[{"oa":1,"file_date_updated":"2023-11-15T09:52:54Z","month":"11","language":[{"iso":"eng"}],"date_published":"2023-11-16T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"date_updated":"2026-04-07T13:29:13Z","oa_version":"Updated Version","type":"dissertation","_id":"14530","citation":{"ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>."},"alternative_title":["ISTA Thesis"],"status":"public","day":"16","page":"260","article_processing_charge":"No","abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order.  In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex.  ","lang":"eng"}],"publication_status":"published","title":"Synchronization in collectively moving active matter","degree_awarded":"PhD","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","first_name":"Michael"}],"OA_place":"publisher","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"461","status":"public"},{"relation":"part_of_dissertation","id":"10791","status":"public"},{"status":"public","id":"7932","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10703"},{"id":"12726","relation":"old_edition","status":"public"}]},"corr_author":"1","file":[{"date_created":"2023-11-15T09:52:54Z","file_name":"Thesis_Riedl_2023_corr.pdf","content_type":"application/pdf","creator":"mriedl","success":1,"file_id":"14536","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","relation":"main_file","access_level":"open_access","file_size":36743942,"date_updated":"2023-11-15T09:52:54Z"}],"has_accepted_license":"1","ddc":["530","570"],"year":"2023","date_created":"2023-11-15T09:59:03Z","doi":"10.15479/14530","publication_identifier":{"issn":["2663-337X"]}},{"doi":"10.15479/14539","publication_identifier":{"isbn":["978-3-99078-036-7"],"issn":["2663-337X"]},"date_created":"2023-11-15T13:39:10Z","year":"2023","ddc":["000"],"file":[{"success":1,"creator":"cchlebak","file_name":"main.pdf","content_type":"application/pdf","date_created":"2023-11-15T13:43:28Z","date_updated":"2023-11-15T13:43:28Z","file_size":2116426,"access_level":"open_access","relation":"main_file","checksum":"f23e002b0059ca78e1fbb864da52dd7e","file_id":"14540"},{"creator":"cchlebak","date_created":"2023-11-15T13:44:24Z","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","checksum":"80ca37618a3c7b59866875f8be9b15ed","relation":"source_file","access_level":"closed","file_size":35884057,"date_updated":"2023-11-15T13:44:24Z","file_id":"14541"}],"corr_author":"1","related_material":{"record":[{"status":"public","id":"10414","relation":"part_of_dissertation"},{"id":"12000","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9644"},{"status":"public","id":"12511","relation":"part_of_dissertation"},{"status":"public","id":"14600","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14601"},{"relation":"part_of_dissertation","id":"1194","status":"public"}]},"OA_place":"publisher","author":[{"first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"}],"title":"Automated verification and control of infinite state stochastic systems","degree_awarded":"PhD","publication_status":"published","abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}],"article_processing_charge":"No","page":"256","status":"public","day":"15","alternative_title":["ISTA Thesis"],"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"ec_funded":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"citation":{"ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>","apa":"Zikelic, D. (2023). <i>Automated verification and control of infinite state stochastic systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>.","mla":"Zikelic, Dorde. <i>Automated Verification and Control of Infinite State Stochastic Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>."},"_id":"14539","type":"dissertation","oa_version":"Published Version","date_updated":"2026-04-07T13:27:56Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","date_published":"2023-11-15T00:00:00Z","month":"11","language":[{"iso":"eng"}],"file_date_updated":"2023-11-15T13:44:24Z","oa":1},{"corr_author":"1","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2023_CellSystems_Briffa.pdf","date_created":"2023-11-20T11:22:52Z","creator":"dernst","success":1,"file_id":"14580","file_size":5587897,"date_updated":"2023-11-20T11:22:52Z","checksum":"101fdac59e6f1102d68ef91f2b5bd51a","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","ddc":["570"],"date_created":"2023-11-19T23:00:54Z","year":"2023","publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"doi":"10.1016/j.cels.2023.10.007","issue":"11","publication":"Cell Systems","article_processing_charge":"Yes (via OA deal)","page":"953-967","publication_status":"published","external_id":{"pmid":["37944515"],"isi":["001113459100001"]},"abstract":[{"text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.","lang":"eng"}],"title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","first_name":"Elizabeth","last_name":"Hollwey"},{"first_name":"Zaigham","last_name":"Shahzad","full_name":"Shahzad, Zaigham"},{"first_name":"Jonathan D.","last_name":"Moore","full_name":"Moore, Jonathan D."},{"first_name":"David B.","last_name":"Lyons","full_name":"Lyons, David B."},{"full_name":"Howard, Martin","last_name":"Howard","first_name":"Martin"},{"first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"volume":14,"pmid":1,"citation":{"mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>.","apa":"Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., &#38; Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>","chicago":"Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>.","ama":"Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. 2023;14(11):953-967. doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>","ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.","short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","ieee":"A. Briffa <i>et al.</i>, “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” <i>Cell Systems</i>, vol. 14, no. 11. Elsevier, pp. 953–967, 2023."},"project":[{"call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin","_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746"}],"tmp":{"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)","short":"CC BY (4.0)"},"ec_funded":1,"day":"15","status":"public","isi":1,"file_date_updated":"2023-11-20T11:22:52Z","oa":1,"date_published":"2023-11-15T00:00:00Z","language":[{"iso":"eng"}],"month":"11","date_updated":"2025-09-09T13:28:50Z","publisher":"Elsevier","department":[{"_id":"DaZi"}],"intvolume":"        14","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z.","scopus_import":"1","_id":"14551"},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"14579"}]},"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Robinson, M. L.","first_name":"M. L.","last_name":"Robinson"},{"full_name":"Hahn, P. G.","last_name":"Hahn","first_name":"P. G."},{"first_name":"B. D.","last_name":"Inouye","full_name":"Inouye, B. D."},{"first_name":"N.","last_name":"Underwood","full_name":"Underwood, N."},{"full_name":"Whitehead, S. R.","first_name":"S. R.","last_name":"Whitehead"},{"full_name":"Abbott, K. C.","last_name":"Abbott","first_name":"K. C."},{"full_name":"Bruna, E. M.","last_name":"Bruna","first_name":"E. M."},{"full_name":"Cacho, N. I.","first_name":"N. I.","last_name":"Cacho"},{"full_name":"Dyer, L. A.","first_name":"L. A.","last_name":"Dyer"},{"last_name":"Abdala-Roberts","first_name":"L.","full_name":"Abdala-Roberts, L."},{"full_name":"Allen, W. J.","last_name":"Allen","first_name":"W. J."},{"first_name":"J. F.","last_name":"Andrade","full_name":"Andrade, J. F."},{"first_name":"D. F.","last_name":"Angulo","full_name":"Angulo, D. F."},{"full_name":"Anjos, D.","last_name":"Anjos","first_name":"D."},{"first_name":"D. N.","last_name":"Anstett","full_name":"Anstett, D. N."},{"last_name":"Bagchi","first_name":"R.","full_name":"Bagchi, R."},{"last_name":"Bagchi","first_name":"S.","full_name":"Bagchi, S."},{"last_name":"Barbosa","first_name":"M.","full_name":"Barbosa, M."},{"full_name":"Barrett, S.","first_name":"S.","last_name":"Barrett"},{"last_name":"Baskett","first_name":"Carina","full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574"},{"full_name":"Ben-Simchon, E.","last_name":"Ben-Simchon","first_name":"E."},{"first_name":"K. J.","last_name":"Bloodworth","full_name":"Bloodworth, K. J."},{"full_name":"Bronstein, J. L.","first_name":"J. L.","last_name":"Bronstein"},{"last_name":"Buckley","first_name":"Y. M.","full_name":"Buckley, Y. M."},{"full_name":"Burghardt, K. T.","last_name":"Burghardt","first_name":"K. T."},{"first_name":"C.","last_name":"Bustos-Segura","full_name":"Bustos-Segura, C."},{"first_name":"E. S.","last_name":"Calixto","full_name":"Calixto, E. S."},{"full_name":"Carvalho, R. L.","first_name":"R. L.","last_name":"Carvalho"},{"last_name":"Castagneyrol","first_name":"B.","full_name":"Castagneyrol, B."},{"full_name":"Chiuffo, M. C.","last_name":"Chiuffo","first_name":"M. C."},{"first_name":"D.","last_name":"Cinoğlu","full_name":"Cinoğlu, D."},{"full_name":"Cinto Mejía, E.","first_name":"E.","last_name":"Cinto Mejía"},{"last_name":"Cock","first_name":"M. C.","full_name":"Cock, M. C."},{"last_name":"Cogni","first_name":"R.","full_name":"Cogni, R."},{"first_name":"O. L.","last_name":"Cope","full_name":"Cope, O. L."},{"full_name":"Cornelissen, T.","last_name":"Cornelissen","first_name":"T."},{"full_name":"Cortez, D. R.","first_name":"D. R.","last_name":"Cortez"},{"last_name":"Crowder","first_name":"D. W.","full_name":"Crowder, D. W."},{"first_name":"C.","last_name":"Dallstream","full_name":"Dallstream, C."},{"first_name":"W.","last_name":"Dáttilo","full_name":"Dáttilo, W."},{"last_name":"Davis","first_name":"J. K.","full_name":"Davis, J. K."},{"last_name":"Dimarco","first_name":"R. D.","full_name":"Dimarco, R. D."},{"full_name":"Dole, H. E.","first_name":"H. E.","last_name":"Dole"},{"first_name":"I. N.","last_name":"Egbon","full_name":"Egbon, I. N."},{"last_name":"Eisenring","first_name":"M.","full_name":"Eisenring, M."},{"first_name":"A.","last_name":"Ejomah","full_name":"Ejomah, A."},{"full_name":"Elderd, B. D.","last_name":"Elderd","first_name":"B. D."},{"full_name":"Endara, M. J.","first_name":"M. J.","last_name":"Endara"},{"first_name":"M. D.","last_name":"Eubanks","full_name":"Eubanks, M. D."},{"last_name":"Everingham","first_name":"S. E.","full_name":"Everingham, S. E."},{"last_name":"Farah","first_name":"K. N.","full_name":"Farah, K. N."},{"full_name":"Farias, R. P.","first_name":"R. P.","last_name":"Farias"},{"full_name":"Fernandes, A. P.","last_name":"Fernandes","first_name":"A. P."},{"first_name":"G. W.","last_name":"Fernandes","full_name":"Fernandes, G. W."},{"full_name":"Ferrante, M.","first_name":"M.","last_name":"Ferrante"},{"full_name":"Finn, A.","last_name":"Finn","first_name":"A."},{"full_name":"Florjancic, G. A.","last_name":"Florjancic","first_name":"G. A."},{"full_name":"Forister, M. L.","first_name":"M. L.","last_name":"Forister"},{"full_name":"Fox, Q. N.","last_name":"Fox","first_name":"Q. N."},{"full_name":"Frago, E.","last_name":"Frago","first_name":"E."},{"last_name":"França","first_name":"F. M.","full_name":"França, F. M."},{"full_name":"Getman-Pickering, A. S.","last_name":"Getman-Pickering","first_name":"A. S."},{"full_name":"Getman-Pickering, Z.","first_name":"Z.","last_name":"Getman-Pickering"},{"full_name":"Gianoli, E.","first_name":"E.","last_name":"Gianoli"},{"last_name":"Gooden","first_name":"B.","full_name":"Gooden, B."},{"full_name":"Gossner, M. M.","last_name":"Gossner","first_name":"M. M."},{"first_name":"K. A.","last_name":"Greig","full_name":"Greig, K. A."},{"first_name":"S.","last_name":"Gripenberg","full_name":"Gripenberg, S."},{"full_name":"Groenteman, R.","first_name":"R.","last_name":"Groenteman"},{"full_name":"Grof-Tisza, P.","last_name":"Grof-Tisza","first_name":"P."},{"full_name":"Haack, N.","last_name":"Haack","first_name":"N."},{"last_name":"Hahn","first_name":"L.","full_name":"Hahn, L."},{"last_name":"Haq","first_name":"S. M.","full_name":"Haq, S. M."},{"full_name":"Helms, A. M.","last_name":"Helms","first_name":"A. M."},{"last_name":"Hennecke","first_name":"J.","full_name":"Hennecke, J."},{"full_name":"Hermann, S. L.","last_name":"Hermann","first_name":"S. L."},{"full_name":"Holeski, L. M.","first_name":"L. M.","last_name":"Holeski"},{"full_name":"Holm, S.","last_name":"Holm","first_name":"S."},{"full_name":"Hutchinson, M. C.","first_name":"M. C.","last_name":"Hutchinson"},{"full_name":"Jackson, E. E.","first_name":"E. E.","last_name":"Jackson"},{"full_name":"Kagiya, S.","last_name":"Kagiya","first_name":"S."},{"last_name":"Kalske","first_name":"A.","full_name":"Kalske, A."},{"first_name":"M.","last_name":"Kalwajtys","full_name":"Kalwajtys, M."},{"first_name":"R.","last_name":"Karban","full_name":"Karban, R."},{"first_name":"R.","last_name":"Kariyat","full_name":"Kariyat, R."},{"last_name":"Keasar","first_name":"T.","full_name":"Keasar, T."},{"first_name":"M. F.","last_name":"Kersch-Becker","full_name":"Kersch-Becker, M. F."},{"last_name":"Kharouba","first_name":"H. M.","full_name":"Kharouba, H. M."},{"last_name":"Kim","first_name":"T. N.","full_name":"Kim, T. N."},{"last_name":"Kimuyu","first_name":"D. M.","full_name":"Kimuyu, D. M."},{"last_name":"Kluse","first_name":"J.","full_name":"Kluse, J."},{"first_name":"S. E.","last_name":"Koerner","full_name":"Koerner, S. E."},{"full_name":"Komatsu, K. J.","first_name":"K. J.","last_name":"Komatsu"},{"last_name":"Krishnan","first_name":"S.","full_name":"Krishnan, S."},{"last_name":"Laihonen","first_name":"M.","full_name":"Laihonen, M."},{"last_name":"Lamelas-López","first_name":"L.","full_name":"Lamelas-López, L."},{"full_name":"Lascaleia, M. C.","last_name":"Lascaleia","first_name":"M. C."},{"full_name":"Lecomte, N.","last_name":"Lecomte","first_name":"N."},{"last_name":"Lehn","first_name":"C. R.","full_name":"Lehn, C. R."},{"full_name":"Li, X.","first_name":"X.","last_name":"Li"},{"full_name":"Lindroth, R. L.","last_name":"Lindroth","first_name":"R. L."},{"first_name":"E. F.","last_name":"Lopresti","full_name":"Lopresti, E. F."},{"last_name":"Losada","first_name":"M.","full_name":"Losada, M."},{"full_name":"Louthan, A. M.","first_name":"A. M.","last_name":"Louthan"},{"full_name":"Luizzi, V. J.","last_name":"Luizzi","first_name":"V. J."},{"first_name":"S. C.","last_name":"Lynch","full_name":"Lynch, S. C."},{"first_name":"J. S.","last_name":"Lynn","full_name":"Lynn, J. S."},{"full_name":"Lyon, N. J.","last_name":"Lyon","first_name":"N. J."},{"full_name":"Maia, L. F.","first_name":"L. F.","last_name":"Maia"},{"first_name":"R. A.","last_name":"Maia","full_name":"Maia, R. A."},{"full_name":"Mannall, T. L.","first_name":"T. L.","last_name":"Mannall"},{"last_name":"Martin","first_name":"B. S.","full_name":"Martin, B. S."},{"last_name":"Massad","first_name":"T. J.","full_name":"Massad, T. J."},{"last_name":"Mccall","first_name":"A. C.","full_name":"Mccall, A. C."},{"first_name":"K.","last_name":"Mcgurrin","full_name":"Mcgurrin, K."},{"full_name":"Merwin, A. C.","first_name":"A. C.","last_name":"Merwin"},{"last_name":"Mijango-Ramos","first_name":"Z.","full_name":"Mijango-Ramos, Z."},{"last_name":"Mills","first_name":"C. H.","full_name":"Mills, C. H."},{"first_name":"A. T.","last_name":"Moles","full_name":"Moles, A. T."},{"full_name":"Moore, C. M.","first_name":"C. M.","last_name":"Moore"},{"full_name":"Moreira, X.","first_name":"X.","last_name":"Moreira"},{"full_name":"Morrison, C. R.","first_name":"C. R.","last_name":"Morrison"},{"full_name":"Moshobane, M. C.","first_name":"M. C.","last_name":"Moshobane"},{"last_name":"Muola","first_name":"A.","full_name":"Muola, A."},{"last_name":"Nakadai","first_name":"R.","full_name":"Nakadai, R."},{"last_name":"Nakajima","first_name":"K.","full_name":"Nakajima, K."},{"first_name":"S.","last_name":"Novais","full_name":"Novais, S."},{"full_name":"Ogbebor, C. O.","last_name":"Ogbebor","first_name":"C. O."},{"first_name":"H.","last_name":"Ohsaki","full_name":"Ohsaki, H."},{"last_name":"Pan","first_name":"V. S.","full_name":"Pan, V. S."},{"full_name":"Pardikes, N. A.","first_name":"N. A.","last_name":"Pardikes"},{"last_name":"Pareja","first_name":"M.","full_name":"Pareja, M."},{"full_name":"Parthasarathy, N.","first_name":"N.","last_name":"Parthasarathy"},{"full_name":"Pawar, R. R.","last_name":"Pawar","first_name":"R. R."},{"full_name":"Paynter, Q.","first_name":"Q.","last_name":"Paynter"},{"last_name":"Pearse","first_name":"I. S.","full_name":"Pearse, I. S."},{"full_name":"Penczykowski, R. M.","last_name":"Penczykowski","first_name":"R. M."},{"full_name":"Pepi, A. A.","last_name":"Pepi","first_name":"A. A."},{"first_name":"C. C.","last_name":"Pereira","full_name":"Pereira, C. C."},{"full_name":"Phartyal, S. S.","first_name":"S. S.","last_name":"Phartyal"},{"first_name":"F. I.","last_name":"Piper","full_name":"Piper, F. I."},{"full_name":"Poveda, K.","first_name":"K.","last_name":"Poveda"},{"first_name":"E. G.","last_name":"Pringle","full_name":"Pringle, E. G."},{"full_name":"Puy, J.","first_name":"J.","last_name":"Puy"},{"full_name":"Quijano, T.","last_name":"Quijano","first_name":"T."},{"last_name":"Quintero","first_name":"C.","full_name":"Quintero, C."},{"full_name":"Rasmann, S.","first_name":"S.","last_name":"Rasmann"},{"first_name":"C.","last_name":"Rosche","full_name":"Rosche, C."},{"full_name":"Rosenheim, L. Y.","last_name":"Rosenheim","first_name":"L. Y."},{"full_name":"Rosenheim, J. A.","last_name":"Rosenheim","first_name":"J. A."},{"first_name":"J. B.","last_name":"Runyon","full_name":"Runyon, J. B."},{"full_name":"Sadeh, A.","last_name":"Sadeh","first_name":"A."},{"full_name":"Sakata, Y.","last_name":"Sakata","first_name":"Y."},{"full_name":"Salcido, D. M.","last_name":"Salcido","first_name":"D. M."},{"full_name":"Salgado-Luarte, C.","last_name":"Salgado-Luarte","first_name":"C."},{"last_name":"Santos","first_name":"B. A.","full_name":"Santos, B. A."},{"full_name":"Sapir, Y.","last_name":"Sapir","first_name":"Y."},{"full_name":"Sasal, Y.","first_name":"Y.","last_name":"Sasal"},{"full_name":"Sato, Y.","first_name":"Y.","last_name":"Sato"},{"first_name":"M.","last_name":"Sawant","full_name":"Sawant, M."},{"last_name":"Schroeder","first_name":"H.","full_name":"Schroeder, H."},{"last_name":"Schumann","first_name":"I.","full_name":"Schumann, I."},{"first_name":"M.","last_name":"Segoli","full_name":"Segoli, M."},{"last_name":"Segre","first_name":"H.","full_name":"Segre, H."},{"last_name":"Shelef","first_name":"O.","full_name":"Shelef, O."},{"first_name":"N.","last_name":"Shinohara","full_name":"Shinohara, N."},{"last_name":"Singh","first_name":"R. P.","full_name":"Singh, R. P."},{"full_name":"Smith, D. S.","first_name":"D. S.","last_name":"Smith"},{"full_name":"Sobral, M.","first_name":"M.","last_name":"Sobral"},{"full_name":"Stotz, G. C.","first_name":"G. C.","last_name":"Stotz"},{"last_name":"Tack","first_name":"A. J.M.","full_name":"Tack, A. J.M."},{"full_name":"Tayal, M.","last_name":"Tayal","first_name":"M."},{"full_name":"Tooker, J. F.","first_name":"J. F.","last_name":"Tooker"},{"full_name":"Torrico-Bazoberry, D.","last_name":"Torrico-Bazoberry","first_name":"D."},{"full_name":"Tougeron, K.","last_name":"Tougeron","first_name":"K."},{"first_name":"A. M.","last_name":"Trowbridge","full_name":"Trowbridge, A. M."},{"first_name":"S.","last_name":"Utsumi","full_name":"Utsumi, S."},{"last_name":"Uyi","first_name":"O.","full_name":"Uyi, O."},{"full_name":"Vaca-Uribe, J. L.","last_name":"Vaca-Uribe","first_name":"J. L."},{"full_name":"Valtonen, A.","last_name":"Valtonen","first_name":"A."},{"full_name":"Van Dijk, L. J.A.","first_name":"L. J.A.","last_name":"Van Dijk"},{"full_name":"Vandvik, V.","first_name":"V.","last_name":"Vandvik"},{"last_name":"Villellas","first_name":"J.","full_name":"Villellas, J."},{"first_name":"L. P.","last_name":"Waller","full_name":"Waller, L. P."},{"full_name":"Weber, M. G.","first_name":"M. G.","last_name":"Weber"},{"first_name":"A.","last_name":"Yamawo","full_name":"Yamawo, A."},{"first_name":"S.","last_name":"Yim","full_name":"Yim, S."},{"full_name":"Zarnetske, P. L.","first_name":"P. L.","last_name":"Zarnetske"},{"last_name":"Zehr","first_name":"L. N.","full_name":"Zehr, L. N."},{"full_name":"Zhong, Z.","last_name":"Zhong","first_name":"Z."},{"first_name":"W. C.","last_name":"Wetzel","full_name":"Wetzel, W. C."}],"OA_place":"repository","volume":382,"title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","page":"679-683","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth."}],"publication_status":"published","external_id":{"pmid":["37943897"],"isi":["001138596500033"]},"issue":"6671","doi":"10.1126/science.adh8830","publication_identifier":{"eissn":["1095-9203"]},"publication":"Science","year":"2023","date_created":"2023-11-19T23:00:54Z","main_file_link":[{"url":"https://centaur.reading.ac.uk/113962/1/adh8830_CombinedPDF_v6.pdf","open_access":"1"}],"quality_controlled":"1","_id":"14552","scopus_import":"1","article_type":"original","intvolume":"       382","oa_version":"Submitted Version","type":"journal_article","acknowledgement":"The authors acknowledge funding for central project coordination from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution, and Behavior Program at Michigan State University; and AgBioResearch at Michigan State University. Site-specific funding is listed in the supplementary materials.","month":"11","language":[{"iso":"eng"}],"date_published":"2023-11-09T00:00:00Z","publisher":"AAAS","department":[{"_id":"NiBa"}],"date_updated":"2025-09-09T13:23:56Z","isi":1,"oa":1,"status":"public","day":"09","OA_type":"green","citation":{"ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. <i>Science</i>. 2023;382(6671):679-683. doi:<a href=\"https://doi.org/10.1126/science.adh8830\">10.1126/science.adh8830</a>","ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683.","ieee":"M. L. Robinson <i>et al.</i>, “Plant size, latitude, and phylogeny explain within-population variability in herbivory,” <i>Science</i>, vol. 382, no. 6671. AAAS, pp. 679–683, 2023.","mla":"Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” <i>Science</i>, vol. 382, no. 6671, AAAS, 2023, pp. 679–83, doi:<a href=\"https://doi.org/10.1126/science.adh8830\">10.1126/science.adh8830</a>.","apa":"Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R., Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain within-population variability in herbivory. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adh8830\">https://doi.org/10.1126/science.adh8830</a>","chicago":"Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead, K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” <i>Science</i>. AAAS, 2023. <a href=\"https://doi.org/10.1126/science.adh8830\">https://doi.org/10.1126/science.adh8830</a>."}},{"title":"Continuous-variable quantum tomography of high-amplitude states","article_processing_charge":"No","external_id":{"arxiv":["2212.07406"]},"publication_status":"published","abstract":[{"text":"Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-7242-015X","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab","full_name":"Fedotova, Ekaterina","last_name":"Fedotova","first_name":"Ekaterina"},{"first_name":"Nikolai","last_name":"Kuznetsov","full_name":"Kuznetsov, Nikolai"},{"full_name":"Tiunov, Egor","last_name":"Tiunov","first_name":"Egor"},{"last_name":"Ulanov","first_name":"A. E.","full_name":"Ulanov, A. E."},{"full_name":"Lvovsky, A. I.","last_name":"Lvovsky","first_name":"A. I."}],"volume":108,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.07406"}],"corr_author":"1","quality_controlled":"1","doi":"10.1103/PhysRevA.108.042430","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"issue":"4","publication":"Physical Review A","date_created":"2023-11-19T23:00:54Z","year":"2023","article_number":"042430","date_published":"2023-10-30T00:00:00Z","language":[{"iso":"eng"}],"month":"10","date_updated":"2024-10-09T21:07:19Z","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"arxiv":1,"oa":1,"scopus_import":"1","_id":"14553","oa_version":"Preprint","intvolume":"       108","article_type":"original","type":"journal_article","citation":{"mla":"Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude States.” <i>Physical Review A</i>, vol. 108, no. 4, 042430, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">10.1103/PhysRevA.108.042430</a>.","chicago":"Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">https://doi.org/10.1103/PhysRevA.108.042430</a>.","apa":"Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., &#38; Lvovsky, A. I. (2023). Continuous-variable quantum tomography of high-amplitude states. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">https://doi.org/10.1103/PhysRevA.108.042430</a>","ama":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable quantum tomography of high-amplitude states. <i>Physical Review A</i>. 2023;108(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">10.1103/PhysRevA.108.042430</a>","ista":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.","ieee":"E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable quantum tomography of high-amplitude states,” <i>Physical Review A</i>, vol. 108, no. 4. American Physical Society, 2023.","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023)."},"status":"public","day":"30"},{"corr_author":"1","quality_controlled":"1","file":[{"date_created":"2023-11-20T08:34:57Z","content_type":"application/pdf","file_name":"2023_ESAIM_Cornalba.pdf","success":1,"creator":"dernst","file_id":"14560","access_level":"open_access","checksum":"3aef1475b1882c8dec112df9a5167c39","relation":"main_file","date_updated":"2023-11-20T08:34:57Z","file_size":1508534}],"has_accepted_license":"1","ddc":["510"],"year":"2023","date_created":"2023-11-19T23:00:55Z","issue":"5","doi":"10.1051/m2an/2023077","publication_identifier":{"eissn":["2804-7214"],"issn":["2822-7840"]},"publication":"ESAIM: Mathematical Modelling and Numerical Analysis","page":"3061-3090","article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format."}],"publication_status":"published","external_id":{"isi":["001087237700001"]},"title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime","author":[{"first_name":"Federico","last_name":"Cornalba","orcid":"0000-0002-6269-5149","id":"2CEB641C-A400-11E9-A717-D712E6697425","full_name":"Cornalba, Federico"},{"full_name":"Shardlow, Tony","last_name":"Shardlow","first_name":"Tony"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":57,"related_material":{"link":[{"url":"https://github.com/tonyshardlow/RIDK-FD","relation":"software"}]},"citation":{"apa":"Cornalba, F., &#38; Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/m2an/2023077\">https://doi.org/10.1051/m2an/2023077</a>","chicago":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences, 2023. <a href=\"https://doi.org/10.1051/m2an/2023077\">https://doi.org/10.1051/m2an/2023077</a>.","mla":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 57, no. 5, EDP Sciences, 2023, pp. 3061–90, doi:<a href=\"https://doi.org/10.1051/m2an/2023077\">10.1051/m2an/2023077</a>.","ieee":"F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime,” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 57, no. 5. EDP Sciences, pp. 3061–3090, 2023.","short":"F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.","ista":"Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.","ama":"Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. 2023;57(5):3061-3090. doi:<a href=\"https://doi.org/10.1051/m2an/2023077\">10.1051/m2an/2023077</a>"},"project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"ec_funded":1,"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","day":"01","isi":1,"oa":1,"file_date_updated":"2023-11-20T08:34:57Z","month":"09","language":[{"iso":"eng"}],"date_published":"2023-09-01T00:00:00Z","publisher":"EDP Sciences","department":[{"_id":"JuFi"}],"date_updated":"2025-09-09T13:21:05Z","article_type":"original","intvolume":"        57","oa_version":"Published Version","acknowledgement":"The authors thank the anonymous referees for their careful reading of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered the first part of this project).","type":"journal_article","_id":"14554","scopus_import":"1"},{"citation":{"ieee":"M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 11. Frontiers, 2023.","short":"M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).","ama":"Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. <i>Frontiers in Cell and Developmental Biology</i>. 2023;11. doi:<a href=\"https://doi.org/10.3389/fcell.2023.1287420\">10.3389/fcell.2023.1287420</a>","ista":"Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11, 1287420.","chicago":"Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fcell.2023.1287420\">https://doi.org/10.3389/fcell.2023.1287420</a>.","apa":"Riedl, M., &#38; Sixt, M. K. (2023). The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fcell.2023.1287420\">https://doi.org/10.3389/fcell.2023.1287420</a>","mla":"Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 11, 1287420, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fcell.2023.1287420\">10.3389/fcell.2023.1287420</a>."},"tmp":{"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)","short":"CC BY (4.0)"},"day":"31","status":"public","file_date_updated":"2023-11-20T08:41:15Z","oa":1,"isi":1,"date_updated":"2025-09-09T13:22:00Z","department":[{"_id":"MiSi"}],"publisher":"Frontiers","date_published":"2023-10-31T00:00:00Z","language":[{"iso":"eng"}],"month":"10","acknowledgement":"The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.","type":"journal_article","intvolume":"        11","oa_version":"Published Version","article_type":"original","scopus_import":"1","_id":"14555","quality_controlled":"1","file":[{"file_id":"14561","access_level":"open_access","relation":"main_file","checksum":"61857fc3ebf019354932e7ee684658ce","file_size":2047622,"date_updated":"2023-11-20T08:41:15Z","date_created":"2023-11-20T08:41:15Z","content_type":"application/pdf","file_name":"2023_FrontiersCellDevBio_Riedl.pdf","success":1,"creator":"dernst"}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1","article_number":"1287420","date_created":"2023-11-19T23:00:55Z","year":"2023","publication":"Frontiers in Cell and Developmental Biology","publication_identifier":{"eissn":["2296-634X"]},"doi":"10.3389/fcell.2023.1287420","publication_status":"published","external_id":{"isi":["001100762800001"],"pmid":["38020899"]},"abstract":[{"lang":"eng","text":"The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems."}],"article_processing_charge":"Yes","title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","volume":11,"author":[{"orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael"},{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1},{"type":"journal_article","acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","article_type":"review","intvolume":"        36","oa_version":"Published Version","_id":"14556","scopus_import":"1","oa":1,"file_date_updated":"2024-07-16T08:16:31Z","isi":1,"department":[{"_id":"NiBa"}],"publisher":"Wiley","date_updated":"2025-09-09T13:22:35Z","month":"12","language":[{"iso":"eng"}],"date_published":"2023-12-01T00:00:00Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"status":"public","day":"01","citation":{"chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” <i>Journal of Evolutionary Biology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/jeb.14242\">https://doi.org/10.1111/jeb.14242</a>.","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.14242\">https://doi.org/10.1111/jeb.14242</a>","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” <i>Journal of Evolutionary Biology</i>, vol. 36, no. 12, 14242, Wiley, 2023, doi:<a href=\"https://doi.org/10.1111/jeb.14242\">10.1111/jeb.14242</a>.","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology 36 (2023).","ieee":"E. L. Berdan <i>et al.</i>, “How chromosomal inversions reorient the evolutionary process,” <i>Journal of Evolutionary Biology</i>, vol. 36, no. 12. Wiley, 2023.","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 36(12), 14242.","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. <i>Journal of Evolutionary Biology</i>. 2023;36(12). doi:<a href=\"https://doi.org/10.1111/jeb.14242\">10.1111/jeb.14242</a>"},"volume":36,"author":[{"full_name":"Berdan, Emma L.","first_name":"Emma L.","last_name":"Berdan"},{"first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Fragata, Inês","last_name":"Fragata","first_name":"Inês"},{"last_name":"Gilbert","first_name":"Kimberly J.","full_name":"Gilbert, Kimberly J."},{"full_name":"Jay, Paul","last_name":"Jay","first_name":"Paul"},{"full_name":"Kapun, Martin","first_name":"Martin","last_name":"Kapun"},{"last_name":"Lotterhos","first_name":"Katie E.","full_name":"Lotterhos, Katie E."},{"full_name":"Mérot, Claire","last_name":"Mérot","first_name":"Claire"},{"last_name":"Durmaz Mitchell","first_name":"Esra","full_name":"Durmaz Mitchell, Esra"},{"first_name":"Marta","last_name":"Pascual","full_name":"Pascual, Marta"},{"last_name":"Peichel","first_name":"Catherine L.","full_name":"Peichel, Catherine L."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram"},{"last_name":"Schaeffer","first_name":"Stephen W.","full_name":"Schaeffer, Stephen W."},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Flatt, Thomas","last_name":"Flatt","first_name":"Thomas"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"abstract":[{"text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001098690500001"],"pmid":["37942504"]},"article_processing_charge":"Yes (in subscription journal)","title":"How chromosomal inversions reorient the evolutionary process","article_number":"14242","year":"2023","date_created":"2023-11-19T23:00:55Z","publication":"Journal of Evolutionary Biology","issue":"12","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"doi":"10.1111/jeb.14242","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2023_JourEvolutionaryBio_Berdan.pdf","date_created":"2024-07-16T08:16:31Z","creator":"dernst","success":1,"file_id":"17253","date_updated":"2024-07-16T08:16:31Z","file_size":1401726,"relation":"main_file","checksum":"93ae4fa700aab8646bc62f0adeed8f8f","access_level":"open_access"}],"ddc":["570"],"has_accepted_license":"1"},{"isi":1,"publisher":"Taylor & Francis","department":[{"_id":"HeEd"}],"date_updated":"2025-09-09T13:23:12Z","month":"11","language":[{"iso":"eng"}],"date_published":"2023-11-01T00:00:00Z","acknowledgement":"The first and second named authors are members of GNSAGA – INdAM.\r\nThe third named author was supported by the FWF Grant, Project number I4245–N35","type":"journal_article","article_type":"original","intvolume":"        46","oa_version":"None","_id":"14557","scopus_import":"1","project":[{"grant_number":"I04245","_id":"26AD5D90-B435-11E9-9278-68D0E5697425","name":"Algebraic Footprints of Geometric Features in Homology","call_identifier":"FWF"}],"citation":{"ama":"Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of categories of semilattices. <i>Quaestiones Mathematicae</i>. 2023;46(S1):191-221. doi:<a href=\"https://doi.org/10.2989/16073606.2023.2247731\">10.2989/16073606.2023.2247731</a>","ista":"Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.","ieee":"D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators of categories of semilattices,” <i>Quaestiones Mathematicae</i>, vol. 46, no. S1. Taylor &#38; Francis, pp. 191–221, 2023.","short":"D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023) 191–221.","mla":"Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of Semilattices.” <i>Quaestiones Mathematicae</i>, vol. 46, no. S1, Taylor &#38; Francis, 2023, pp. 191–221, doi:<a href=\"https://doi.org/10.2989/16073606.2023.2247731\">10.2989/16073606.2023.2247731</a>.","chicago":"Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure Operators of Categories of Semilattices.” <i>Quaestiones Mathematicae</i>. Taylor &#38; Francis, 2023. <a href=\"https://doi.org/10.2989/16073606.2023.2247731\">https://doi.org/10.2989/16073606.2023.2247731</a>.","apa":"Dikranjan, D., Giordano Bruno, A., &#38; Zava, N. (2023). Epimorphisms and closure operators of categories of semilattices. <i>Quaestiones Mathematicae</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.2989/16073606.2023.2247731\">https://doi.org/10.2989/16073606.2023.2247731</a>"},"day":"01","status":"public","abstract":[{"lang":"eng","text":"Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem."}],"publication_status":"published","external_id":{"isi":["001098712000006"]},"page":"191-221","article_processing_charge":"No","title":"Epimorphisms and closure operators of categories of semilattices","volume":46,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"D.","last_name":"Dikranjan","full_name":"Dikranjan, D."},{"last_name":"Giordano Bruno","first_name":"A.","full_name":"Giordano Bruno, A."},{"full_name":"Zava, Nicolò","orcid":"0000-0001-8686-1888","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","first_name":"Nicolò","last_name":"Zava"}],"quality_controlled":"1","year":"2023","date_created":"2023-11-19T23:00:55Z","publication":"Quaestiones Mathematicae","issue":"S1","doi":"10.2989/16073606.2023.2247731","publication_identifier":{"issn":["1607-3606"],"eissn":["1727-933X"]}},{"volume":52,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"},{"first_name":"Xiaowei","last_name":"Wu","full_name":"Wu, Xiaowei"}],"external_id":{"isi":["001116719500002"]},"publication_status":"published","abstract":[{"lang":"eng","text":"n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1)  O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with  amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f\r\n in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m\r\n and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds."}],"article_processing_charge":"No","page":"1132-1192","title":"Deterministic near-optimal approximation algorithms for dynamic set cover","date_created":"2023-11-19T23:00:56Z","year":"2023","publication":"SIAM Journal on Computing","doi":"10.1137/21M1428649","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"issue":"5","quality_controlled":"1","type":"journal_article","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures (MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council, UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer (ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I 5982-N, and project Z 422-N. The third author was also supported by the Swedish Research Council (Reg. No. 2015-04659). The fourth author was also supported by the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ, 0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023).","oa_version":"None","intvolume":"        52","article_type":"original","scopus_import":"1","_id":"14558","isi":1,"date_updated":"2025-09-09T13:19:49Z","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"MoHe"}],"date_published":"2023-10-01T00:00:00Z","month":"10","language":[{"iso":"eng"}],"ec_funded":1,"day":"01","status":"public","project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"},{"name":"Efficient algorithms","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"}],"citation":{"mla":"Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” <i>SIAM Journal on Computing</i>, vol. 52, no. 5, Society for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:<a href=\"https://doi.org/10.1137/21M1428649\">10.1137/21M1428649</a>.","chicago":"Bhattacharya, Sayan, Monika Henzinger, Danupon Nanongkai, and Xiaowei Wu. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” <i>SIAM Journal on Computing</i>. 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Wu, “Deterministic near-optimal approximation algorithms for dynamic set cover,” <i>SIAM Journal on Computing</i>, vol. 52, no. 5. Society for Industrial and Applied Mathematics, pp. 1132–1192, 2023.","short":"S. Bhattacharya, M. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing 52 (2023) 1132–1192."}},{"ec_funded":1,"alternative_title":["LNCS"],"status":"public","day":"22","citation":{"mla":"Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, vol. 14215, Springer Nature, 2023, pp. 357–79, doi:<a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">10.1007/978-3-031-45329-8_17</a>.","apa":"Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., &#38; Zikelic, D. (2023). Learning provably stabilizing neural controllers for discrete-time stochastic systems. In <i>21st International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 14215, pp. 357–379). Singapore, Singapore: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">https://doi.org/10.1007/978-3-031-45329-8_17</a>","chicago":"Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” In <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, 14215:357–79. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">https://doi.org/10.1007/978-3-031-45329-8_17</a>.","ama":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably stabilizing neural controllers for discrete-time stochastic systems. In: <i>21st International Symposium on Automated Technology for Verification and Analysis</i>. Vol 14215. Springer Nature; 2023:357-379. doi:<a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">10.1007/978-3-031-45329-8_17</a>","ista":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning provably stabilizing neural controllers for discrete-time stochastic systems. 21st International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.","short":"M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, 21st International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2023, pp. 357–379.","ieee":"M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “Learning provably stabilizing neural controllers for discrete-time stochastic systems,” in <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, Singapore, Singapore, 2023, vol. 14215, pp. 357–379."},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","intvolume":"     14215","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","type":"conference","scopus_import":"1","_id":"14559","isi":1,"oa":1,"date_published":"2023-10-22T00:00:00Z","language":[{"iso":"eng"}],"month":"10","date_updated":"2025-09-09T13:20:26Z","publisher":"Springer Nature","arxiv":1,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_created":"2023-11-19T23:00:56Z","year":"2023","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031453281"]},"doi":"10.1007/978-3-031-45329-8_17","publication":"21st International Symposium on Automated Technology for Verification and Analysis","corr_author":"1","quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2210.05304","open_access":"1"}],"conference":{"start_date":"2023-10-24","name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2023-10-27","location":"Singapore, Singapore"},"author":[{"last_name":"Ansaripour","first_name":"Matin","full_name":"Ansaripour, Matin"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":14215,"article_processing_charge":"No","page":"357-379","publication_status":"published","external_id":{"arxiv":["2210.05304"],"isi":["001456127300017"]},"abstract":[{"text":"We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.","lang":"eng"}],"title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"related_material":{"record":[{"id":"12334","relation":"used_in_publication","status":"public"}]},"article_processing_charge":"No","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP 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Version","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","type":"research_data","_id":"14562","oa":1,"file_date_updated":"2023-11-20T11:49:58Z","month":"11","date_published":"2023-11-21T00:00:00Z","department":[{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2025-04-23T08:46:21Z","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"day":"21","status":"public","citation":{"ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","short":"F.K. Schur, (2023).","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>.","mla":"Schur, Florian KM. <i>Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>."},"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}]},{"scopus_import":"1","_id":"14564","intvolume":"        15","oa_version":"Published Version","article_type":"original","acknowledgement":"The research of B.K. is supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020). This research was conducted during the visits of P.M. Krishna to the Center for Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November 2018 to June 2019 and July 2019 and October 2019, respectively. The authors are very grateful to the three anonymous reviewers who provided very thoughtful and constructive comments during the review process that helped greatly improve and shape the final version of the manuscript.","type":"journal_article","date_published":"2023-11-01T00:00:00Z","language":[{"iso":"eng"}],"month":"11","date_updated":"2025-09-09T13:29:45Z","department":[{"_id":"CaMu"}],"publisher":"American Geophysical Union","isi":1,"file_date_updated":"2023-11-20T11:29:16Z","oa":1,"day":"01","status":"public","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"citation":{"ieee":"B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 11. American Geophysical Union, 2023.","short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023).","ista":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.","ama":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. <i>Journal of Advances in Modeling Earth Systems</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1029/2022ms003391\">10.1029/2022ms003391</a>","chicago":"Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2022ms003391\">https://doi.org/10.1029/2022ms003391</a>.","apa":"Khouider, B., GOSWAMI, B. B., Phani, R., &#38; Majda, A. J. (2023). A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2022ms003391\">https://doi.org/10.1029/2022ms003391</a>","mla":"Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2022ms003391\">10.1029/2022ms003391</a>."},"author":[{"last_name":"Khouider","first_name":"B.","full_name":"Khouider, B."},{"orcid":"0000-0001-8602-3083","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"GOSWAMI, BIDYUT B","first_name":"BIDYUT B","last_name":"GOSWAMI"},{"last_name":"Phani","first_name":"R.","full_name":"Phani, R."},{"full_name":"Majda, A. J.","last_name":"Majda","first_name":"A. J."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":15,"keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","article_processing_charge":"Yes","publication_status":"published","external_id":{"isi":["001106311000001"]},"abstract":[{"lang":"eng","text":"Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized."}],"publication_identifier":{"eissn":["1942-2466"]},"doi":"10.1029/2022ms003391","issue":"11","publication":"Journal of Advances in Modeling Earth Systems","date_created":"2023-11-20T09:18:21Z","year":"2023","article_number":"e2022MS003391","has_accepted_license":"1","ddc":["550"],"quality_controlled":"1","file":[{"relation":"main_file","checksum":"e30329dd985559de0ddc7021ca7382b4","access_level":"open_access","file_size":6435697,"date_updated":"2023-11-20T11:29:16Z","file_id":"14582","creator":"dernst","success":1,"date_created":"2023-11-20T11:29:16Z","file_name":"2023_JAMES_Khoulder.pdf","content_type":"application/pdf"}]},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n"}],"oa":1,"month":"07","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","date_published":"2023-07-11T00:00:00Z","department":[{"_id":"NiBa"}],"publisher":"Zenodo","date_updated":"2025-09-09T13:23:55Z","oa_version":"Published Version","author":[{"first_name":"William","last_name":"Wetzel","full_name":"Wetzel, William"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14552"}]},"_id":"14579","citation":{"ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>","ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>.","short":"W. Wetzel, (2023).","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","mla":"Wetzel, William. <i>HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>.","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133117\">https://doi.org/10.5281/ZENODO.8133117</a>.","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133117\">https://doi.org/10.5281/ZENODO.8133117</a>"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"ddc":["570"],"year":"2023","date_created":"2023-11-20T11:07:45Z","doi":"10.5281/ZENODO.8133117","day":"11","status":"public"},{"year":"2023","date_created":"2023-11-21T11:41:05Z","doi":"10.15479/at:ista:14587","publication_identifier":{"issn":["2663-337X"]},"file":[{"file_id":"14626","file_size":2881100,"date_updated":"2023-11-29T09:09:31Z","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"thesis_Marveggio.pdf","date_created":"2023-11-29T09:09:31Z","creator":"amarvegg","success":1},{"file_size":10189696,"date_updated":"2024-03-20T12:28:32Z","access_level":"closed","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","relation":"source_file","file_id":"14627","creator":"amarvegg","file_name":"Thesis_Marveggio.zip","content_type":"application/zip","date_created":"2023-11-29T09:10:19Z"}],"corr_author":"1","ddc":["515"],"has_accepted_license":"1","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Marveggio, Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","first_name":"Alice","last_name":"Marveggio"}],"related_material":{"record":[{"status":"public","id":"11842","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14597"}]},"abstract":[{"text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.","lang":"eng"}],"publication_status":"published","page":"228","article_processing_charge":"No","degree_awarded":"PhD","title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","supervisor":[{"first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"status":"public","day":"21","alternative_title":["ISTA Thesis"],"project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"citation":{"ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","apa":"Marveggio, A. (2023). <i>Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>.","mla":"Marveggio, Alice. <i>Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>."},"acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","type":"dissertation","oa_version":"Published Version","_id":"14587","oa":1,"file_date_updated":"2024-03-20T12:28:32Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"date_updated":"2026-04-07T13:28:13Z","language":[{"iso":"eng"}],"month":"11","date_published":"2023-11-21T00:00:00Z"},{"type":"journal_article","acknowledgement":"All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript.","article_type":"original","intvolume":"        77","oa_version":"Published Version","_id":"14604","scopus_import":"1","oa":1,"file_date_updated":"2023-11-28T08:12:15Z","isi":1,"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","date_updated":"2025-09-09T13:32:06Z","language":[{"iso":"eng"}],"month":"11","date_published":"2023-11-02T00:00:00Z","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","day":"02","citation":{"mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>.","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. 2023;77(11):2504-2511. doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” <i>Evolution</i>, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023.","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511."},"volume":77,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"related_material":{"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}],"record":[{"id":"14616","relation":"research_data","status":"public"},{"status":"public","id":"14617","relation":"research_data"}]},"pmid":1,"abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001170341900014"],"pmid":["37738212"]},"page":"2504-2511","article_processing_charge":"Yes (in subscription journal)","title":"The X chromosome of insects likely predates the origin of class Insecta","year":"2023","date_created":"2023-11-26T23:00:54Z","publication":"Evolution","issue":"11","publication_identifier":{"eissn":["1558-5646"]},"doi":"10.1093/evolut/qpad169","quality_controlled":"1","file":[{"success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2023_Evolution_Toups.pdf","date_created":"2023-11-28T08:12:15Z","file_size":1399102,"date_updated":"2023-11-28T08:12:15Z","access_level":"open_access","relation":"main_file","checksum":"b66dc10edae92d38918d534e64dda77c","file_id":"14618"}],"ddc":["570"],"has_accepted_license":"1"},{"page":"1062-1069","article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001105882300018"],"pmid":["37968398"]},"title":"Stress granules plug and stabilize damaged endolysosomal membranes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Claudio","last_name":"Bussi","full_name":"Bussi, Claudio"},{"full_name":"Mangiarotti, Agustín","first_name":"Agustín","last_name":"Mangiarotti"},{"first_name":"Christian Eduardo","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"first_name":"Beren","last_name":"Aylan","full_name":"Aylan, Beren"},{"last_name":"Pellegrino","first_name":"Enrica","full_name":"Pellegrino, Enrica"},{"full_name":"Athanasiadi, Natalia","last_name":"Athanasiadi","first_name":"Natalia"},{"full_name":"Fearns, Antony","first_name":"Antony","last_name":"Fearns"},{"first_name":"Angela","last_name":"Rodgers","full_name":"Rodgers, Angela"},{"last_name":"Franzmann","first_name":"Titus M.","full_name":"Franzmann, Titus M."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"full_name":"Gutierrez, Maximiliano G.","first_name":"Maximiliano G.","last_name":"Gutierrez"}],"volume":623,"related_material":{"record":[{"id":"14472","relation":"research_data","status":"public"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}]},"pmid":1,"quality_controlled":"1","file":[{"file_id":"17248","file_size":17047711,"date_updated":"2024-07-16T07:41:39Z","access_level":"open_access","checksum":"b939a19e4c228fbf3beca298ac2ac014","relation":"main_file","content_type":"application/pdf","file_name":"2023_Nature_Bussi.pdf","date_created":"2024-07-16T07:41:39Z","success":1,"creator":"dernst"}],"has_accepted_license":"1","ddc":["570"],"year":"2023","date_created":"2023-11-27T07:56:37Z","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"doi":"10.1038/s41586-023-06726-w","publication":"Nature","isi":1,"oa":1,"file_date_updated":"2024-07-16T07:41:39Z","month":"11","language":[{"iso":"eng"}],"date_published":"2023-11-30T00:00:00Z","department":[{"_id":"AnSa"}],"publisher":"Springer Nature","date_updated":"2025-09-09T13:30:34Z","article_type":"original","intvolume":"       623","oa_version":"Published Version","type":"journal_article","acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). 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. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","_id":"14610","scopus_import":"1","citation":{"chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>.","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, vol. 623, Springer Nature, 2023, pp. 1062–69, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>.","short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature 623 (2023) 1062–1069.","ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>, vol. 623. Springer Nature, pp. 1062–1069, 2023.","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023;623:1062-1069. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 623, 1062–1069."},"tmp":{"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)","short":"CC BY (4.0)"},"day":"30","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"first_name":"Clementine","last_name":"Lasne","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616","full_name":"Lasne, Clementine"},{"last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"type":"research_data","_id":"14614","related_material":{"record":[{"status":"public","id":"14613","relation":"used_in_publication"}]},"article_processing_charge":"No","file_date_updated":"2023-11-30T14:16:59Z","oa":1,"abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"date_published":"2023-12-01T00:00:00Z","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"month":"12","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","date_updated":"2025-09-09T13:33:22Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"}],"date_created":"2023-11-27T16:39:19Z","year":"2023","tmp":{"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)","short":"CC BY (4.0)"},"contributor":[{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","contributor_type":"researcher"}],"doi":"10.15479/AT:ISTA:14614","status":"public","day":"01","citation":{"short":"C. Lasne, M.N. Elkrewi, (2023).","ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023.","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>","chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>.","apa":"Lasne, C., &#38; Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>","mla":"Lasne, Clementine, and Marwan N. Elkrewi. <i>The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>."},"corr_author":"1","file":[{"success":1,"creator":"clasne","date_created":"2023-11-28T13:15:26Z","content_type":"application/zip","file_name":"panorpaX.zip","access_level":"open_access","checksum":"cd0f13322b5156819ecaebd2bc8e7d12","relation":"main_file","file_size":404968272,"date_updated":"2023-11-28T13:15:26Z","file_id":"14625"},{"date_updated":"2023-11-30T14:16:59Z","file_size":2625,"access_level":"open_access","checksum":"9ff600416577687a737cb3c96dfcb26c","relation":"main_file","file_id":"14634","success":1,"creator":"clasne","file_name":"panorpa_readme.txt","content_type":"text/plain","date_created":"2023-11-30T14:16:59Z"}],"has_accepted_license":"1","ddc":["576"]},{"date_created":"2023-11-28T08:01:53Z","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"doi":"10.5061/DRYAD.HX3FFBGKT","day":"15","status":"public","citation":{"chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Dryad, 2023, doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","short":"M.A. Toups, B. Vicoso, (2023).","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.hx3ffbgkt"}],"has_accepted_license":"1","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"}],"type":"research_data_reference","related_material":{"record":[{"status":"public","id":"14604","relation":"used_in_publication"}]},"_id":"14616","article_processing_charge":"No","oa":1,"abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"date_published":"2023-09-15T00:00:00Z","month":"09","title":"The X chromosome of insects likely predates the origin of Class Insecta","date_updated":"2025-09-09T13:32:05Z","publisher":"Dryad","department":[{"_id":"BeVi"}]},{"status":"public","day":"15","doi":"10.5281/ZENODO.8138705","date_created":"2023-11-28T08:04:03Z","year":"2023","ddc":["570"],"has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8138705","open_access":"1"}],"citation":{"ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","short":"M.A. Toups, B. Vicoso, (2023).","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>."},"related_material":{"record":[{"status":"public","id":"14604","relation":"used_in_publication"}]},"_id":"14617","type":"research_data_reference","other_data_license":"MIT License","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"oa_version":"Published Version","date_updated":"2025-09-09T13:32:05Z","publisher":"Zenodo","department":[{"_id":"BeVi"}],"date_published":"2023-09-15T00:00:00Z","title":"The X chromosome of insects likely predates the origin of Class Insecta","month":"09","oa":1,"abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"article_processing_charge":"No"}]