[{"intvolume":"        25","date_updated":"2025-09-08T08:06:56Z","article_type":"letter_note","citation":{"chicago":"Lembo, Sergio, and Michael K Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” <i>Nature Immunology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41590-024-01881-2\">https://doi.org/10.1038/s41590-024-01881-2</a>.","apa":"Lembo, S., &#38; Sixt, M. K. (2024). Nuclear squeezing wakes up dendritic cells. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-024-01881-2\">https://doi.org/10.1038/s41590-024-01881-2</a>","ista":"Lembo S, Sixt MK. 2024. Nuclear squeezing wakes up dendritic cells. Nature Immunology. 25, 1131–1132.","ama":"Lembo S, Sixt MK. Nuclear squeezing wakes up dendritic cells. <i>Nature Immunology</i>. 2024;25:1131–1132. doi:<a href=\"https://doi.org/10.1038/s41590-024-01881-2\">10.1038/s41590-024-01881-2</a>","ieee":"S. Lembo and M. K. Sixt, “Nuclear squeezing wakes up dendritic cells,” <i>Nature Immunology</i>, vol. 25. Springer Nature, pp. 1131–1132, 2024.","mla":"Lembo, Sergio, and Michael K. Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” <i>Nature Immunology</i>, vol. 25, Springer Nature, 2024, pp. 1131–1132, doi:<a href=\"https://doi.org/10.1038/s41590-024-01881-2\">10.1038/s41590-024-01881-2</a>.","short":"S. Lembo, M.K. Sixt, Nature Immunology 25 (2024) 1131–1132."},"language":[{"iso":"eng"}],"date_created":"2024-06-30T22:01:05Z","publication":"Nature Immunology","scopus_import":"1","oa_version":"None","corr_author":"1","type":"journal_article","abstract":[{"text":"Dendritic cells migrate to and from lymph nodes in response to chemokine gradients.Data now show that steady-state migration of these cells can be triggered by a mechanosensitive pathway.","lang":"eng"}],"external_id":{"pmid":["38907047"],"isi":["001251509300001"]},"status":"public","volume":25,"month":"06","year":"2024","publication_status":"published","pmid":1,"page":"1131–1132 ","author":[{"last_name":"Lembo","orcid":"0000-0002-2253-8771","first_name":"Sergio","full_name":"Lembo, Sergio","id":"d993a7b2-292f-11ed-aaac-fb045a912e31"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1038/s41590-024-01881-2","isi":1,"publisher":"Springer Nature","_id":"17191","quality_controlled":"1","date_published":"2024-06-21T00:00:00Z","day":"21","department":[{"_id":"MiSi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Nuclear squeezing wakes up dendritic cells","article_processing_charge":"No","publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]}},{"related_material":{"record":[{"relation":"used_in_publication","id":"17202","status":"public"}]},"month":"07","year":"2024","file_date_updated":"2024-07-04T10:11:40Z","contributor":[{"last_name":"Crippa","orcid":"0000-0002-2968-611X","first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","contributor_type":"project_member"},{"first_name":"Marco","last_name":"Valentini","contributor_type":"project_member","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"last_name":"Janik","first_name":"Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"first_name":"Levon","last_name":"Baghumyan","contributor_type":"project_member","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7"},{"first_name":"Giorgio","last_name":"Fabris","contributor_type":"project_member","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352"},{"last_name":"Kapoor","first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","contributor_type":"project_member"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773"},{"contributor_type":"project_member","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"},{"last_name":"Calcaterra","first_name":"Stefano","contributor_type":"project_member"},{"last_name":"Chrastina","first_name":"Daniel","contributor_type":"project_member"},{"last_name":"Isella","first_name":"Giovanni","contributor_type":"project_member"},{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"author":[{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","first_name":"Oliver","last_name":"Sagi"}],"project":[{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507"}],"date_updated":"2026-04-16T12:20:39Z","ddc":["530"],"citation":{"ieee":"O. Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and Technology Austria, 2024.","ista":"Sagi O. 2024. A gate-tunable transmon in planar Ge, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>.","ama":"Sagi O. A gate-tunable transmon in planar Ge. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>","apa":"Sagi, O. (2024). A gate-tunable transmon in planar Ge. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">https://doi.org/10.15479/AT:ISTA:17196</a>","short":"O. Sagi, (2024).","mla":"Sagi, Oliver. <i>A Gate-Tunable Transmon in Planar Ge</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>.","chicago":"Sagi, Oliver. “A Gate-Tunable Transmon in Planar Ge.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">https://doi.org/10.15479/AT:ISTA:17196</a>."},"oa_version":"Published Version","date_created":"2024-07-04T10:14:34Z","corr_author":"1","type":"research_data","abstract":[{"text":"This .zip File contains the data for the figures presented in the main text and supplementary material of \"A gate tunable transmon qubit in planar Ge\" by O.Sagi et al. The measurements were done using Qcodes. The description of the files and the instructions on opening the data can be found in the Readme. An additional Jupyter Notebook is attached that walks through the data analysis.","lang":"eng"}],"has_accepted_license":"1","status":"public","day":"04","department":[{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"JoFi"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","oa":1,"title":"A gate-tunable transmon in planar Ge","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"checksum":"a9f640a0b72a92171353f3ea14406f0b","success":1,"file_id":"17197","file_name":"GeGatemon_DataAnalysis.ipynb","date_updated":"2024-07-04T10:01:51Z","file_size":1960182,"content_type":"application/octet-stream","date_created":"2024-07-04T10:01:51Z","creator":"osagi","relation":"main_file","access_level":"open_access"},{"access_level":"open_access","creator":"osagi","relation":"main_file","date_created":"2024-07-04T10:01:50Z","content_type":"application/vnd.openxmlformats-officedocument.presentationml.presentation","file_size":34194,"file_id":"17198","file_name":"OlSa_Readme.pptx","date_updated":"2024-07-04T10:01:50Z","success":1,"checksum":"f0feec931233e8e845ade56165c1588f"},{"file_size":72939292,"date_updated":"2024-07-04T10:11:16Z","file_id":"17199","file_name":"Al_Transmon.zip","success":1,"checksum":"92bb11e3a508d736d01ff0738a1172c7","access_level":"open_access","relation":"main_file","creator":"osagi","date_created":"2024-07-04T10:11:16Z","content_type":"application/x-zip-compressed"},{"date_updated":"2024-07-04T10:11:40Z","file_id":"17200","file_name":"Gatemon_RT_5nm_1.zip","success":1,"checksum":"871e96fe0ecc97581196e883045cd516","file_size":465618029,"content_type":"application/x-zip-compressed","date_created":"2024-07-04T10:11:40Z","access_level":"open_access","relation":"main_file","creator":"osagi"},{"date_created":"2024-07-04T10:11:35Z","content_type":"application/x-zip-compressed","creator":"osagi","relation":"main_file","access_level":"open_access","success":1,"checksum":"a3e141af90f0104b7269c8a72370848a","file_id":"17201","file_name":"Gatemon_RT_5nm_2.zip","date_updated":"2024-07-04T10:11:35Z","file_size":281503513}],"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. ","doi":"10.15479/AT:ISTA:17196","publisher":"Institute of Science and Technology Austria","date_published":"2024-07-04T00:00:00Z","_id":"17196"},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2041-1723"]},"APC_amount":"6828 EUR","article_processing_charge":"Yes","title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MaJö"}],"day":"12","article_number":"8830","date_published":"2024-10-12T00:00:00Z","_id":"18444","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance with the reconstruction experiments. We would also like to thank Laura Burnett for drawing scientific illustrations used in the figures. We are particularly grateful to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing material support and technical advice. We are grateful to Daria Siekhaus, Eugenia Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory for valuable discussions and comments on the manuscript. Stocks from the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center were used in this study. The Scientific Service Units of ISTA supported the project through resources provided by the Imaging and Optics Facility, MIBA Machine Shop, and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) as part of the SPP 2205 – 429960716 (M.J.).","file":[{"file_size":8276667,"checksum":"2af4d6e7364329107aa94d072d594ce0","success":1,"date_updated":"2024-10-21T12:11:10Z","file_id":"18459","file_name":"2024_NatureComm_Pokusaeva.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2024-10-21T12:11:10Z","content_type":"application/pdf"}],"doi":"10.1038/s41467-024-53173-w","isi":1,"author":[{"orcid":"0000-0001-7660-444X","first_name":"Victoria","last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0009-0006-2974-5075","first_name":"Roshan K","last_name":"Satapathy","full_name":"Satapathy, Roshan K","id":"46046B7A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2012-9947","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"pmid":1,"file_date_updated":"2024-10-21T12:11:10Z","publication_status":"published","year":"2024","month":"10","volume":15,"related_material":{"record":[{"relation":"dissertation_contains","id":"18568","status":"public"},{"relation":"research_data","status":"public","id":"17488"}]},"has_accepted_license":"1","status":"public","external_id":{"pmid":["39396050"],"isi":["001336422500001"]},"abstract":[{"lang":"eng","text":"Animals rely on compensatory actions to maintain stability and navigate their environment efficiently. These actions depend on global visual motion cues known as optic-flow. While the optomotor response has been the traditional focus for studying optic-flow compensation in insects, its simplicity has been insufficient to determine the role of the intricate optic-flow processing network involved in visual course control. Here, we reveal a series of course control behaviours in Drosophila and link them to specific neural circuits. We show that bilateral electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate are required for a proper course control. This electrical interaction works alongside chemical synapses within the HS-H2 network to control the dynamics and direction of turning behaviours. Our findings reveal how insects use bilateral motion cues for navigation, assigning a new functional significance to the HS-H2 network and suggesting a previously unknown role for gap junctions in non-linear operations."}],"type":"journal_article","corr_author":"1","publication":"Nature Communications","oa_version":"Published Version","scopus_import":"1","date_created":"2024-10-20T22:02:05Z","language":[{"iso":"eng"}],"article_type":"original","DOAJ_listed":"1","citation":{"chicago":"Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>.","apa":"Pokusaeva, V., Satapathy, R. K., Symonova, O., &#38; Jösch, M. A. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>","ama":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>","ista":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. 15, 8830.","ieee":"V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","mla":"Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>, vol. 15, 8830, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>.","short":"V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications 15 (2024)."},"ddc":["570"],"date_updated":"2026-06-10T07:58:34Z","intvolume":"        15","OA_place":"publisher","OA_type":"gold","project":[{"_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","name":"Evolution of Sensorimotor Transformation Across Diptera","grant_number":"429960716"}]},{"author":[{"full_name":"Zupančič, Maja","last_name":"Zupančič","first_name":"Maja"},{"last_name":"Keimpema","first_name":"Erik","full_name":"Keimpema, Erik"},{"full_name":"Tretiakov, Evgenii O.","last_name":"Tretiakov","first_name":"Evgenii O."},{"full_name":"Eder, Stephanie J.","first_name":"Stephanie J.","last_name":"Eder"},{"full_name":"Lev, Itamar","first_name":"Itamar","last_name":"Lev"},{"full_name":"Englmaier, Lukas","first_name":"Lukas","last_name":"Englmaier"},{"first_name":"Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"full_name":"Fietz, Simone A.","last_name":"Fietz","first_name":"Simone A."},{"full_name":"Härtig, Wolfgang","last_name":"Härtig","first_name":"Wolfgang"},{"full_name":"Renaux, Estelle","last_name":"Renaux","first_name":"Estelle"},{"full_name":"Villunger, Andreas","first_name":"Andreas","last_name":"Villunger"},{"full_name":"Hökfelt, Tomas","first_name":"Tomas","last_name":"Hökfelt"},{"full_name":"Zimmer, Manuel","last_name":"Zimmer","first_name":"Manuel"},{"full_name":"Clotman, Frédéric","first_name":"Frédéric","last_name":"Clotman"},{"full_name":"Harkany, Tibor","first_name":"Tibor","last_name":"Harkany"}],"pmid":1,"file_date_updated":"2024-10-21T12:15:38Z","publication_status":"published","year":"2024","month":"10","volume":15,"abstract":[{"text":"Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus.","lang":"eng"}],"status":"public","external_id":{"isi":["001409493300014"],"pmid":["39366958"]},"has_accepted_license":"1","scopus_import":"1","date_created":"2024-10-20T22:02:05Z","publication":"Nature Communications","oa_version":"Published Version","type":"journal_article","DOAJ_listed":"1","article_type":"original","citation":{"chicago":"Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder, Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>.","short":"M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier, P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer, F. Clotman, T. Harkany, Nature Communications 15 (2024).","mla":"Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>, vol. 15, 8631, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>.","ieee":"M. Zupančič <i>et al.</i>, “Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>","ista":"Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F, Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.","apa":"Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier, L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>"},"language":[{"iso":"eng"}],"date_updated":"2025-09-08T14:25:06Z","ddc":["570"],"OA_place":"publisher","intvolume":"        15","OA_type":"gold","publication_identifier":{"eissn":["2041-1723"]},"PlanS_conform":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","oa":1,"title":"Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"RySh"}],"day":"05","article_number":"8631","quality_controlled":"1","_id":"18445","date_published":"2024-10-05T00:00:00Z","publisher":"Springer Nature","file":[{"file_size":7215329,"checksum":"03d6dd1b84efa24e9e9ede748d08764d","success":1,"file_name":"2024_NatureComm_Zupancic.pdf","file_id":"18460","date_updated":"2024-10-21T12:15:38Z","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_created":"2024-10-21T12:15:38Z"}],"doi":"10.1038/s41467-024-52762-z","isi":1,"acknowledgement":"The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility, Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher (Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their technical assistance. C. elegans strains were provided by the National Bioresource Project for the nematode, Japan, and the CGC, with the latter being funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council (2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden, FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.), the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21, to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L). E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska Institute."},{"status":"public","external_id":{"pmid":["39388574"],"isi":["001422132300018"]},"abstract":[{"lang":"eng","text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning."}],"corr_author":"1","type":"journal_article","main_file_link":[{"url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf","open_access":"1"}],"oa_version":"Submitted Version","publication":"Science","scopus_import":"1","date_created":"2024-10-20T22:02:06Z","language":[{"iso":"eng"}],"citation":{"apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>","ieee":"D. Fabrèges <i>et al.</i>, “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” <i>Science</i>, vol. 386, no. 6718. AAAS, 2024.","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.","ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. 2024;386(6718). doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>.","short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>."},"article_type":"original","date_updated":"2025-09-08T14:22:13Z","OA_place":"repository","intvolume":"       386","OA_type":"green","author":[{"full_name":"Fabrèges, Dimitri","last_name":"Fabrèges","first_name":"Dimitri"},{"last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat"},{"last_name":"Moghe","first_name":"Prachiti","full_name":"Moghe, Prachiti"},{"full_name":"Kickuth, Alison","last_name":"Kickuth","first_name":"Alison"},{"first_name":"Takafumi","last_name":"Ichikawa","full_name":"Ichikawa, Takafumi"},{"full_name":"Iwatani, Chizuru","last_name":"Iwatani","first_name":"Chizuru"},{"last_name":"Tsukiyama","first_name":"Tomoyuki","full_name":"Tsukiyama, Tomoyuki"},{"full_name":"Daniel, Nathalie","last_name":"Daniel","first_name":"Nathalie"},{"full_name":"Gering, Julie","last_name":"Gering","first_name":"Julie"},{"full_name":"Stokkermans, Anniek","last_name":"Stokkermans","first_name":"Anniek"},{"last_name":"Wolny","first_name":"Adrian","full_name":"Wolny, Adrian"},{"full_name":"Kreshuk, Anna","first_name":"Anna","last_name":"Kreshuk"},{"full_name":"Duranthon, Véronique","first_name":"Véronique","last_name":"Duranthon"},{"full_name":"Uhlman, Virginie","last_name":"Uhlman","first_name":"Virginie"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Takashi","last_name":"Hiiragi","full_name":"Hiiragi, Takashi"}],"pmid":1,"publication_status":"published","year":"2024","month":"10","volume":386,"issue":"6718","article_number":"eadh1145","_id":"18446","quality_controlled":"1","date_published":"2024-10-11T00:00:00Z","publisher":"AAAS","isi":1,"doi":"10.1126/science.adh1145","acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","publication_identifier":{"eissn":["1095-9203"]},"article_processing_charge":"No","title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"EdHa"}],"day":"11"},{"month":"12","issue":"45","volume":11,"file_date_updated":"2025-01-13T09:16:25Z","publication_status":"published","year":"2024","pmid":1,"author":[{"full_name":"Zhou, Yu","last_name":"Zhou","first_name":"Yu"},{"full_name":"Shaukat, Ahmed","last_name":"Shaukat","first_name":"Ahmed"},{"full_name":"Seitsonen, Jani","first_name":"Jani","last_name":"Seitsonen"},{"first_name":"Carlo","last_name":"Rigoni","id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0","full_name":"Rigoni, Carlo"},{"full_name":"Timonen, Jaakko V.I.","first_name":"Jaakko V.I.","last_name":"Timonen"},{"last_name":"Kostiainen","first_name":"Mauri A.","full_name":"Kostiainen, Mauri A."}],"OA_type":"gold","date_updated":"2025-09-08T14:20:31Z","ddc":["540"],"intvolume":"        11","OA_place":"publisher","article_type":"original","citation":{"chicago":"Zhou, Yu, Ahmed Shaukat, Jani Seitsonen, Carlo Rigoni, Jaakko V.I. Timonen, and Mauri A. Kostiainen. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” <i>Advanced Science</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/advs.202408416\">https://doi.org/10.1002/advs.202408416</a>.","mla":"Zhou, Yu, et al. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” <i>Advanced Science</i>, vol. 11, no. 45, 2408416, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/advs.202408416\">10.1002/advs.202408416</a>.","short":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen, Advanced Science 11 (2024).","apa":"Zhou, Y., Shaukat, A., Seitsonen, J., Rigoni, C., Timonen, J. V. I., &#38; Kostiainen, M. A. (2024). Protein cage directed assembly of binary nanoparticle superlattices. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.202408416\">https://doi.org/10.1002/advs.202408416</a>","ieee":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J. V. I. Timonen, and M. A. Kostiainen, “Protein cage directed assembly of binary nanoparticle superlattices,” <i>Advanced Science</i>, vol. 11, no. 45. Wiley, 2024.","ama":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. Protein cage directed assembly of binary nanoparticle superlattices. <i>Advanced Science</i>. 2024;11(45). doi:<a href=\"https://doi.org/10.1002/advs.202408416\">10.1002/advs.202408416</a>","ista":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. 2024. Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. 11(45), 2408416."},"DOAJ_listed":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Inorganic nanoparticles can be assembled into superlattices with unique optical and magnetic properties arising from collective behavior. Protein cages can be utilized to guide this assembly by encapsulating nanoparticles and promoting their assembly into ordered structures. However, creating ordered multi-component structures with different protein cage types and sizes remains a challenge. Here, the co-crystallization of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized by opposing surface charges and unequal diameter is shown. Precise tuning of the electrostatic attraction between the cages enabled the preparation of binary crystals with dimensions up to several tens of micrometers. Additionally, binary metal nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles inside the cavities of the protein cages. The resulting structure adopts an AB2FCC configuration that also impacts the dipolar coupling between the particles and hence the optical properties of the crystals, providing key insight for the future preparation of plasmonic and magnetic nanoparticle metamaterials."}],"has_accepted_license":"1","status":"public","external_id":{"pmid":["39401426"],"isi":["001330745600001"]},"publication":"Advanced Science","scopus_import":"1","oa_version":"Published Version","date_created":"2024-10-20T22:02:07Z","type":"journal_article","department":[{"_id":"RaKl"}],"day":"04","oa":1,"title":"Protein cage directed assembly of binary nanoparticle superlattices","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2198-3844"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","publisher":"Wiley","doi":"10.1002/advs.202408416","isi":1,"file":[{"file_size":7040083,"date_updated":"2025-01-13T09:16:25Z","file_id":"18834","file_name":"2024_AdvancedScience_Zhou.pdf","checksum":"00451eeb2c9eecf1ff41ad243c793a51","success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2025-01-13T09:16:25Z"}],"acknowledgement":"This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 101002258). The authors acknowledge the provision of facilities and technical support by Aalto University Bioeconomy Facilities and OtaNanoNanomicroscopy Center (Aalto-NMC). This work was carried out under the Academy of Finland's Centers of Excellence Programme, Life Inspired Hybrid Materials (LIBER) Center of Excellence (2022–2029), project number 346110 and 346112.","article_number":"2408416","_id":"18451","date_published":"2024-12-04T00:00:00Z","quality_controlled":"1"},{"article_type":"original","citation":{"apa":"Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes, U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>","ista":"Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 59(14), S1534-5807(24)00569–0.","ama":"Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. 2024;59(14):S1534-5807(24)00569-0. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>","ieee":"D. Janacek <i>et al.</i>, “Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport,” <i>Developmental Cell</i>, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024.","mla":"Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>.","short":"D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml, K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0.","chicago":"Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.","lang":"eng"}],"status":"public","has_accepted_license":"1","external_id":{"isi":["001390774300001"],"pmid":["39413780"]},"publication":"Developmental Cell","oa_version":"Published Version","date_created":"2024-10-23T08:41:27Z","scopus_import":"1","type":"journal_article","OA_type":"hybrid","date_updated":"2025-09-08T14:33:17Z","ddc":["570"],"intvolume":"        59","OA_place":"publisher","page":"S1534-5807(24)00569-0","pmid":1,"author":[{"first_name":"DP","last_name":"Janacek","full_name":"Janacek, DP"},{"first_name":"M","last_name":"Kolb","full_name":"Kolb, M"},{"last_name":"Schulz","first_name":"L","full_name":"Schulz, L"},{"last_name":"Mergner","first_name":"J","full_name":"Mergner, J"},{"full_name":"Kuster, B","first_name":"B","last_name":"Kuster"},{"orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Ten Tusscher","first_name":"K","full_name":"Ten Tusscher, K"},{"first_name":"C","last_name":"Schwechheimer","full_name":"Schwechheimer, C"},{"first_name":"UZ","last_name":"Hammes","full_name":"Hammes, UZ"}],"month":"12","issue":"14","volume":59,"publication_status":"published","file_date_updated":"2025-01-13T09:20:15Z","year":"2024","date_published":"2024-12-16T00:00:00Z","_id":"18465","quality_controlled":"1","publisher":"Elsevier","acknowledgement":"This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H. We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished results and valuable discussions.","file":[{"content_type":"application/pdf","date_created":"2025-01-13T09:20:15Z","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"34423ee9fb4e30334f3572eddf1da2ae","success":1,"date_updated":"2025-01-13T09:20:15Z","file_id":"18835","file_name":"2024_DevelopmentalCell_Janacek.pdf","file_size":3675955}],"isi":1,"doi":"10.1016/j.devcel.2024.09.020","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"JiFr"}],"day":"16","oa":1,"title":"Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"eissn":["1091-6490"]},"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"BeVi"}],"day":"29","title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"e2406335121","date_published":"2024-10-29T00:00:00Z","_id":"18479","quality_controlled":"1","publisher":"National Academy of Sciences","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.","doi":"10.1073/pnas.2406335121","isi":1,"file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2024-11-04T10:29:43Z","content_type":"application/pdf","file_size":1299095,"checksum":"73db3c87b35753e0f4324417f164a35e","success":1,"date_updated":"2024-11-04T10:29:43Z","file_id":"18501","file_name":"2024_PNAS_McDonough.pdf"}],"pmid":1,"author":[{"last_name":"Mcdonough","first_name":"Yasmine","full_name":"Mcdonough, Yasmine"},{"id":"347955dd-57b0-11ee-9095-c28bdd368f4b","full_name":"Ruzicka, Filip","first_name":"Filip","last_name":"Ruzicka"},{"first_name":"Tim","last_name":"Connallon","full_name":"Connallon, Tim"}],"month":"10","volume":121,"issue":"44","file_date_updated":"2024-11-04T10:29:43Z","publication_status":"published","year":"2024","language":[{"iso":"eng"}],"article_type":"original","citation":{"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>.","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>","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.","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>","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.","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>.","short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"ec_funded":1,"status":"public","external_id":{"isi":["001359216400017"],"pmid":["39436652"]},"has_accepted_license":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2024-10-27T23:01:44Z","oa_version":"Published Version","scopus_import":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"OA_type":"hybrid","ddc":["570"],"date_updated":"2025-09-08T14:31:58Z","OA_place":"publisher","intvolume":"       121"},{"file":[{"date_created":"2024-11-04T10:37:56Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"checksum":"b936b1c047f41cd427f00e3dc79327d3","file_name":"2024_NatureComm_dosSantos.pdf","file_id":"18502","date_updated":"2024-11-04T10:37:56Z","file_size":7358742}],"isi":1,"doi":"10.1038/s41467-024-53127-2","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.","publisher":"Springer Nature","quality_controlled":"1","_id":"18480","date_published":"2024-10-21T00:00:00Z","article_number":"9063","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice","oa":1,"day":"21","department":[{"_id":"MaHe"}],"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2041-1723"]},"intvolume":"        15","OA_place":"publisher","ddc":["570"],"date_updated":"2025-09-08T14:32:38Z","OA_type":"gold","type":"journal_article","scopus_import":"1","date_created":"2024-10-27T23:01:44Z","oa_version":"Published Version","publication":"Nature Communications","external_id":{"pmid":["39433757"],"isi":["001426270600023"]},"has_accepted_license":"1","status":"public","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."}],"language":[{"iso":"eng"}],"citation":{"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>.","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.","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>","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>","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).","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>."},"DOAJ_listed":"1","article_type":"original","year":"2024","file_date_updated":"2024-11-04T10:37:56Z","publication_status":"published","volume":15,"month":"10","author":[{"first_name":"Cristiane","last_name":"Dos Santos","full_name":"Dos Santos, Cristiane"},{"full_name":"Cambraia, Amanda","first_name":"Amanda","last_name":"Cambraia"},{"last_name":"Shrestha","first_name":"Shristi","full_name":"Shrestha, Shristi"},{"full_name":"Cutler, Melanie","last_name":"Cutler","first_name":"Melanie"},{"first_name":"Matthew","last_name":"Cottam","full_name":"Cottam, Matthew"},{"last_name":"Perkins","first_name":"Guy","full_name":"Perkins, Guy"},{"full_name":"Lev-Ram, Varda","first_name":"Varda","last_name":"Lev-Ram"},{"full_name":"Roy, Birbickram","last_name":"Roy","first_name":"Birbickram"},{"full_name":"Acree, Christopher","last_name":"Acree","first_name":"Christopher"},{"first_name":"Keun Young","last_name":"Kim","full_name":"Kim, Keun Young"},{"full_name":"Deerinck, Thomas","first_name":"Thomas","last_name":"Deerinck"},{"last_name":"Dean","first_name":"Danielle","full_name":"Dean, Danielle"},{"full_name":"Cartailler, Jean Philippe","last_name":"Cartailler","first_name":"Jean Philippe"},{"full_name":"Macdonald, Patrick E.","first_name":"Patrick E.","last_name":"Macdonald"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"Hetzer, Martin W","first_name":"Martin W","orcid":"0000-0002-2111-992X","last_name":"Hetzer"},{"last_name":"Ellisman","first_name":"Mark","full_name":"Ellisman, Mark"},{"first_name":"Rafael","last_name":"Arrojo E Drigo","full_name":"Arrojo E Drigo, Rafael"}],"pmid":1},{"OA_type":"gold","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"}],"OA_place":"publisher","intvolume":"        20","date_updated":"2026-04-07T12:31:58Z","ddc":["570"],"DOAJ_listed":"1","article_type":"original","citation":{"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>.","short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","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>.","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>","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.","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.","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>"},"language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","publication":"PLoS Computational Biology","date_created":"2024-10-27T23:01:45Z","type":"journal_article","corr_author":"1","abstract":[{"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.","lang":"eng"}],"status":"public","has_accepted_license":"1","external_id":{"isi":["001331700300003"],"pmid":["39401260"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20393"}]},"volume":20,"month":"10","year":"2024","publication_status":"published","file_date_updated":"2024-10-29T11:59:09Z","pmid":1,"author":[{"full_name":"Ho, Richard D.J.G.","first_name":"Richard D.J.G.","last_name":"Ho"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","first_name":"Kasumi","orcid":"0000-0001-6060-4795","last_name":"Kishi"},{"full_name":"Majka, Maciej","first_name":"Maciej","last_name":"Majka"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762"}],"file":[{"file_size":3732443,"checksum":"42fa714459943cb3961b40fab8fd82c8","success":1,"date_updated":"2024-10-29T11:59:09Z","file_id":"18487","file_name":"2024_PloSComBio_Ho.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2024-10-29T11:59:09Z","content_type":"application/pdf"}],"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.","isi":1,"doi":"10.1371/journal.pcbi.1012508","publisher":"Public Library of Science","_id":"18481","date_published":"2024-10-14T00:00:00Z","quality_controlled":"1","article_number":"e1012508","day":"14","department":[{"_id":"AnKi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Dynamics of morphogen source formation in a growing tissue","article_processing_charge":"No","APC_amount":"3197,23 EUR","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"title":"An algorithm for finding the generalized Chebyshev center of sets defined via their support functions","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"GradSch"}],"day":"01","publication_identifier":{"issn":["0005-1179"],"eissn":["1608-3032"]},"article_processing_charge":"No","publisher":"Springer Nature","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.","isi":1,"doi":"10.1134/S0005117924060031","_id":"18482","date_published":"2024-06-01T00:00:00Z","quality_controlled":"1","publication_status":"published","year":"2024","month":"06","issue":"6","volume":85,"author":[{"full_name":"Arkhipov, Pavel","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","last_name":"Arkhipov","first_name":"Pavel"}],"page":"522-532","date_updated":"2025-09-08T14:27:08Z","intvolume":"        85","OA_type":"closed access","abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["001338721700007"]},"status":"public","scopus_import":"1","oa_version":"None","date_created":"2024-10-27T23:01:45Z","publication":"Automation and Remote Control","corr_author":"1","type":"journal_article","citation":{"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.","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>","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>","short":"P. Arkhipov, Automation and Remote Control 85 (2024) 522–532.","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>.","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>."},"article_type":"original","language":[{"iso":"eng"}]},{"file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2025-01-13T09:14:24Z","content_type":"application/pdf","file_size":2260980,"checksum":"e7fcd9f78beb40408c7d858ac0625e27","success":1,"date_updated":"2025-01-13T09:14:24Z","file_name":"2024_GeometricFunctionalAnalysis_Kaloshin.pdf","file_id":"18833"}],"isi":1,"doi":"10.1007/s00039-024-00695-6","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).","publisher":"Springer Nature","_id":"18483","date_published":"2024-12-01T00:00:00Z","quality_controlled":"1","day":"01","department":[{"_id":"VaKa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Birkhoff conjecture for nearly centrally symmetric domains","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1420-8970"],"issn":["1016-443X"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"OA_type":"hybrid","intvolume":"        34","OA_place":"publisher","date_updated":"2025-09-08T14:27:45Z","ddc":["510"],"arxiv":1,"ec_funded":1,"citation":{"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.","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>","ista":"Kaloshin V, Koudjinan E, Zhang K. 2024. Birkhoff conjecture for nearly centrally symmetric domains. Geometric and Functional Analysis. 34, 1973–2007.","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>","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.","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>."},"article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2024-10-27T23:01:45Z","publication":"Geometric and Functional Analysis","oa_version":"Published Version","corr_author":"1","type":"journal_article","abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","status":"public","external_id":{"isi":["001329804200001"],"arxiv":["2306.12301"]},"volume":34,"month":"12","year":"2024","file_date_updated":"2025-01-13T09:14:24Z","publication_status":"published","page":"1973-2007","author":[{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"orcid":"0000-0003-2640-4049","first_name":"Edmond","last_name":"Koudjinan","full_name":"Koudjinan, Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E"},{"last_name":"Zhang","first_name":"Ke","full_name":"Zhang, Ke"}]},{"quality_controlled":"1","_id":"18488","date_published":"2024-10-23T00:00:00Z","article_number":"040311","isi":1,"doi":"10.1103/prxquantum.5.040311","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).","file":[{"file_size":1151431,"date_updated":"2024-10-30T08:59:09Z","file_id":"18489","file_name":"2024_PRXQuantum_Ljubotina.pdf","success":1,"checksum":"2e057ba021744d0a74602517935326b3","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2024-10-30T08:59:09Z"}],"publisher":"American Physical Society","article_processing_charge":"Yes","APC_amount":"3711,01 EUR","publication_identifier":{"eissn":["2691-3399"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Tangent space generators of matrix product states and exact floquet quantum scars","day":"23","department":[{"_id":"MaSe"}],"publication":"PRX Quantum","scopus_import":"1","oa_version":"Published Version","date_created":"2024-10-29T16:04:05Z","type":"journal_article","corr_author":"1","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."}],"external_id":{"arxiv":["2403.12325"],"isi":["001346198800001"]},"has_accepted_license":"1","status":"public","article_type":"original","citation":{"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>.","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.","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>","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>","short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).","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>."},"DOAJ_listed":"1","ec_funded":1,"language":[{"iso":"eng"}],"OA_place":"publisher","intvolume":"         5","date_updated":"2025-09-08T14:26:29Z","ddc":["530"],"arxiv":1,"OA_type":"gold","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"author":[{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","first_name":"Marko","orcid":"0000-0003-0038-7068","last_name":"Ljubotina"},{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","full_name":"Petrova, Elena","first_name":"Elena","last_name":"Petrova"},{"full_name":"Schuch, Norbert","first_name":"Norbert","last_name":"Schuch"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","publication_status":"published","file_date_updated":"2024-10-30T08:59:09Z","issue":"4","volume":5,"month":"10"},{"file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_created":"2024-11-04T08:54:26Z","file_size":911476,"file_id":"18497","file_name":"2024_JourLondonMathSoc_Schiavo.pdf","date_updated":"2024-11-04T08:54:26Z","success":1,"checksum":"143816823b5f43bd3748da8e3e91cef5"}],"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.","doi":"10.1112/jlms.70003","isi":1,"publisher":"London Mathematical Society","_id":"18490","date_published":"2024-11-01T00:00:00Z","quality_controlled":"1","article_number":"e70003","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension","day":"01","department":[{"_id":"JaMa"}],"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_place":"publisher","intvolume":"       110","date_updated":"2025-09-08T14:29:45Z","ddc":["510"],"project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"OA_type":"hybrid","date_created":"2024-11-03T23:01:44Z","oa_version":"Published Version","publication":"Journal of the London Mathematical Society","scopus_import":"1","type":"journal_article","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. "}],"external_id":{"isi":["001351918100029"]},"status":"public","has_accepted_license":"1","article_type":"original","ec_funded":1,"citation":{"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>.","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.","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.","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>","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>","short":"L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Journal of the London Mathematical Society 110 (2024).","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>."},"language":[{"iso":"eng"}],"year":"2024","publication_status":"published","file_date_updated":"2024-11-04T08:54:26Z","issue":"5","volume":110,"month":"11","author":[{"last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E"},{"full_name":"Herry, Ronan","last_name":"Herry","first_name":"Ronan"},{"full_name":"Kopfer, Eva","last_name":"Kopfer","first_name":"Eva"},{"last_name":"Sturm","first_name":"Karl Theodor","full_name":"Sturm, Karl Theodor"}]},{"article_processing_charge":"Yes","APC_amount":"4569,23 EUR","publication_identifier":{"eissn":["2375-2548"]},"PlanS_conform":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"11","department":[{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails","_id":"18491","quality_controlled":"1","date_published":"2024-10-11T00:00:00Z","article_number":"eadp2102","isi":1,"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.).","doi":"10.1126/sciadv.adp2102","file":[{"date_created":"2024-11-04T09:35:49Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"96aa0d3640fa9401975138e59054f84e","success":1,"file_name":"2024_ScienceAdv_Castillo.pdf","file_id":"18499","date_updated":"2024-11-04T09:35:49Z","file_size":1154107}],"publisher":"AAAS","author":[{"last_name":"Garcia Castillo","first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","full_name":"Garcia Castillo, Diego Fernando"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"}],"related_material":{"link":[{"url":"https://github.com/fernandoGarcia21/littorina_saxatilis_skerry","relation":"software"}],"record":[{"id":"18498","status":"public","relation":"research_data"},{"id":"20991","status":"public","relation":"dissertation_contains"}]},"issue":"41","volume":10,"month":"10","year":"2024","file_date_updated":"2024-11-04T09:35:49Z","publication_status":"published","citation":{"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>","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.","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.","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>","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>."},"DOAJ_listed":"1","article_type":"original","language":[{"iso":"eng"}],"publication":"Science Advances","scopus_import":"1","oa_version":"Published Version","date_created":"2024-11-03T23:01:44Z","corr_author":"1","type":"journal_article","abstract":[{"lang":"eng","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."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["001354405400018"]},"project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"OA_type":"gold","intvolume":"        10","OA_place":"publisher","date_updated":"2026-04-07T11:42:09Z","ddc":["570"]},{"volume":974,"issue":"2","month":"10","year":"2024","publication_status":"published","file_date_updated":"2024-11-04T08:42:23Z","author":[{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"last_name":"Mackenzie","first_name":"Ruari","full_name":"Mackenzie, Ruari"},{"full_name":"Pizzati, Elia","last_name":"Pizzati","first_name":"Elia"},{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"full_name":"Hennawi, Joseph F.","last_name":"Hennawi","first_name":"Joseph F."},{"full_name":"Zhang, Haowen","last_name":"Zhang","first_name":"Haowen"},{"full_name":"Bordoloi, Rongmon","first_name":"Rongmon","last_name":"Bordoloi"},{"full_name":"Kashino, Daichi","last_name":"Kashino","first_name":"Daichi"},{"full_name":"Lilly, Simon J.","first_name":"Simon J.","last_name":"Lilly"},{"full_name":"Naidu, Rohan P.","first_name":"Rohan P.","last_name":"Naidu"},{"last_name":"Simcoe","first_name":"Robert A.","full_name":"Simcoe, Robert A."},{"full_name":"Yue, Minghao","first_name":"Minghao","last_name":"Yue"},{"first_name":"Carlos S.","last_name":"Frenk","full_name":"Frenk, Carlos S."},{"full_name":"Helly, John C.","last_name":"Helly","first_name":"John C."},{"full_name":"Schaller, Matthieu","last_name":"Schaller","first_name":"Matthieu"},{"full_name":"Schaye, Joop","first_name":"Joop","last_name":"Schaye"}],"project":[{"grant_number":"101076224","name":"Young galaxies as tracers and agents of cosmic reionization","_id":"bd9b2118-d553-11ed-ba76-db24564edfea"}],"OA_type":"gold","intvolume":"       974","OA_place":"publisher","ddc":["520"],"date_updated":"2025-09-08T14:29:05Z","language":[{"iso":"eng"}],"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).","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.","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>","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>","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>."},"DOAJ_listed":"1","article_type":"original","type":"journal_article","oa_version":"Published Version","scopus_import":"1","publication":"Astrophysical Journal","date_created":"2024-11-03T23:01:45Z","external_id":{"isi":["001338877100001"]},"status":"public","has_accepted_license":"1","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."}],"day":"01","department":[{"_id":"JoMa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6","oa":1,"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"file":[{"file_size":1042470,"checksum":"1fcac3d11d01d91cf2bb4963b6e10b22","success":1,"file_id":"18496","file_name":"2024_AstrophysicalJour_Eilers.pdf","date_updated":"2024-11-04T08:42:23Z","creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2024-11-04T08:42:23Z","content_type":"application/pdf"}],"isi":1,"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).","doi":"10.3847/1538-4357/ad778b","publisher":"IOP Publishing","quality_controlled":"1","_id":"18494","date_published":"2024-10-01T00:00:00Z","article_number":"275"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","title":"Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails","oa":1,"day":"19","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20991"},{"id":"18491","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"NiBa"}],"month":"06","author":[{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","full_name":"Garcia Castillo, Diego Fernando","last_name":"Garcia Castillo","first_name":"Diego Fernando"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Larsson, Jenny","last_name":"Larsson","first_name":"Jenny"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_place":"repository","ddc":["570"],"date_updated":"2026-04-16T12:20:37Z","doi":"10.5281/ZENODO.12159343","publisher":"Zenodo","type":"research_data_reference","corr_author":"1","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.12159344","open_access":"1"}],"date_created":"2024-11-04T09:33:17Z","oa_version":"Published Version","has_accepted_license":"1","status":"public","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"}],"_id":"18498","date_published":"2024-06-19T00:00:00Z","citation":{"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>.","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>.","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>","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.","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>","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, (2024).","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>."}},{"year":"2024","publication_status":"published","month":"01","author":[{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Li, Jason","first_name":"Jason","last_name":"Li"},{"first_name":"Satish","last_name":"Rao","full_name":"Rao, Satish"},{"full_name":"Wang, Di","first_name":"Di","last_name":"Wang"}],"page":"3089-3139","OA_place":"repository","date_updated":"2025-06-24T12:09:26Z","arxiv":1,"project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms","grant_number":"Z00422"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"OA_type":"free access","scopus_import":"1","publication":"35th Annual ACM-SIAM Symposium on Discrete Algorithms","oa_version":"Preprint","date_created":"2024-11-04T10:54:21Z","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2401.05627"}],"type":"conference","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."}],"external_id":{"arxiv":["2401.05627"]},"status":"public","ec_funded":1,"citation":{"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.","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>.","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.","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.","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>","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>","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>."},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Deterministic near-linear time minimum cut in weighted graphs","day":"04","department":[{"_id":"MoHe"}],"article_processing_charge":"No","publication_identifier":{"eisbn":["9781611977912"]},"conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2024-01-10","start_date":"2024-01-07","location":"Alexandria, VA,  United States"},"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.","doi":"10.1137/1.9781611977912.111","publisher":"Society for Industrial and Applied Mathematics","date_published":"2024-01-04T00:00:00Z","_id":"18503","quality_controlled":"1"},{"file":[{"relation":"main_file","creator":"psurendr","access_level":"open_access","date_created":"2024-11-07T10:59:29Z","content_type":"application/pdf","file_size":37019760,"success":1,"checksum":"c32cf7bc75748d9c551d8eb70178bbec","date_updated":"2024-11-07T10:59:29Z","file_id":"18519","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf"},{"date_created":"2024-11-07T10:59:42Z","content_type":"application/zip","access_level":"closed","creator":"psurendr","relation":"source_file","file_id":"18520","file_name":"PhD Thesis- Parvathy_071124.zip","date_updated":"2024-11-07T10:59:42Z","checksum":"4417e02d54084d89e75734e18caaa96d","file_size":41198857}],"doi":"10.15479/at:ista:18515","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.","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"date_published":"2024-11-07T00:00:00Z","_id":"18515","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","oa":1,"day":"07","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","ddc":["576"],"date_updated":"2026-04-07T12:56:52Z","OA_type":"gold","project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"type":"dissertation","corr_author":"1","date_created":"2024-11-06T21:25:37Z","oa_version":"Published Version","has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"citation":{"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>","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","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>","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","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>.","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","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>."},"year":"2024","publication_status":"published","file_date_updated":"2024-11-07T10:59:42Z","month":"11","alternative_title":["ISTA Thesis"],"author":[{"first_name":"Parvathy","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"page":"219"},{"page":"282-301","alternative_title":["LNCS"],"author":[{"last_name":"Bonakdarpour","first_name":"Borzoo","full_name":"Bonakdarpour, Borzoo"},{"full_name":"Momtaz, Anik","first_name":"Anik","last_name":"Momtaz"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac"}],"volume":15191,"month":"10","year":"2024","file_date_updated":"2024-11-11T09:42:28Z","publication_status":"published","ec_funded":1,"citation":{"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>.","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>","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>","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.","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.","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."},"language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2024-11-10T23:01:58Z","publication":"24th International Conference on Runtime Verification","scopus_import":"1","type":"conference","corr_author":"1","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."}],"has_accepted_license":"1","status":"public","external_id":{"arxiv":["2408.05033"],"isi":["001420093700018"]},"OA_type":"hybrid","project":[{"name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093"}],"intvolume":"     15191","OA_place":"publisher","date_updated":"2026-05-20T08:43:20Z","ddc":["000"],"arxiv":1,"article_processing_charge":"Yes (in subscription journal)","APC_amount":"2748 EUR","publication_identifier":{"isbn":["9783031742330"],"eissn":["1611-3349"],"issn":["0302-9743"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"12","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","_id":"18521","quality_controlled":"1","date_published":"2024-10-12T00:00:00Z","file":[{"checksum":"7b8ca21b8c19ab796fa445b0e54003ca","success":1,"date_updated":"2024-11-11T09:42:28Z","file_name":"2024_LNCS_Bonakdarpour.pdf","file_id":"18539","file_size":1897101,"date_created":"2024-11-11T09:42:28Z","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access"}],"isi":1,"doi":"10.1007/978-3-031-74234-7_18","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).","publisher":"Springer Nature","conference":{"end_date":"2024-10-17","location":"Istanbul, Turkey","start_date":"2024-10-15","name":"RV: Conference on Runtime Verification"}}]