name":"Simcoe","full_name":"Simcoe, Robert A.","first_name":"Robert A."},{"last_name":"Yue","full_name":"Yue, Minghao","first_name":"Minghao"},{"full_name":"Frenk, Carlos S.","first_name":"Carlos S.","last_name":"Frenk"},{"last_name":"Helly","first_name":"John C.","full_name":"Helly, John C."},{"last_name":"Schaller","first_name":"Matthieu","full_name":"Schaller, Matthieu"},{"last_name":"Schaye","full_name":"Schaye, Joop","first_name":"Joop"}],"ddc":["520"],"day":"01","issue":"2","title":"EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6","abstract":[{"lang":"eng","text":"We expect luminous (M 1450 ≲ −26.5) high-redshift quasars to trace the highest-density peaks in the early Universe. Here, we present observations of four z ≳ 6 quasar fields using JWST/NIRCam in the imaging and wide-field slitless spectroscopy mode and report a wide range in the number of detected [O iii]-emitting galaxies in the quasars’ environments, ranging between a density enhancement of δ ≈ 65 within a 2 cMpc radius—one of the largest protoclusters during the Epoch of Reionization discovered to date—to a density contrast consistent with zero, indicating the presence of a UV-luminous quasar in a region comparable to the average density of the Universe. By measuring the two-point cross-correlation function of quasars and their surrounding galaxies, as well as the galaxy autocorrelation function, we infer a correlation length of quasars at 〈z〉 = 6.25 of r 0 QQ = 22.0 − 2.9 + 3.0 cMpc h − 1 , while we obtain a correlation length of the [O iii]-emitting galaxies of r 0 GG = 4.1 ± 0.3 cMpc h − 1 . By comparing the correlation functions to dark-matter-only simulations we estimate the minimum mass of the quasars’ host dark matter halos to be log 10 ( M halo , min / M ⊙ ) = 12.43 − 0.15 + 0.13 (and log 10 ( M halo , min [ OIII ] / M ⊙ ) = 10.56 − 0.03 + 0.05 for the [O iii] emitters), indicating that (a) luminous quasars do not necessarily reside within the most overdense regions in the early Universe, and that (b) the UV-luminous duty cycle of quasar activity at these redshifts is f duty ≪ 1. Such short quasar activity timescales challenge our understanding of early supermassive black hole growth and provide evidence for highly dust-obscured growth phases or episodic, radiatively inefficient accretion rates."}],"acknowledgement":"The authors would like to thank the anonymous referee for the thoughtful comments, which significantly improved our manuscript, and Jan-Torge Schindler, Jiamu Huang, and Feige Wang for helpful discussions.\r\n\r\nJ.F.H. and E.P. acknowledge support from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation program (grant agreement No. 885301). J.M. acknowledges support from the European Union (ERC, AGENTS, 101076224).\r\n\r\nThis work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The JWST data presented in this article were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The specific observations analyzed are associated with program #1243 and can be accessed via doi:10.17909/m5mp-5v90.\r\n\r\nThis work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Directors Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded DiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure.\r\n\r\nWe thank the Instituto de Astrofisica de Andalucia (IAA-CSIC), Centro de Supercomputacion de Galicia (CESGA), and Spanish Academic and Research Network (RedIRIS) in Spain for hosting Uchuu DR1, DR2, and DR3 in the Skies & Universes site for cosmological simulations. The Uchuu simulations were carried out on the Aterui II supercomputer at the Center for Computational Astrophysics, CfCA, of the National Astronomical Observatory of Japan, and the K computer at the RIKEN Advanced Institute for Computational Science. The Uchuu Data Releases efforts have made use of the skunIAA_RedIRIS and skun6IAA computer facilities managed by the IAA-CSIC in Spain (MICINN EU-Feder grant EQC2018-004366-P).","publication_status":"published","publication":"Astrophysical Journal","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":1042470,"date_created":"2024-11-04T08:42:23Z","date_updated":"2024-11-04T08:42:23Z","success":1,"creator":"dernst","checksum":"1fcac3d11d01d91cf2bb4963b6e10b22","relation":"main_file","file_id":"18496","file_name":"2024_AstrophysicalJour_Eilers.pdf"}],"isi":1,"publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"external_id":{"isi":["001338877100001"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"original"},{"publisher":"Zenodo","department":[{"_id":"NiBa"}],"year":"2024","corr_author":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Garcia Castillo, Diego Fernando, et al. <i>Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>.","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, (2024).","ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>","ieee":"D. F. Garcia Castillo <i>et al.</i>, “Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails.” Zenodo, 2024.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>"},"date_published":"2024-06-19T00:00:00Z","author":[{"last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Larsson","first_name":"Jenny","full_name":"Larsson, Jenny"},{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"}],"ddc":["570"],"day":"19","related_material":{"record":[{"status":"public","id":"20991","relation":"used_in_publication"},{"id":"18491","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","article_processing_charge":"No","OA_place":"repository","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"has_accepted_license":"1","doi":"10.5281/ZENODO.12159343","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.12159344","open_access":"1"}],"title":"Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails","_id":"18498","oa_version":"Published Version","month":"06","abstract":[{"text":"Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715","lang":"eng"}],"date_created":"2024-11-04T09:33:17Z","date_updated":"2026-04-16T12:20:37Z"},{"conference":{"start_date":"2024-01-07","location":"Alexandria, VA,  United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2024-01-10"},"type":"conference","date_updated":"2025-06-24T12:09:26Z","quality_controlled":"1","date_created":"2024-11-04T10:54:21Z","oa_version":"Preprint","_id":"18503","month":"01","project":[{"call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures"},{"grant_number":"Z00422","name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2401.05627"}],"doi":"10.1137/1.9781611977912.111","department":[{"_id":"MoHe"}],"publisher":"Society for Industrial and Applied Mathematics","date_published":"2024-01-04T00:00:00Z","citation":{"ieee":"M. Henzinger, J. Li, S. Rao, and D. Wang, “Deterministic near-linear time minimum cut in weighted graphs,” in <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Alexandria, VA,  United States, 2024, pp. 3089–3139.","apa":"Henzinger, M., Li, J., Rao, S., &#38; Wang, D. (2024). Deterministic near-linear time minimum cut in weighted graphs. In <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 3089–3139). Alexandria, VA,  United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977912.111\">https://doi.org/10.1137/1.9781611977912.111</a>","ama":"Henzinger M, Li J, Rao S, Wang D. Deterministic near-linear time minimum cut in weighted graphs. In: <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2024:3089-3139. doi:<a href=\"https://doi.org/10.1137/1.9781611977912.111\">10.1137/1.9781611977912.111</a>","short":"M. Henzinger, J. Li, S. Rao, D. Wang, in:, 35th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 3089–3139.","chicago":"Henzinger, Monika, Jason Li, Satish Rao, and Di Wang. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” In <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 3089–3139. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/1.9781611977912.111\">https://doi.org/10.1137/1.9781611977912.111</a>.","mla":"Henzinger, Monika, et al. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2024, pp. 3089–139, doi:<a href=\"https://doi.org/10.1137/1.9781611977912.111\">10.1137/1.9781611977912.111</a>.","ista":"Henzinger M, Li J, Rao S, Wang D. 2024. Deterministic near-linear time minimum cut in weighted graphs. 35th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 3089–3139."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"corr_author":"1","status":"public","arxiv":1,"OA_place":"repository","oa":1,"article_processing_charge":"No","OA_type":"free access","day":"04","author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"last_name":"Li","first_name":"Jason","full_name":"Li, Jason"},{"first_name":"Satish","full_name":"Rao, Satish","last_name":"Rao"},{"first_name":"Di","full_name":"Wang, Di","last_name":"Wang"}],"abstract":[{"lang":"eng","text":"In 1996, Karger [Kar96] gave a startling randomized algorithm that finds a minimum-cut in a (weighted) graph in time O(m log3 n) which he termed near-linear time meaning linear (in the size of the input) times a polylogarthmic factor. In this paper, we give the first deterministic algorithm which runs in near-linear time for weighted graphs.\r\nPreviously, the breakthrough results of Kawarabayashi and Thorup [KT19] gave a near-linear time algorithm for simple graphs (which was improved to have running time O(m log2 n log log n) in [HRW20].) The main technique here is a clustering procedure that perfectly preserves minimum cuts. Recently, Li [Li21] gave an m1+o(1) deterministic minimum-cut algorithm for weighted graphs; this form of running time has been termed “almost-linear”. Li uses almost-linear time deterministic expander decompositions which do not perfectly preserve minimum cuts, but he can use these clusterings to, in a sense, “derandomize” the methods of Karger.\r\nIn terms of techniques, we provide a structural theorem that says there exists a sparse clustering that preserves minimum cuts in a weighted graph with o(1) error. In addition, we construct it deterministically in near linear time. This was done exactly for simple graphs in [KT19, HRW20] and with polylogarithmic error for weighted graphs in [Li21]. Extending the techniques in [KT19, HRW20] to weighted graphs presents significant challenges, and moreover, the algorithm can only polylogarithmically approximately preserve minimum cuts. A remaining challenge is to reduce the polylogarithmic-approximate clusterings to 1 + o(1/ log n)-approximate so that they can be applied recursively as in [Li21] over O(log n) many levels. This is an additional challenge that requires building on properties of tree-packings in the presence of a wide range of edge weights to, for example, find sources for local flow computations which identify minimum cuts that cross clusters."}],"title":"Deterministic near-linear time minimum cut in weighted graphs","page":"3089-3139","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDyn-Struct)” and the Austrian Science Fund (FWF) project Z 422-N, project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","publication":"35th Annual ACM-SIAM Symposium on Discrete Algorithms","publication_identifier":{"eisbn":["9781611977912"]},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2401.05627"]},"year":"2024"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2024-11-07T10:59:42Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","corr_author":"1","status":"public","alternative_title":["ISTA Thesis"],"date_published":"2024-11-07T00:00:00Z","citation":{"chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","doi":"10.15479/at:ista:18515","date_updated":"2026-04-07T12:56:52Z","date_created":"2024-11-06T21:25:37Z","month":"11","_id":"18515","oa_version":"Published Version","project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"creator":"psurendr","success":1,"file_size":37019760,"date_updated":"2024-11-07T10:59:29Z","date_created":"2024-11-07T10:59:29Z","access_level":"open_access","content_type":"application/pdf","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","relation":"main_file","file_id":"18519","checksum":"c32cf7bc75748d9c551d8eb70178bbec"},{"checksum":"4417e02d54084d89e75734e18caaa96d","file_name":"PhD Thesis- Parvathy_071124.zip","relation":"source_file","file_id":"18520","access_level":"closed","content_type":"application/zip","creator":"psurendr","date_created":"2024-11-07T10:59:42Z","file_size":41198857,"date_updated":"2024-11-07T10:59:42Z"}],"year":"2024","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"ddc":["576"],"day":"07","author":[{"first_name":"Parvathy","full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"OA_place":"publisher","degree_awarded":"PhD","article_processing_charge":"No","OA_type":"gold","page":"219","publication_status":"published","acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","abstract":[{"text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations.","lang":"eng"}],"title":"Effect of population structure on neutral genetic variation and barriers to gene exchange"},{"file_date_updated":"2024-11-11T09:42:28Z","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     15191","date_published":"2024-10-12T00:00:00Z","citation":{"mla":"Bonakdarpour, Borzoo, et al. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” <i>24th International Conference on Runtime Verification</i>, vol. 15191, Springer Nature, 2024, pp. 282–301, doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>.","short":"B. Bonakdarpour, A. Momtaz, D. Nickovic, N.E. Sarac, in:, 24th International Conference on Runtime Verification, Springer Nature, 2024, pp. 282–301.","chicago":"Bonakdarpour, Borzoo, Anik Momtaz, Dejan Nickovic, and Naci E Sarac. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” In <i>24th International Conference on Runtime Verification</i>, 15191:282–301. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>.","ista":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. 2024. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. 24th International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 15191, 282–301.","apa":"Bonakdarpour, B., Momtaz, A., Nickovic, D., &#38; Sarac, N. E. (2024). Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In <i>24th International Conference on Runtime Verification</i> (Vol. 15191, pp. 282–301). Istanbul, Turkey: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>","ieee":"B. Bonakdarpour, A. Momtaz, D. Nickovic, and N. E. Sarac, “Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy,” in <i>24th International Conference on Runtime Verification</i>, Istanbul, Turkey, 2024, vol. 15191, pp. 282–301.","ama":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In: <i>24th International Conference on Runtime Verification</i>. Vol 15191. Springer Nature; 2024:282-301. doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>"},"arxiv":1,"alternative_title":["LNCS"],"status":"public","corr_author":"1","ec_funded":1,"type":"conference","conference":{"location":"Istanbul, Turkey","name":"RV: Conference on Runtime Verification","end_date":"2024-10-17","start_date":"2024-10-15"},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","project":[{"name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020"}],"_id":"18521","oa_version":"Published Version","month":"10","quality_controlled":"1","date_updated":"2026-05-20T08:43:20Z","volume":15191,"date_created":"2024-11-10T23:01:58Z","doi":"10.1007/978-3-031-74234-7_18","publication":"24th International Conference on Runtime Verification","file":[{"file_id":"18539","relation":"main_file","file_name":"2024_LNCS_Bonakdarpour.pdf","checksum":"7b8ca21b8c19ab796fa445b0e54003ca","date_updated":"2024-11-11T09:42:28Z","file_size":1897101,"date_created":"2024-11-11T09:42:28Z","creator":"dernst","success":1,"content_type":"application/pdf","access_level":"open_access"}],"isi":1,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031742330"]},"external_id":{"arxiv":["2408.05033"],"isi":["001420093700018"]},"language":[{"iso":"eng"}],"year":"2024","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","oa":1,"OA_place":"publisher","author":[{"last_name":"Bonakdarpour","full_name":"Bonakdarpour, Borzoo","first_name":"Borzoo"},{"full_name":"Momtaz, Anik","first_name":"Anik","last_name":"Momtaz"},{"last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"first_name":"Naci E","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"ddc":["000"],"day":"12","title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","abstract":[{"lang":"eng","text":"In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples."}],"APC_amount":"2748 EUR","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. This work is sponsored in part by the United States NSF CCF-2118356 award. This research was partially funded by A-IQ Ready (Chips JU, grant agreement No. 101096658).","publication_status":"published","page":"282-301"},{"external_id":{"isi":["001335663900008"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"original","publication":"Monthly Notices of the Royal Astronomical Society","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"file":[{"file_id":"18542","relation":"main_file","file_name":"2024_MonthlyNRoyalAstronSoc_Pizzati.pdf","checksum":"9ea6285dd1d04d7a9e7b40a4c9e11edb","file_size":2954312,"date_updated":"2024-11-12T07:17:26Z","date_created":"2024-11-12T07:17:26Z","success":1,"creator":"dernst","content_type":"application/pdf","access_level":"open_access"}],"isi":1,"abstract":[{"lang":"eng","text":"Recent observations from the EIGER JWST program have measured for the first time the quasar–galaxy cross-correlation function at z ≈ 6. The autocorrelation function of faint z ≈ 6 quasars was also recently estimated. These measurements provide key insights into the properties of quasars and galaxies at high redshift and their relation with the host dark matter haloes. In this work, we interpret these data building upon an empirical quasar population model that has been applied successfully to quasar clustering and demographic measurements at z ≈ 2–4. We use a new, large-volume N-body simulation with more than a trillion particles, FLAMINGO-10k, to model quasars and galaxies simultaneously. We successfully reproduce observations of z ≈ 6 quasars and galaxies (i.e. their clustering properties and luminosity functions), and infer key quantities such as their luminosity–halo mass relation, the mass function of their host haloes, and their duty cycle/occupation fraction. Our key findings\r\nare (i) quasars reside on average in ≈ 1012.5 M haloes (corresponding to ≈ 5σ fluctuations in the initial conditions of the linear density field), but the distribution of host halo masses is quite broad; (ii) the duty cycle of (UV-bright) quasar activity is relatively low (≈ 1 per cent); (iii) galaxies (that are bright in [O III]) live in much smaller haloes (≈ 1010.9 M) and have a larger duty cycle (occupation fraction) of ≈ 13 per cent. Finally, we focus on the inferred properties of quasars and present a homogeneous analysis of their evolution with redshift. The picture that emerges reveals a strong evolution of the host halo mass and duty cycle of quasars at z ≈ 2–6, and calls for new investigations of the role of quasar activity across cosmic time."}],"title":"A unified model for the clustering of quasars and galaxies at z ≈ 6","publication_status":"published","page":"3155-3175","acknowledgement":"We are grateful to Junya Arita and the SHELLQs team for sharing their data on the quasar autocorrelation function and to Jan-Torge Schindler for discussion on the QLF. We acknowledge helpful conversations with the ENIGMA group at UC Santa Barbara and Leiden University. EP is grateful to Rob McGibbon and Victor Forouhar Moreno for help with the simulation outputs, and to Timo Kist, Jiamu Huang, and Vikram Khaire for comments on an early version of the manuscript. JFH and EP acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 885301). This work is partly supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 860744 (BiD4BESt). FW acknowledges support from NSF grant AST-2308258. This work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Director’s Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded\r\nDiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University, and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure.","oa":1,"OA_place":"publisher","OA_type":"gold","article_processing_charge":"Yes","issue":"4","author":[{"last_name":"Pizzati","full_name":"Pizzati, Elia","first_name":"Elia"},{"first_name":"Joseph F.","full_name":"Hennawi, Joseph F.","last_name":"Hennawi"},{"full_name":"Schaye, Joop","first_name":"Joop","last_name":"Schaye"},{"full_name":"Schaller, Matthieu","first_name":"Matthieu","last_name":"Schaller"},{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"first_name":"Feige","full_name":"Wang, Feige","last_name":"Wang"},{"last_name":"Frenk","first_name":"Carlos S.","full_name":"Frenk, Carlos S."},{"first_name":"Willem","full_name":"Elbers, Willem","last_name":"Elbers"},{"first_name":"John C.","full_name":"Helly, John C.","last_name":"Helly"},{"last_name":"Mackenzie","first_name":"Ruari","full_name":"Mackenzie, Ruari"},{"first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"full_name":"Bordoloi, Rongmon","first_name":"Rongmon","last_name":"Bordoloi"},{"first_name":"Daichi","full_name":"Kashino, Daichi","last_name":"Kashino"},{"last_name":"Naidu","first_name":"Rohan P.","full_name":"Naidu, Rohan P."},{"full_name":"Yue, Minghao","first_name":"Minghao","last_name":"Yue"}],"day":"01","ddc":["520"],"citation":{"ista":"Pizzati E, Hennawi JF, Schaye J, Schaller M, Eilers AC, Wang F, Frenk CS, Elbers W, Helly JC, Mackenzie R, Matthee JJ, Bordoloi R, Kashino D, Naidu RP, Yue M. 2024. A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. 534(4), 3155–3175.","mla":"Pizzati, Elia, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 4, Oxford University Press, 2024, pp. 3155–75, doi:<a href=\"https://doi.org/10.1093/mnras/stae2307\">10.1093/mnras/stae2307</a>.","chicago":"Pizzati, Elia, Joseph F. Hennawi, Joop Schaye, Matthieu Schaller, Anna Christina Eilers, Feige Wang, Carlos S. Frenk, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stae2307\">https://doi.org/10.1093/mnras/stae2307</a>.","short":"E. Pizzati, J.F. Hennawi, J. Schaye, M. Schaller, A.C. Eilers, F. Wang, C.S. Frenk, W. Elbers, J.C. Helly, R. Mackenzie, J.J. Matthee, R. Bordoloi, D. Kashino, R.P. Naidu, M. Yue, Monthly Notices of the Royal Astronomical Society 534 (2024) 3155–3175.","ama":"Pizzati E, Hennawi JF, Schaye J, et al. A unified model for the clustering of quasars and galaxies at z ≈ 6. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;534(4):3155-3175. doi:<a href=\"https://doi.org/10.1093/mnras/stae2307\">10.1093/mnras/stae2307</a>","apa":"Pizzati, E., Hennawi, J. F., Schaye, J., Schaller, M., Eilers, A. C., Wang, F., … Yue, M. (2024). A unified model for the clustering of quasars and galaxies at z ≈ 6. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stae2307\">https://doi.org/10.1093/mnras/stae2307</a>","ieee":"E. Pizzati <i>et al.</i>, “A unified model for the clustering of quasars and galaxies at z ≈ 6,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 4. Oxford University Press, pp. 3155–3175, 2024."},"date_published":"2024-11-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       534","DOAJ_listed":"1","status":"public","file_date_updated":"2024-11-12T07:17:26Z","department":[{"_id":"JoMa"}],"publisher":"Oxford University Press","_id":"18523","oa_version":"Published Version","month":"11","date_created":"2024-11-10T23:01:58Z","volume":534,"date_updated":"2025-09-08T14:40:22Z","quality_controlled":"1","scopus_import":"1","doi":"10.1093/mnras/stae2307","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article"},{"isi":1,"file":[{"access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"date_created":"2024-11-11T09:20:45Z","file_size":34634395,"date_updated":"2024-11-11T09:20:45Z","checksum":"0e9bb88b5048ecc782ac27953c84b8ce","file_name":"2024_AstrophysicalJour_Grady.pdf","relation":"main_file","file_id":"18535"}],"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"publication":"Astrophysical Journal","article_type":"original","year":"2024","language":[{"iso":"eng"}],"external_id":{"arxiv":["2406.17177"],"isi":["001339486900001"]},"day":"01","ddc":["520"],"author":[{"first_name":"Anna J.G.","full_name":"O’Grady, Anna J.G.","last_name":"O’Grady"},{"first_name":"Maria R.","full_name":"Drout, Maria R.","last_name":"Drout"},{"last_name":"Neugent","first_name":"Kathryn F.","full_name":"Neugent, Kathryn F."},{"last_name":"Ludwig","first_name":"Bethany","full_name":"Ludwig, Bethany"},{"full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","last_name":"Götberg","orcid":"0000-0002-6960-6911"},{"full_name":"Gaensler, B. M.","first_name":"B. M.","last_name":"Gaensler"}],"article_processing_charge":"No","OA_type":"gold","oa":1,"OA_place":"publisher","acknowledgement":"The authors thank Aaron Tohuvavohu, Katie Breivik, Marten van Kerkwijk, Jakub Klencki, Eva Laplace, and Dae-Sik Moon for helpful discussions, and Adiv Paradise for helpful edits. The authors also thank the anonymous reviewer for a helpful and constructive referee report.\r\nThe authors at the University of Toronto acknowledge that the land on which the University of Toronto operates is the traditional territory of the Huron–Wendat, the Seneca, and the Mississaugas of the Credit River. They are grateful to have the opportunity to work on this land.\r\nThe Dunlap Institute is funded through an endowment established by the David Dunlap family and the University of Toronto.\r\nA.J.G.O. is supported by a McWilliams Fellowship at Carnegie Mellon University. M.R.D. acknowledges support from the NSERC through grant RGPIN-2019-06186, the Canada Research Chairs Program, and the Dunlap Institute at the University of Toronto. B.M.G. acknowledges the support of the Natural Sciences and Engineering Research Council of Canada (NSERC) through grant RGPIN-2022-03163, and of the Canada Research Chairs program. Support for this work was provided by NASA through the NASA Hubble Fellowship Program grant Nos. HST-HF2-51457.001-A and HST-HF2-51516 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555.\r\nThis research has made use of the SIMBAD database (M. Wenger et al. 2000), operated at CDS, Strasbourg, France, and the SVO Filter Profile Service 13 supported by the Spanish MINECO through grant AYA2017-84089 (C. Rodrigo et al. 2012, 2020).\r\nThis research has made use of the following software: astropy (Astropy Collaboration et al. 2013, 2018, 2022), IRAF (D. Tody 1986, 1993), and TOPCAT (M. B. Taylor 2005).","publication_status":"published","title":"Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification","abstract":[{"lang":"eng","text":"Recent works have constrained the binary fraction of evolved populations of massive stars in local galaxies such as red supergiants and Wolf–Rayet stars, but the binary fraction of yellow supergiants (YSGs) in the Hertzsprung gap remains unconstrained. Binary evolution theory predicts that the Hertzsprung gap is home to multiple populations of binary systems with varied evolutionary histories. In this paper, we develop a method to distinguish single YSGs from YSG plus O- or B-type main-sequence binaries using optical and ultraviolet photometry, and then apply this method to identify candidate YSG binaries in the Magellanic Clouds. After constructing a set of combined stellar atmosphere models, we find that optical photometry is, given typical measurement and reddening uncertainties, sufficient to discern single YSGs from YSG+OB binaries if the OB-star is at least ∼5M⊙ for Teff,YSG ∼ 4000 K, but requires a ∼20M⊙ OB star for YSGs up to Teff,YSG ∼ 9000 K. For these hotter YSG temperatures, ultraviolet photometry allows binaries with OB companions as small as ∼7M⊙ to be identified. We use color–color spaces developed from these models to search for evidence of excess blue or ultraviolet light in a set of ∼1000 YSG candidates in the Magellanic Clouds. We identify hundreds of candidate YSG binary systems and report a preliminary fraction of YSGs that show a blue/UV color excess of 20%–60%. Spectroscopic follow-up is now required to confirm the true nature of this population."}],"publisher":"IOP Publishing","department":[{"_id":"YlGo"}],"file_date_updated":"2024-11-11T09:20:45Z","article_number":"29","arxiv":1,"status":"public","DOAJ_listed":"1","intvolume":"       975","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-11-01T00:00:00Z","citation":{"ama":"O’Grady AJG, Drout MR, Neugent KF, Ludwig B, Götberg YLL, Gaensler BM. Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification. <i>Astrophysical Journal</i>. 2024;975. doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778a\">10.3847/1538-4357/ad778a</a>","ieee":"A. J. G. O’Grady, M. R. Drout, K. F. Neugent, B. Ludwig, Y. L. L. Götberg, and B. M. Gaensler, “Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification,” <i>Astrophysical Journal</i>, vol. 975. IOP Publishing, 2024.","apa":"O’Grady, A. J. G., Drout, M. R., Neugent, K. F., Ludwig, B., Götberg, Y. L. L., &#38; Gaensler, B. M. (2024). Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad778a\">https://doi.org/10.3847/1538-4357/ad778a</a>","ista":"O’Grady AJG, Drout MR, Neugent KF, Ludwig B, Götberg YLL, Gaensler BM. 2024. Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification. Astrophysical Journal. 975, 29.","chicago":"O’Grady, Anna J.G., Maria R. Drout, Kathryn F. Neugent, Bethany Ludwig, Ylva Louise Linsdotter Götberg, and B. M. Gaensler. “Binary Yellow Supergiants in the Magellanic Clouds. I. Photometric Candidate Identification.” <i>Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad778a\">https://doi.org/10.3847/1538-4357/ad778a</a>.","short":"A.J.G. O’Grady, M.R. Drout, K.F. Neugent, B. Ludwig, Y.L.L. Götberg, B.M. Gaensler, Astrophysical Journal 975 (2024).","mla":"O’Grady, Anna J. G., et al. “Binary Yellow Supergiants in the Magellanic Clouds. I. Photometric Candidate Identification.” <i>Astrophysical Journal</i>, vol. 975, 29, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778a\">10.3847/1538-4357/ad778a</a>."},"type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","doi":"10.3847/1538-4357/ad778a","scopus_import":"1","volume":975,"date_created":"2024-11-10T23:01:59Z","date_updated":"2025-09-08T14:37:18Z","quality_controlled":"1","_id":"18524","month":"11","oa_version":"Published Version"},{"file":[{"file_id":"18536","relation":"main_file","file_name":"2024_PNAS_Ruzickova.pdf","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","file_size":25529709,"date_updated":"2024-11-11T09:31:00Z","date_created":"2024-11-11T09:31:00Z","creator":"dernst","success":1,"content_type":"application/pdf","access_level":"open_access"}],"isi":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2024","article_type":"original","external_id":{"pmid":["39441639"],"isi":["001349462600001"]},"pmid":1,"language":[{"iso":"eng"}],"author":[{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","full_name":"Ruzickova, Natalia","first_name":"Natalia"},{"last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","first_name":"Michal"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"day":"29","ddc":["570"],"issue":"44","OA_type":"hybrid","article_processing_charge":"Yes","oa":1,"OA_place":"publisher","acknowledgement":"N.R.acknowledges the support of the Austrian Academy of Sciences through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences 26917. M.H. and G.T. were supported in part by the Human Frontiers Science Program Grant RGP0034/2018. We thank Nicholas H. Barton, Fyodor Kondrashov, and Matthew R. Robinson for fruitful discussions.","publication_status":"published","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","abstract":[{"lang":"eng","text":"As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects."}],"APC_amount":"3062,93 EUR","publisher":"National Academy of Sciences","file_date_updated":"2024-11-11T09:31:00Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"article_number":"e2402340121","status":"public","corr_author":"1","intvolume":"       121","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-29T00:00:00Z","citation":{"chicago":"Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>.","short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>.","ista":"Ruzickova N, Hledik M, Tkačik G. 2024. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2402340121.","ieee":"N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","apa":"Ruzickova, N., Hledik, M., &#38; Tkačik, G. (2024). Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>","ama":"Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>"},"related_material":{"record":[{"id":"20357","relation":"dissertation_contains","status":"public"}]},"type":"journal_article","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.1073/pnas.2402340121","scopus_import":"1","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"oa_version":"Published Version","_id":"18525","month":"10","quality_controlled":"1","date_updated":"2026-04-07T12:02:39Z","volume":121,"date_created":"2024-11-10T23:01:59Z"},{"status":"public","ec_funded":1,"article_number":"e2409407121","date_published":"2024-10-29T00:00:00Z","citation":{"ista":"Weiner E, Berryman E, Frey FF, Solís AG, Leier A, Lago TM, Šarić A, Otegui MS. 2024. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2409407121.","mla":"Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>.","chicago":"Weiner, Ethan, Elizabeth Berryman, Felix F Frey, Ariadna González Solís, André Leier, Tatiana Marquez Lago, Anđela Šarić, and Marisa S. Otegui. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>.","short":"E. Weiner, E. Berryman, F.F. Frey, A.G. Solís, A. Leier, T.M. Lago, A. Šarić, M.S. Otegui, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in plants. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>","apa":"Weiner, E., Berryman, E., Frey, F. F., Solís, A. G., Leier, A., Lago, T. M., … Otegui, M. S. (2024). Endosomal membrane budding patterns in plants. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>","ieee":"E. Weiner <i>et al.</i>, “Endosomal membrane budding patterns in plants,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024."},"intvolume":"       121","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"National Academy of Sciences","file_date_updated":"2024-11-11T09:35:15Z","department":[{"_id":"AnSa"}],"doi":"10.1073/pnas.2409407121","month":"10","_id":"18526","oa_version":"Published Version","date_updated":"2025-09-08T14:38:35Z","date_created":"2024-11-10T23:01:59Z","volume":121,"quality_controlled":"1","scopus_import":"1","project":[{"grant_number":"802960","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"has_accepted_license":"1","type":"journal_article","year":"2024","article_type":"original","external_id":{"isi":["001349500800007"],"pmid":["39441629"]},"pmid":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"file":[{"date_updated":"2024-11-11T09:35:15Z","file_size":5268074,"date_created":"2024-11-11T09:35:15Z","creator":"dernst","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"18538","relation":"main_file","file_name":"2024_PNAS_Weiner.pdf","checksum":"21c82d2ab58ff99b2bd0489797be42e5"}],"isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_status":"published","acknowledgement":"We would like to thank Janice Pennington for her support with electron tomography data collection, Dr. Ingrid Jordon-Thaden, director of the Botany Garden and Greenhouse of University of Wisconsin Madison, for her invaluable assistance collecting plant materials, Dr. Marie Trest for providing Chara specimens, and Dr. Nicholas Keuler for his advice on statistical analyses. We thank Charlie Hamilton for exploring the initial computational model. This work was supported by grant NSF MCB 2114603 and NIH 1S10OD026769-01 to M.S.O. F.F acknowledges support as a NOMIS Fellow from the NOMIS Foundation. A.Š. acknowledges ERC Starting Grant “NEPA” 802960.","abstract":[{"lang":"eng","text":"Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets."}],"title":"Endosomal membrane budding patterns in plants","issue":"44","author":[{"last_name":"Weiner","full_name":"Weiner, Ethan","first_name":"Ethan"},{"last_name":"Berryman","first_name":"Elizabeth","full_name":"Berryman, Elizabeth"},{"first_name":"Felix F","full_name":"Frey, Felix F","orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","last_name":"Frey"},{"full_name":"Solís, Ariadna González","first_name":"Ariadna González","last_name":"Solís"},{"last_name":"Leier","first_name":"André","full_name":"Leier, André"},{"last_name":"Lago","first_name":"Tatiana Marquez","full_name":"Lago, Tatiana Marquez"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"first_name":"Marisa S.","full_name":"Otegui, Marisa S.","last_name":"Otegui"}],"day":"29","ddc":["570"],"OA_place":"publisher","oa":1,"OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)"},{"language":[{"iso":"eng"}],"pmid":1,"external_id":{"pmid":["39547223"],"isi":["001395711300001"]},"article_type":"original","year":"2024","publication":"Molecular Cell","publication_identifier":{"issn":["1097-2765"]},"isi":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_size":25071994,"date_updated":"2025-01-13T11:17:35Z","date_created":"2025-01-13T11:17:35Z","success":1,"creator":"dernst","checksum":"e051e2766b2d424983778f742cb7c5ed","relation":"main_file","file_id":"18844","file_name":"2024_MolecularCell_Ramadhin.pdf"}],"abstract":[{"text":"Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component.","lang":"eng"}],"title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","page":"4740-4757.e12","publication_status":"published","acknowledgement":"We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF) and the Preclinical Facility (PCF). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer Institute is supported by institutional grants of the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI (VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for Scientific Research.","OA_place":"publisher","oa":1,"article_processing_charge":"No","OA_type":"hybrid","issue":"24","ddc":["570"],"day":"19","author":[{"first_name":"Anisha R.","full_name":"Ramadhin, Anisha R.","last_name":"Ramadhin"},{"first_name":"Shun-Hsiao","full_name":"Lee, Shun-Hsiao","last_name":"Lee"},{"full_name":"Zhou, Di","first_name":"Di","last_name":"Zhou"},{"first_name":"Anita P","full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo"},{"first_name":"Camila","full_name":"Gonzalo-Hansen, Camila","last_name":"Gonzalo-Hansen"},{"last_name":"van Sluis","full_name":"van Sluis, Marjolein","first_name":"Marjolein"},{"full_name":"Blom, Cindy M.A.","first_name":"Cindy M.A.","last_name":"Blom"},{"full_name":"Janssens, Roel C.","first_name":"Roel C.","last_name":"Janssens"},{"last_name":"Raams","full_name":"Raams, Anja","first_name":"Anja"},{"first_name":"Dick","full_name":"Dekkers, Dick","last_name":"Dekkers"},{"full_name":"Bezstarosti, Karel","first_name":"Karel","last_name":"Bezstarosti"},{"full_name":"Slade, Dea","first_name":"Dea","last_name":"Slade"},{"first_name":"Wim","full_name":"Vermeulen, Wim","last_name":"Vermeulen"},{"last_name":"Pines","first_name":"Alex","full_name":"Pines, Alex"},{"first_name":"Jeroen A.A.","full_name":"Demmers, Jeroen A.A.","last_name":"Demmers"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A"},{"last_name":"Sixma","first_name":"Titia K.","full_name":"Sixma, Titia K."},{"first_name":"Jurgen A.","full_name":"Marteijn, Jurgen A.","last_name":"Marteijn"}],"citation":{"ista":"Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 4740–4757.e12.","chicago":"Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>.","short":"A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen, M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti, D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A. Marteijn, Molecular Cell 84 (2024) 4740–4757.e12.","mla":"Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>.","ama":"Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. 2024;84(24):4740-4757.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>","ieee":"A. R. Ramadhin <i>et al.</i>, “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” <i>Molecular Cell</i>, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024.","apa":"Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen, C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>"},"date_published":"2024-12-19T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        84","status":"public","department":[{"_id":"CaBe"}],"file_date_updated":"2025-01-13T11:17:35Z","publisher":"Elsevier","volume":84,"date_created":"2024-11-15T12:12:54Z","quality_controlled":"1","date_updated":"2025-09-08T14:42:50Z","_id":"18553","month":"12","oa_version":"Published Version","scopus_import":"1","doi":"10.1016/j.molcel.2024.10.030","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article"},{"scopus_import":"1","date_updated":"2026-04-07T12:32:19Z","quality_controlled":"1","volume":405,"date_created":"2024-11-17T23:01:46Z","_id":"18554","oa_version":"Published Version","month":"12","doi":"10.1007/s00220-024-05143-y","type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20575"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       405","date_published":"2024-12-01T00:00:00Z","citation":{"apa":"Erdös, L., &#38; Riabov, V. (2024). Eigenstate Thermalization Hypothesis for Wigner-type matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-024-05143-y\">https://doi.org/10.1007/s00220-024-05143-y</a>","ieee":"L. Erdös and V. Riabov, “Eigenstate Thermalization Hypothesis for Wigner-type matrices,” <i>Communications in Mathematical Physics</i>, vol. 405, no. 12. Springer Nature, 2024.","ama":"Erdös L, Riabov V. Eigenstate Thermalization Hypothesis for Wigner-type matrices. <i>Communications in Mathematical Physics</i>. 2024;405(12). doi:<a href=\"https://doi.org/10.1007/s00220-024-05143-y\">10.1007/s00220-024-05143-y</a>","mla":"Erdös, László, and Volodymyr Riabov. “Eigenstate Thermalization Hypothesis for Wigner-Type Matrices.” <i>Communications in Mathematical Physics</i>, vol. 405, no. 12, 282, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00220-024-05143-y\">10.1007/s00220-024-05143-y</a>.","short":"L. Erdös, V. Riabov, Communications in Mathematical Physics 405 (2024).","chicago":"Erdös, László, and Volodymyr Riabov. “Eigenstate Thermalization Hypothesis for Wigner-Type Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00220-024-05143-y\">https://doi.org/10.1007/s00220-024-05143-y</a>.","ista":"Erdös L, Riabov V. 2024. Eigenstate Thermalization Hypothesis for Wigner-type matrices. Communications in Mathematical Physics. 405(12), 282."},"arxiv":1,"article_number":"282","corr_author":"1","status":"public","department":[{"_id":"LaEr"}],"file_date_updated":"2024-11-18T08:15:07Z","publisher":"Springer Nature","title":"Eigenstate Thermalization Hypothesis for Wigner-type matrices","abstract":[{"text":"We prove the Eigenstate Thermalization Hypothesis for general Wigner-type matrices in the bulk of the self-consistent spectrum, with optimal control on the fluctuations for obs ervables of arbitrary rank. As the main technical ingredient, we prove rank-uniform optimal local laws for one and two resolvents of a Wigner-type matrix with regular observables. Our results hold under very general conditions on the variance profile, even allowing many vanishing entries, demonstrating that Eigenstate Thermalization occurs robustly across a diverse class of random matrix ensembles, for which the underlying quantum system has a non-trivial spatial structure.","lang":"eng"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"published","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","OA_place":"publisher","oa":1,"ddc":["510"],"day":"01","author":[{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László"},{"first_name":"Volodymyr","full_name":"Riabov, Volodymyr","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","last_name":"Riabov"}],"issue":"12","language":[{"iso":"eng"}],"external_id":{"arxiv":["2403.10359"],"isi":["001348943900004"],"pmid":["39526190"]},"pmid":1,"article_type":"original","year":"2024","publication":"Communications in Mathematical Physics","isi":1,"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-11-18T08:15:07Z","file_size":1426046,"date_updated":"2024-11-18T08:15:07Z","creator":"dernst","success":1,"checksum":"c9ae0ea195bd39b8b3a630d492fb00dc","relation":"main_file","file_id":"18562","file_name":"2024_CommMathPhysics_Erdoes.pdf"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]}},{"title":"The Euclidean MST-ratio for bi-colored lattices","abstract":[{"text":"Given a finite set, A ⊆ ℝ², and a subset, B ⊆ A, the MST-ratio is the combined length of the minimum spanning trees of B and A⧵B divided by the length of the minimum spanning tree of A. The question of the supremum, over all sets A, of the maximum, over all subsets B, is related to the Steiner ratio, and we prove this sup-max is between 2.154 and 2.427. Restricting ourselves to 2-dimensional lattices, we prove that the sup-max is 2, while the inf-max is 1.25. By some margin the most difficult of these results is the upper bound for the inf-max, which we prove by showing that the hexagonal lattice cannot have MST-ratio larger than 1.25.","lang":"eng"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, \"Discretization in Geometry and Dynamics\", Austrian Science Fund (FWF), grant no. I 02979-N35.","publication_status":"published","article_processing_charge":"Yes","OA_type":"gold","oa":1,"OA_place":"publisher","ddc":["510"],"day":"28","author":[{"orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano"},{"first_name":"Ondrej","full_name":"Draganov, Ondrej","orcid":"0000-0003-0464-3823","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov"},{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"first_name":"Morteza","full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2403.10204"],"isi":["001540278400001"]},"year":"2024","publication":"32nd International Symposium on Graph Drawing and Network Visualization","isi":1,"file":[{"content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","date_updated":"2024-11-18T07:49:25Z","file_size":908541,"date_created":"2024-11-18T07:49:25Z","checksum":"5f9b35e115c3d375e99be78da9054cb4","file_name":"2024_LIPIcs_CultreradiMontesano.pdf","file_id":"18560","relation":"main_file"}],"publication_identifier":{"isbn":["9783959773430"],"issn":["1868-8969"]},"project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"scopus_import":"1","date_created":"2024-11-17T23:01:47Z","volume":320,"quality_controlled":"1","date_updated":"2025-12-02T13:50:50Z","oa_version":"Published Version","_id":"18556","month":"10","doi":"10.4230/LIPIcs.GD.2024.3","type":"conference","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","conference":{"start_date":"2024-09-18","end_date":"2024-09-20","location":"Vienna, Austria","name":"GD: Graph Drawing and Network Visualization"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       320","date_published":"2024-10-28T00:00:00Z","citation":{"ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. The Euclidean MST-ratio for bi-colored lattices. In: <i>32nd International Symposium on Graph Drawing and Network Visualization</i>. Vol 320. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">10.4230/LIPIcs.GD.2024.3</a>","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “The Euclidean MST-ratio for bi-colored lattices,” in <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, Vienna, Austria, 2024, vol. 320.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (2024). The Euclidean MST-ratio for bi-colored lattices. In <i>32nd International Symposium on Graph Drawing and Network Visualization</i> (Vol. 320). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">https://doi.org/10.4230/LIPIcs.GD.2024.3</a>","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. 2024. The Euclidean MST-ratio for bi-colored lattices. 32nd International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LIPIcs, vol. 320, 3.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, in:, 32nd International Symposium on Graph Drawing and Network Visualization, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “The Euclidean MST-Ratio for Bi-Colored Lattices.” In <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, Vol. 320. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">https://doi.org/10.4230/LIPIcs.GD.2024.3</a>.","mla":"Cultrera di Montesano, Sebastiano, et al. “The Euclidean MST-Ratio for Bi-Colored Lattices.” <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, vol. 320, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">10.4230/LIPIcs.GD.2024.3</a>."},"alternative_title":["LIPIcs"],"article_number":"3","arxiv":1,"ec_funded":1,"corr_author":"1","status":"public","department":[{"_id":"HeEd"}],"file_date_updated":"2024-11-18T07:49:25Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"}]