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Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>.","ista":"Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>.","ama":"Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>","ieee":"J. Binysh <i>et al.</i>, “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1.” Zenodo, 2023.","short":"J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023).","chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8329143\">https://doi.org/10.5281/ZENODO.8329143</a>.","apa":"Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J., &#38; Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8329143\">https://doi.org/10.5281/ZENODO.8329143</a>"},"year":"2023"},{"day":"15","issue":"11","article_type":"original","publisher":"Elsevier","department":[{"_id":"DaZi"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"year":"2023","page":"953-967","month":"11","oa":1,"oa_version":"Published Version","status":"public","file_date_updated":"2023-11-20T11:22:52Z","_id":"14551","ddc":["570"],"intvolume":"        14","scopus_import":"1","doi":"10.1016/j.cels.2023.10.007","date_created":"2023-11-19T23:00:54Z","volume":14,"author":[{"last_name":"Briffa","full_name":"Briffa, Amy","first_name":"Amy"},{"first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","last_name":"Hollwey","full_name":"Hollwey, Elizabeth"},{"last_name":"Shahzad","full_name":"Shahzad, Zaigham","first_name":"Zaigham"},{"full_name":"Moore, Jonathan D.","last_name":"Moore","first_name":"Jonathan D."},{"first_name":"David B.","full_name":"Lyons, David B.","last_name":"Lyons"},{"last_name":"Howard","full_name":"Howard, Martin","first_name":"Martin"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"file":[{"checksum":"101fdac59e6f1102d68ef91f2b5bd51a","content_type":"application/pdf","relation":"main_file","file_id":"14580","file_size":5587897,"creator":"dernst","access_level":"open_access","date_updated":"2023-11-20T11:22:52Z","success":1,"date_created":"2023-11-20T11:22:52Z","file_name":"2023_CellSystems_Briffa.pdf"}],"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.","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","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>.","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>.","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.","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.","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>"},"publication":"Cell Systems","publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"corr_author":"1","ec_funded":1,"date_published":"2023-11-15T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37944515"],"isi":["001113459100001"]},"isi":1,"date_updated":"2025-09-09T13:28:50Z","publication_status":"published","title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","project":[{"grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin","_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020"}],"abstract":[{"lang":"eng","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."}],"quality_controlled":"1"},{"publication":"Science","pmid":1,"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>","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.","ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","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>.","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","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.","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."}],"quality_controlled":"1","date_published":"2023-11-09T00:00:00Z","isi":1,"external_id":{"isi":["001138596500033"],"pmid":["37943897"]},"publication_status":"published","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","date_updated":"2025-09-09T13:23:56Z","publication_identifier":{"eissn":["1095-9203"]},"page":"679-683","year":"2023","language":[{"iso":"eng"}],"OA_type":"green","department":[{"_id":"NiBa"}],"article_processing_charge":"No","day":"09","issue":"6671","publisher":"AAAS","article_type":"original","volume":382,"related_material":{"record":[{"relation":"research_data","id":"14579","status":"public"}]},"date_created":"2023-11-19T23:00:54Z","author":[{"full_name":"Robinson, M. L.","last_name":"Robinson","first_name":"M. L."},{"first_name":"P. G.","last_name":"Hahn","full_name":"Hahn, P. G."},{"first_name":"B. D.","full_name":"Inouye, B. D.","last_name":"Inouye"},{"first_name":"N.","last_name":"Underwood","full_name":"Underwood, N."},{"first_name":"S. R.","full_name":"Whitehead, S. R.","last_name":"Whitehead"},{"last_name":"Abbott","full_name":"Abbott, K. C.","first_name":"K. C."},{"full_name":"Bruna, E. M.","last_name":"Bruna","first_name":"E. M."},{"full_name":"Cacho, N. I.","last_name":"Cacho","first_name":"N. I."},{"last_name":"Dyer","full_name":"Dyer, L. A.","first_name":"L. A."},{"first_name":"L.","full_name":"Abdala-Roberts, L.","last_name":"Abdala-Roberts"},{"first_name":"W. J.","last_name":"Allen","full_name":"Allen, W. J."},{"first_name":"J. F.","last_name":"Andrade","full_name":"Andrade, J. F."},{"first_name":"D. F.","full_name":"Angulo, D. F.","last_name":"Angulo"},{"first_name":"D.","last_name":"Anjos","full_name":"Anjos, D."},{"first_name":"D. N.","full_name":"Anstett, D. N.","last_name":"Anstett"},{"last_name":"Bagchi","full_name":"Bagchi, R.","first_name":"R."},{"full_name":"Bagchi, S.","last_name":"Bagchi","first_name":"S."},{"first_name":"M.","full_name":"Barbosa, M.","last_name":"Barbosa"},{"full_name":"Barrett, S.","last_name":"Barrett","first_name":"S."},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","last_name":"Baskett"},{"first_name":"E.","full_name":"Ben-Simchon, E.","last_name":"Ben-Simchon"},{"last_name":"Bloodworth","full_name":"Bloodworth, K. J.","first_name":"K. J."},{"first_name":"J. L.","last_name":"Bronstein","full_name":"Bronstein, J. L."},{"first_name":"Y. M.","last_name":"Buckley","full_name":"Buckley, Y. M."},{"last_name":"Burghardt","full_name":"Burghardt, K. T.","first_name":"K. T."},{"last_name":"Bustos-Segura","full_name":"Bustos-Segura, C.","first_name":"C."},{"first_name":"E. S.","last_name":"Calixto","full_name":"Calixto, E. S."},{"full_name":"Carvalho, R. L.","last_name":"Carvalho","first_name":"R. L."},{"full_name":"Castagneyrol, B.","last_name":"Castagneyrol","first_name":"B."},{"full_name":"Chiuffo, M. C.","last_name":"Chiuffo","first_name":"M. C."},{"first_name":"D.","full_name":"Cinoğlu, D.","last_name":"Cinoğlu"},{"last_name":"Cinto Mejía","full_name":"Cinto Mejía, E.","first_name":"E."},{"last_name":"Cock","full_name":"Cock, M. C.","first_name":"M. C."},{"first_name":"R.","full_name":"Cogni, R.","last_name":"Cogni"},{"first_name":"O. L.","full_name":"Cope, O. L.","last_name":"Cope"},{"last_name":"Cornelissen","full_name":"Cornelissen, T.","first_name":"T."},{"first_name":"D. R.","last_name":"Cortez","full_name":"Cortez, D. R."},{"full_name":"Crowder, D. W.","last_name":"Crowder","first_name":"D. W."},{"full_name":"Dallstream, C.","last_name":"Dallstream","first_name":"C."},{"first_name":"W.","full_name":"Dáttilo, W.","last_name":"Dáttilo"},{"first_name":"J. K.","full_name":"Davis, J. K.","last_name":"Davis"},{"last_name":"Dimarco","full_name":"Dimarco, R. D.","first_name":"R. D."},{"first_name":"H. E.","full_name":"Dole, H. E.","last_name":"Dole"},{"first_name":"I. N.","full_name":"Egbon, I. N.","last_name":"Egbon"},{"first_name":"M.","last_name":"Eisenring","full_name":"Eisenring, M."},{"first_name":"A.","full_name":"Ejomah, A.","last_name":"Ejomah"},{"last_name":"Elderd","full_name":"Elderd, B. D.","first_name":"B. D."},{"first_name":"M. J.","last_name":"Endara","full_name":"Endara, M. J."},{"first_name":"M. D.","last_name":"Eubanks","full_name":"Eubanks, M. D."},{"last_name":"Everingham","full_name":"Everingham, S. E.","first_name":"S. E."},{"full_name":"Farah, K. N.","last_name":"Farah","first_name":"K. N."},{"full_name":"Farias, R. P.","last_name":"Farias","first_name":"R. P."},{"full_name":"Fernandes, A. P.","last_name":"Fernandes","first_name":"A. P."},{"full_name":"Fernandes, G. W.","last_name":"Fernandes","first_name":"G. W."},{"first_name":"M.","full_name":"Ferrante, M.","last_name":"Ferrante"},{"first_name":"A.","last_name":"Finn","full_name":"Finn, A."},{"last_name":"Florjancic","full_name":"Florjancic, G. A.","first_name":"G. A."},{"full_name":"Forister, M. L.","last_name":"Forister","first_name":"M. L."},{"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","full_name":"França, F. M.","first_name":"F. M."},{"first_name":"A. S.","last_name":"Getman-Pickering","full_name":"Getman-Pickering, A. S."},{"first_name":"Z.","last_name":"Getman-Pickering","full_name":"Getman-Pickering, Z."},{"first_name":"E.","full_name":"Gianoli, E.","last_name":"Gianoli"},{"last_name":"Gooden","full_name":"Gooden, B.","first_name":"B."},{"first_name":"M. M.","full_name":"Gossner, M. M.","last_name":"Gossner"},{"full_name":"Greig, K. A.","last_name":"Greig","first_name":"K. A."},{"first_name":"S.","last_name":"Gripenberg","full_name":"Gripenberg, S."},{"first_name":"R.","full_name":"Groenteman, R.","last_name":"Groenteman"},{"first_name":"P.","last_name":"Grof-Tisza","full_name":"Grof-Tisza, P."},{"first_name":"N.","full_name":"Haack, N.","last_name":"Haack"},{"full_name":"Hahn, L.","last_name":"Hahn","first_name":"L."},{"first_name":"S. M.","full_name":"Haq, S. M.","last_name":"Haq"},{"first_name":"A. M.","full_name":"Helms, A. M.","last_name":"Helms"},{"full_name":"Hennecke, J.","last_name":"Hennecke","first_name":"J."},{"full_name":"Hermann, S. L.","last_name":"Hermann","first_name":"S. L."},{"first_name":"L. M.","full_name":"Holeski, L. M.","last_name":"Holeski"},{"first_name":"S.","full_name":"Holm, S.","last_name":"Holm"},{"last_name":"Hutchinson","full_name":"Hutchinson, M. C.","first_name":"M. C."},{"full_name":"Jackson, E. E.","last_name":"Jackson","first_name":"E. E."},{"full_name":"Kagiya, S.","last_name":"Kagiya","first_name":"S."},{"full_name":"Kalske, A.","last_name":"Kalske","first_name":"A."},{"last_name":"Kalwajtys","full_name":"Kalwajtys, M.","first_name":"M."},{"full_name":"Karban, R.","last_name":"Karban","first_name":"R."},{"first_name":"R.","full_name":"Kariyat, R.","last_name":"Kariyat"},{"last_name":"Keasar","full_name":"Keasar, T.","first_name":"T."},{"full_name":"Kersch-Becker, M. F.","last_name":"Kersch-Becker","first_name":"M. F."},{"last_name":"Kharouba","full_name":"Kharouba, H. M.","first_name":"H. M."},{"full_name":"Kim, T. N.","last_name":"Kim","first_name":"T. N."},{"full_name":"Kimuyu, D. M.","last_name":"Kimuyu","first_name":"D. M."},{"first_name":"J.","full_name":"Kluse, J.","last_name":"Kluse"},{"last_name":"Koerner","full_name":"Koerner, S. E.","first_name":"S. E."},{"full_name":"Komatsu, K. J.","last_name":"Komatsu","first_name":"K. 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M.","last_name":"Moore"},{"last_name":"Moreira","full_name":"Moreira, X.","first_name":"X."},{"last_name":"Morrison","full_name":"Morrison, C. R.","first_name":"C. R."},{"full_name":"Moshobane, M. C.","last_name":"Moshobane","first_name":"M. C."},{"last_name":"Muola","full_name":"Muola, A.","first_name":"A."},{"full_name":"Nakadai, R.","last_name":"Nakadai","first_name":"R."},{"last_name":"Nakajima","full_name":"Nakajima, K.","first_name":"K."},{"first_name":"S.","full_name":"Novais, S.","last_name":"Novais"},{"first_name":"C. O.","last_name":"Ogbebor","full_name":"Ogbebor, C. O."},{"full_name":"Ohsaki, H.","last_name":"Ohsaki","first_name":"H."},{"first_name":"V. S.","full_name":"Pan, V. S.","last_name":"Pan"},{"first_name":"N. A.","full_name":"Pardikes, N. A.","last_name":"Pardikes"},{"full_name":"Pareja, M.","last_name":"Pareja","first_name":"M."},{"first_name":"N.","last_name":"Parthasarathy","full_name":"Parthasarathy, N."},{"full_name":"Pawar, R. R.","last_name":"Pawar","first_name":"R. R."},{"first_name":"Q.","full_name":"Paynter, Q.","last_name":"Paynter"},{"last_name":"Pearse","full_name":"Pearse, I. S.","first_name":"I. S."},{"full_name":"Penczykowski, R. M.","last_name":"Penczykowski","first_name":"R. M."},{"first_name":"A. A.","last_name":"Pepi","full_name":"Pepi, A. A."},{"first_name":"C. C.","full_name":"Pereira, C. C.","last_name":"Pereira"},{"first_name":"S. S.","full_name":"Phartyal, S. S.","last_name":"Phartyal"},{"full_name":"Piper, F. I.","last_name":"Piper","first_name":"F. I."},{"first_name":"K.","full_name":"Poveda, K.","last_name":"Poveda"},{"first_name":"E. G.","last_name":"Pringle","full_name":"Pringle, E. 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J.M.","last_name":"Tack"},{"full_name":"Tayal, M.","last_name":"Tayal","first_name":"M."},{"last_name":"Tooker","full_name":"Tooker, J. F.","first_name":"J. F."},{"first_name":"D.","full_name":"Torrico-Bazoberry, D.","last_name":"Torrico-Bazoberry"},{"first_name":"K.","full_name":"Tougeron, K.","last_name":"Tougeron"},{"first_name":"A. M.","full_name":"Trowbridge, A. M.","last_name":"Trowbridge"},{"first_name":"S.","last_name":"Utsumi","full_name":"Utsumi, S."},{"last_name":"Uyi","full_name":"Uyi, O.","first_name":"O."},{"first_name":"J. L.","full_name":"Vaca-Uribe, J. L.","last_name":"Vaca-Uribe"},{"last_name":"Valtonen","full_name":"Valtonen, A.","first_name":"A."},{"first_name":"L. J.A.","full_name":"Van Dijk, L. J.A.","last_name":"Van Dijk"},{"last_name":"Vandvik","full_name":"Vandvik, V.","first_name":"V."},{"full_name":"Villellas, J.","last_name":"Villellas","first_name":"J."},{"full_name":"Waller, L. P.","last_name":"Waller","first_name":"L. P."},{"last_name":"Weber","full_name":"Weber, M. G.","first_name":"M. G."},{"first_name":"A.","full_name":"Yamawo, A.","last_name":"Yamawo"},{"first_name":"S.","last_name":"Yim","full_name":"Yim, S."},{"last_name":"Zarnetske","full_name":"Zarnetske, P. L.","first_name":"P. L."},{"last_name":"Zehr","full_name":"Zehr, L. N.","first_name":"L. N."},{"last_name":"Zhong","full_name":"Zhong, Z.","first_name":"Z."},{"last_name":"Wetzel","full_name":"Wetzel, W. C.","first_name":"W. C."}],"main_file_link":[{"open_access":"1","url":"https://centaur.reading.ac.uk/113962/1/adh8830_CombinedPDF_v6.pdf"}],"intvolume":"       382","doi":"10.1126/science.adh8830","scopus_import":"1","_id":"14552","status":"public","oa_version":"Submitted Version","month":"11","oa":1},{"arxiv":1,"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"corr_author":"1","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"}],"quality_controlled":"1","date_updated":"2024-10-09T21:07:19Z","publication_status":"published","title":"Continuous-variable quantum tomography of high-amplitude states","date_published":"2023-10-30T00:00:00Z","external_id":{"arxiv":["2212.07406"]},"type":"journal_article","publication":"Physical Review A","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>.","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.","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>","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023).","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>"},"status":"public","oa_version":"Preprint","_id":"14553","article_number":"042430","oa":1,"month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.07406"}],"author":[{"orcid":"0000-0001-7242-015X","full_name":"Fedotova, Ekaterina","last_name":"Fedotova","first_name":"Ekaterina","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab"},{"full_name":"Kuznetsov, Nikolai","last_name":"Kuznetsov","first_name":"Nikolai"},{"last_name":"Tiunov","full_name":"Tiunov, Egor","first_name":"Egor"},{"full_name":"Ulanov, A. E.","last_name":"Ulanov","first_name":"A. E."},{"last_name":"Lvovsky","full_name":"Lvovsky, A. I.","first_name":"A. I."}],"date_created":"2023-11-19T23:00:54Z","volume":108,"scopus_import":"1","doi":"10.1103/PhysRevA.108.042430","intvolume":"       108","article_processing_charge":"No","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","article_type":"original","issue":"4","day":"30","language":[{"iso":"eng"}],"year":"2023"},{"related_material":{"link":[{"url":"https://github.com/tonyshardlow/RIDK-FD","relation":"software"}]},"date_created":"2023-11-19T23:00:55Z","volume":57,"author":[{"orcid":"0000-0002-6269-5149","full_name":"Cornalba, Federico","last_name":"Cornalba","first_name":"Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425"},{"first_name":"Tony","last_name":"Shardlow","full_name":"Shardlow, Tony"}],"intvolume":"        57","scopus_import":"1","doi":"10.1051/m2an/2023077","status":"public","oa_version":"Published Version","ddc":["510"],"_id":"14554","file_date_updated":"2023-11-20T08:34:57Z","month":"09","oa":1,"page":"3061-3090","language":[{"iso":"eng"}],"year":"2023","department":[{"_id":"JuFi"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","issue":"5","day":"01","article_type":"original","publisher":"EDP Sciences","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-09-01T00:00:00Z","external_id":{"isi":["001087237700001"]},"date_updated":"2025-09-09T13:21:05Z","title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"publication_status":"published","ec_funded":1,"publication_identifier":{"eissn":["2804-7214"],"issn":["2822-7840"]},"corr_author":"1","publication":"ESAIM: Mathematical Modelling and Numerical Analysis","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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.","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.","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>","short":"F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.","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>.","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>"},"type":"journal_article","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).","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"3aef1475b1882c8dec112df9a5167c39","file_size":1508534,"file_id":"14560","success":1,"date_updated":"2023-11-20T08:34:57Z","creator":"dernst","access_level":"open_access","file_name":"2023_ESAIM_Cornalba.pdf","date_created":"2023-11-20T08:34:57Z"}]},{"oa_version":"Published Version","status":"public","file_date_updated":"2023-11-20T08:41:15Z","_id":"14555","ddc":["570"],"article_number":"1287420","oa":1,"month":"10","author":[{"last_name":"Riedl","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"}],"date_created":"2023-11-19T23:00:55Z","volume":11,"scopus_import":"1","doi":"10.3389/fcell.2023.1287420","intvolume":"        11","has_accepted_license":"1","article_processing_charge":"Yes","department":[{"_id":"MiSi"}],"publisher":"Frontiers","article_type":"original","day":"31","language":[{"iso":"eng"}],"year":"2023","publication_identifier":{"eissn":["2296-634X"]},"corr_author":"1","quality_controlled":"1","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."}],"date_updated":"2025-09-09T13:22:00Z","publication_status":"published","title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","date_published":"2023-10-31T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"pmid":["38020899"],"isi":["001100762800001"]},"type":"journal_article","acknowledgement":"The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.","file":[{"file_size":2047622,"file_id":"14561","relation":"main_file","content_type":"application/pdf","checksum":"61857fc3ebf019354932e7ee684658ce","file_name":"2023_FrontiersCellDevBio_Riedl.pdf","date_created":"2023-11-20T08:41:15Z","success":1,"date_updated":"2023-11-20T08:41:15Z","creator":"dernst","access_level":"open_access"}],"publication":"Frontiers in Cell and Developmental Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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.","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>","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).","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>","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>."},"pmid":1},{"date_updated":"2025-09-09T13:22:35Z","publication_status":"published","title":"How chromosomal inversions reorient the evolutionary process","date_published":"2023-12-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"isi":1,"external_id":{"pmid":["37942504"],"isi":["001098690500001"]},"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>","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>.","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).","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>","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.","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>.","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."},"pmid":1,"publication":"Journal of Evolutionary Biology","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"93ae4fa700aab8646bc62f0adeed8f8f","file_id":"17253","file_size":1401726,"success":1,"date_updated":"2024-07-16T08:16:31Z","access_level":"open_access","creator":"dernst","file_name":"2023_JourEvolutionaryBio_Berdan.pdf","date_created":"2024-07-16T08:16:31Z"}],"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.","scopus_import":"1","doi":"10.1111/jeb.14242","intvolume":"        36","author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Inês","full_name":"Fragata, Inês","last_name":"Fragata"},{"first_name":"Kimberly J.","last_name":"Gilbert","full_name":"Gilbert, Kimberly J."},{"full_name":"Jay, Paul","last_name":"Jay","first_name":"Paul"},{"first_name":"Martin","last_name":"Kapun","full_name":"Kapun, Martin"},{"first_name":"Katie E.","last_name":"Lotterhos","full_name":"Lotterhos, Katie E."},{"full_name":"Mérot, Claire","last_name":"Mérot","first_name":"Claire"},{"first_name":"Esra","last_name":"Durmaz Mitchell","full_name":"Durmaz Mitchell, Esra"},{"first_name":"Marta","last_name":"Pascual","full_name":"Pascual, Marta"},{"last_name":"Peichel","full_name":"Peichel, Catherine L.","first_name":"Catherine L."},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Stephen W.","last_name":"Schaeffer","full_name":"Schaeffer, Stephen W."},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Flatt","full_name":"Flatt, Thomas","first_name":"Thomas"}],"date_created":"2023-11-19T23:00:55Z","volume":36,"oa":1,"month":"12","status":"public","oa_version":"Published Version","file_date_updated":"2024-07-16T08:16:31Z","_id":"14556","ddc":["570"],"article_number":"14242","language":[{"iso":"eng"}],"year":"2023","license":"https://creativecommons.org/licenses/by-nc/4.0/","publisher":"Wiley","article_type":"review","issue":"12","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"NiBa"}]},{"page":"191-221","language":[{"iso":"eng"}],"year":"2023","article_processing_charge":"No","department":[{"_id":"HeEd"}],"article_type":"original","publisher":"Taylor & Francis","issue":"S1","day":"01","author":[{"full_name":"Dikranjan, D.","last_name":"Dikranjan","first_name":"D."},{"first_name":"A.","full_name":"Giordano Bruno, A.","last_name":"Giordano Bruno"},{"first_name":"Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","orcid":"0000-0001-8686-1888","full_name":"Zava, Nicolò","last_name":"Zava"}],"date_created":"2023-11-19T23:00:55Z","volume":46,"scopus_import":"1","doi":"10.2989/16073606.2023.2247731","intvolume":"        46","status":"public","oa_version":"None","_id":"14557","month":"11","publication":"Quaestiones Mathematicae","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>","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>.","short":"D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023) 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.","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.","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>."},"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","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"date_updated":"2025-09-09T13:23:12Z","title":"Epimorphisms and closure operators of categories of semilattices","publication_status":"published","project":[{"_id":"26AD5D90-B435-11E9-9278-68D0E5697425","name":"Algebraic Footprints of Geometric Features in Homology","call_identifier":"FWF","grant_number":"I04245"}],"date_published":"2023-11-01T00:00:00Z","external_id":{"isi":["001098712000006"]},"isi":1,"publication_identifier":{"issn":["1607-3606"],"eissn":["1727-933X"]}},{"publication":"SIAM Journal on Computing","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/21M1428649\">https://doi.org/10.1137/21M1428649</a>.","apa":"Bhattacharya, S., Henzinger, M., Nanongkai, D., &#38; Wu, X. (2023). Deterministic near-optimal approximation algorithms for dynamic set cover. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1428649\">https://doi.org/10.1137/21M1428649</a>","short":"S. Bhattacharya, M. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing 52 (2023) 1132–1192.","ieee":"S. Bhattacharya, M. Henzinger, D. Nanongkai, and X. 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.","ama":"Bhattacharya S, Henzinger M, Nanongkai D, Wu X. Deterministic near-optimal approximation algorithms for dynamic set cover. <i>SIAM Journal on Computing</i>. 2023;52(5):1132-1192. doi:<a href=\"https://doi.org/10.1137/21M1428649\">10.1137/21M1428649</a>","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>.","ista":"Bhattacharya S, Henzinger M, Nanongkai D, Wu X. 2023. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5), 1132–1192."},"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).","type":"journal_article","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"date_updated":"2025-09-09T13:19:49Z","title":"Deterministic near-optimal approximation algorithms for dynamic set cover","publication_status":"published","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"},{"name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"}],"external_id":{"isi":["001116719500002"]},"date_published":"2023-10-01T00:00:00Z","isi":1,"ec_funded":1,"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"page":"1132-1192","language":[{"iso":"eng"}],"year":"2023","article_processing_charge":"No","department":[{"_id":"MoHe"}],"publisher":"Society for Industrial and Applied Mathematics","article_type":"original","issue":"5","day":"01","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"},{"last_name":"Wu","full_name":"Wu, Xiaowei","first_name":"Xiaowei"}],"date_created":"2023-11-19T23:00:56Z","volume":52,"scopus_import":"1","doi":"10.1137/21M1428649","intvolume":"        52","oa_version":"None","status":"public","_id":"14558","month":"10"},{"language":[{"iso":"eng"}],"year":"2023","page":"357-379","day":"22","publisher":"Springer Nature","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"article_processing_charge":"No","intvolume":"     14215","scopus_import":"1","doi":"10.1007/978-3-031-45329-8_17","date_created":"2023-11-19T23:00:56Z","volume":14215,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2210.05304"}],"author":[{"last_name":"Ansaripour","full_name":"Ansaripour, Matin","first_name":"Matin"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"month":"10","oa":1,"status":"public","oa_version":"Preprint","_id":"14559","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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>.","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.","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>","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.","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.","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>.","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>"},"publication":"21st International Symposium on Automated Technology for Verification and Analysis","alternative_title":["LNCS"],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","location":"Singapore, Singapore","start_date":"2023-10-24","end_date":"2023-10-27"},"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","external_id":{"arxiv":["2210.05304"],"isi":["001456127300017"]},"isi":1,"date_published":"2023-10-22T00:00:00Z","date_updated":"2025-09-09T13:20:26Z","title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","publication_status":"published","project":[{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"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"}],"quality_controlled":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031453281"],"issn":["0302-9743"]},"corr_author":"1","ec_funded":1,"arxiv":1},{"date_created":"2023-11-20T09:22:33Z","related_material":{"record":[{"relation":"used_in_publication","id":"12334","status":"public"}]},"author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"doi":"10.15479/AT:ISTA:14562","status":"public","oa_version":"Published Version","file_date_updated":"2023-11-20T11:49:58Z","ddc":["570"],"_id":"14562","month":"11","oa":1,"license":"https://creativecommons.org/licenses/by-sa/4.0/","contributor":[{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","orcid":"0000-0001-7149-769X","last_name":"Fäßler"},{"first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","contributor_type":"researcher","last_name":"Javoor"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Datler","orcid":"0000-0002-3616-8580","contributor_type":"researcher"},{"first_name":"Hermann","contributor_type":"researcher","last_name":"Döring"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","last_name":"Hofer","contributor_type":"researcher"},{"contributor_type":"researcher","orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Faix","contributor_type":"researcher","first_name":"Jan"},{"first_name":"Klemens","contributor_type":"researcher","last_name":"Rottner"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","contributor_type":"researcher","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"year":"2023","department":[{"_id":"FlSc"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"has_accepted_license":"1","article_processing_charge":"No","day":"21","publisher":"Institute of Science and Technology Austria","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"}],"tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"date_published":"2023-11-21T00:00:00Z","date_updated":"2025-04-23T08:46:21Z","title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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>.","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>","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).","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>."},"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","file":[{"file_size":1581687449,"file_id":"14570","content_type":"application/zip","relation":"main_file","checksum":"e9bab797b44614f144a5b02d9636f8c3","date_created":"2023-11-20T10:27:17Z","file_name":"Figure2.zip","date_updated":"2023-11-20T10:27:17Z","success":1,"creator":"fschur","access_level":"open_access"},{"relation":"main_file","content_type":"application/zip","checksum":"4efd388cccd03c549fc90f6e46d37006","file_id":"14571","file_size":116088565,"date_updated":"2023-11-20T10:29:18Z","success":1,"creator":"fschur","access_level":"open_access","file_name":"SupplementaryFigure3.zip","date_created":"2023-11-20T10:29:18Z"},{"date_created":"2023-11-20T10:44:39Z","file_name":"Figure5.zip","date_updated":"2023-11-20T10:44:39Z","success":1,"access_level":"open_access","creator":"fschur","file_id":"14572","file_size":5154614201,"content_type":"application/zip","relation":"main_file","checksum":"bdeb232dc94d0c22a3f7e0d18189ce89"},{"checksum":"83aee17d621a05d865f68f39c8892d27","relation":"main_file","content_type":"application/zip","file_size":1277893286,"file_id":"14573","creator":"fschur","access_level":"open_access","success":1,"date_updated":"2023-11-20T10:46:00Z","file_name":"SupplementaryFigure7.zip","date_created":"2023-11-20T10:46:00Z"},{"content_type":"application/zip","relation":"main_file","checksum":"fb9beb6fe15c8dac6679dd02044d2ea6","file_size":228485124,"file_id":"14574","success":1,"date_updated":"2023-11-20T10:46:08Z","creator":"fschur","access_level":"open_access","date_created":"2023-11-20T10:46:08Z","file_name":"SupplementaryFigure9.zip"},{"file_id":"14575","file_size":1226788198,"checksum":"4f3644e5feabe4824486d56885bb79fe","relation":"main_file","content_type":"application/zip","file_name":"SupplementaryFigure10.zip","date_created":"2023-11-20T10:46:32Z","creator":"fschur","access_level":"open_access","date_updated":"2023-11-20T10:46:32Z","success":1},{"file_name":"SupplementaryFigure11.zip","date_created":"2023-11-20T10:46:17Z","creator":"fschur","access_level":"open_access","date_updated":"2023-11-20T10:46:17Z","success":1,"file_id":"14576","file_size":277577131,"checksum":"96167f722ed0ca78e30681cd1573b9d7","relation":"main_file","content_type":"application/zip"},{"checksum":"d1e03c9805c18cfbc2e9fdf38a9f556f","relation":"main_file","content_type":"application/zip","file_id":"14577","file_size":591483468,"access_level":"open_access","creator":"fschur","success":1,"date_updated":"2023-11-20T10:46:29Z","file_name":"SupplementaryFigure15.zip","date_created":"2023-11-20T10:46:29Z"},{"date_updated":"2023-11-20T10:47:00Z","success":1,"access_level":"open_access","creator":"fschur","date_created":"2023-11-20T10:47:00Z","file_name":"SupplementaryFigure17.zip","content_type":"application/zip","relation":"main_file","checksum":"4d437c04fdb3c1e699618063c4bd21c3","file_size":1709528579,"file_id":"14578"},{"checksum":"967b5378a4f16c43f490eae328afe50e","relation":"main_file","content_type":"application/zip","file_id":"14581","file_size":1920765280,"access_level":"open_access","creator":"fschur","date_updated":"2023-11-20T11:26:36Z","success":1,"file_name":"SupplementaryFigure4.zip","date_created":"2023-11-20T11:26:36Z"},{"file_id":"14583","file_size":3013566196,"relation":"main_file","content_type":"application/zip","checksum":"11899986cf0b471d258fe168ee33a3ea","file_name":"Figure1_partA.zip","date_created":"2023-11-20T11:38:12Z","success":1,"date_updated":"2023-11-20T11:38:12Z","access_level":"open_access","creator":"fschur"},{"checksum":"c452afe1ab506d58d32e601d5b3878bb","content_type":"application/zip","relation":"main_file","file_size":3250260203,"file_id":"14584","access_level":"open_access","creator":"fschur","success":1,"date_updated":"2023-11-20T11:43:23Z","date_created":"2023-11-20T11:43:23Z","file_name":"Figure1_partB.zip"},{"content_type":"text/rtf","relation":"main_file","checksum":"223c98eceecbe65dd268f4f363a620d8","file_id":"14585","file_size":1460,"date_updated":"2023-11-20T11:49:58Z","success":1,"access_level":"open_access","creator":"fschur","date_created":"2023-11-20T11:49:58Z","file_name":"ReadMe.rtf"}]},{"publication_identifier":{"eissn":["1942-2466"]},"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","date_published":"2023-11-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"external_id":{"isi":["001106311000001"]},"isi":1,"publication_status":"published","title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","date_updated":"2025-09-09T13:29:45Z","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","file":[{"file_size":6435697,"file_id":"14582","content_type":"application/pdf","relation":"main_file","checksum":"e30329dd985559de0ddc7021ca7382b4","date_created":"2023-11-20T11:29:16Z","file_name":"2023_JAMES_Khoulder.pdf","date_updated":"2023-11-20T11:29:16Z","success":1,"access_level":"open_access","creator":"dernst"}],"publication":"Journal of Advances in Modeling Earth Systems","citation":{"short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023).","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>","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.","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>.","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.","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>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"e2022MS003391","file_date_updated":"2023-11-20T11:29:16Z","_id":"14564","ddc":["550"],"status":"public","oa_version":"Published Version","month":"11","oa":1,"volume":15,"date_created":"2023-11-20T09:18:21Z","author":[{"first_name":"B.","last_name":"Khouider","full_name":"Khouider, B."},{"full_name":"GOSWAMI, BIDYUT B","last_name":"GOSWAMI","orcid":"0000-0001-8602-3083","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"BIDYUT B"},{"first_name":"R.","last_name":"Phani","full_name":"Phani, R."},{"first_name":"A. J.","full_name":"Majda, A. J.","last_name":"Majda"}],"intvolume":"        15","doi":"10.1029/2022ms003391","scopus_import":"1","department":[{"_id":"CaMu"}],"article_processing_charge":"Yes","has_accepted_license":"1","issue":"11","day":"01","article_type":"original","publisher":"American Geophysical Union","keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"year":"2023","language":[{"iso":"eng"}]},{"month":"07","oa":1,"_id":"14579","ddc":["570"],"oa_version":"Published Version","status":"public","date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133117","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","date_updated":"2025-09-09T13:23:55Z","date_created":"2023-11-20T11:07:45Z","related_material":{"record":[{"relation":"used_in_publication","id":"14552","status":"public"}]},"author":[{"first_name":"William","full_name":"Wetzel, William","last_name":"Wetzel"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"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"}],"day":"11","publisher":"Zenodo","department":[{"_id":"NiBa"}],"article_processing_charge":"No","type":"research_data_reference","year":"2023","citation":{"ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","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>","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>.","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>.","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>","short":"W. Wetzel, (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","date_updated":"2025-09-09T13:32:46Z","date_published":"2023-11-14T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2308.10886"],"pmid":["37962445"],"isi":["001137066700001"]},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances."}],"corr_author":"1","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"arxiv":1,"citation":{"ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110.","mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>.","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. 2023;159(18). doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>","ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” <i>Journal of Chemical Physics</i>, vol. 159, no. 18. AIP Publishing, 2023.","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>.","apa":"Reinhardt, A., Chew, P. Y., &#38; Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication":"Journal of Chemical Physics","file":[{"access_level":"open_access","creator":"dernst","date_updated":"2023-11-28T08:39:06Z","success":1,"date_created":"2023-11-28T08:39:06Z","file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","checksum":"f668ee0d07096eef81159d05bc27aabc","content_type":"application/pdf","relation":"main_file","file_size":6276059,"file_id":"14620"}],"type":"journal_article","acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","doi":"10.1063/5.0173341","scopus_import":"1","intvolume":"       159","author":[{"first_name":"Aleks","full_name":"Reinhardt, Aleks","last_name":"Reinhardt"},{"first_name":"Pin Yu","last_name":"Chew","full_name":"Chew, Pin Yu"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632"}],"volume":159,"related_material":{"record":[{"status":"public","id":"14619","relation":"research_data"}]},"date_created":"2023-11-26T23:00:54Z","oa":1,"month":"11","_id":"14603","file_date_updated":"2023-11-28T08:39:06Z","ddc":["530","540"],"status":"public","oa_version":"Published Version","article_number":"184110","year":"2023","language":[{"iso":"eng"}],"article_type":"original","publisher":"AIP Publishing","day":"14","issue":"18","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","department":[{"_id":"BiCh"}]},{"file":[{"file_name":"2023_Evolution_Toups.pdf","date_created":"2023-11-28T08:12:15Z","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2023-11-28T08:12:15Z","file_id":"14618","file_size":1399102,"checksum":"b66dc10edae92d38918d534e64dda77c","relation":"main_file","content_type":"application/pdf"}],"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.","type":"journal_article","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","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>","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>.","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>.","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.","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>"},"publication":"Evolution","publication_identifier":{"eissn":["1558-5646"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001170341900014"],"pmid":["37738212"]},"isi":1,"date_published":"2023-11-02T00:00:00Z","date_updated":"2025-09-09T13:32:06Z","publication_status":"published","title":"The X chromosome of insects likely predates the origin of class Insecta","quality_controlled":"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"}],"day":"02","issue":"11","article_type":"original","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"year":"2023","page":"2504-2511","month":"11","oa":1,"status":"public","oa_version":"Published Version","file_date_updated":"2023-11-28T08:12:15Z","_id":"14604","ddc":["570"],"intvolume":"        77","scopus_import":"1","doi":"10.1093/evolut/qpad169","date_created":"2023-11-26T23:00:54Z","related_material":{"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}],"record":[{"id":"14616","relation":"research_data","status":"public"},{"relation":"research_data","id":"14617","status":"public"}]},"volume":77,"author":[{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}]},{"acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (Grants No. 17318122 and No. 17306721). The authors are grateful for the research computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","type":"journal_article","citation":{"short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).","apa":"Ouyang, N., Zeng, Z., Wang, C., Wang, Q., &#38; Chen, Y. (2023). Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>","chicago":"Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>.","ista":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 108(17), 174302.","mla":"Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>, vol. 108, no. 17, 174302, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>.","ieee":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),” <i>Physical Review B</i>, vol. 108, no. 17. American Physical Society, 2023.","ama":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. 2023;108(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Physical Review B","corr_author":"1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"ec_funded":1,"title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","publication_status":"published","project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"date_updated":"2025-09-09T13:31:19Z","date_published":"2023-11-01T00:00:00Z","external_id":{"isi":["001101152500001"]},"isi":1,"quality_controlled":"1","abstract":[{"text":"The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments.","lang":"eng"}],"publisher":"American Physical Society","article_type":"original","issue":"17","day":"01","article_processing_charge":"No","department":[{"_id":"BiCh"}],"year":"2023","language":[{"iso":"eng"}],"month":"11","_id":"14605","status":"public","oa_version":"None","article_number":"174302","doi":"10.1103/PhysRevB.108.174302","scopus_import":"1","intvolume":"       108","author":[{"last_name":"Ouyang","full_name":"Ouyang, Niuchang","first_name":"Niuchang"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng","full_name":"Zeng, Zezhu"},{"full_name":"Wang, Chen","last_name":"Wang","first_name":"Chen"},{"last_name":"Wang","full_name":"Wang, Qi","first_name":"Qi"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"}],"volume":108,"date_created":"2023-11-26T23:00:54Z"},{"scopus_import":"1","intvolume":"         8","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1389"}],"author":[{"first_name":"Sourav","full_name":"Das, Sourav","last_name":"Das"},{"full_name":"Xiang, Zhuolun","last_name":"Xiang","first_name":"Zhuolun"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Ren","full_name":"Ren, Ling","first_name":"Ling"}],"date_created":"2023-11-26T23:00:55Z","volume":8,"oa":1,"month":"08","status":"public","oa_version":"Published Version","ddc":["000"],"_id":"14609","file_date_updated":"2023-11-28T09:14:34Z","language":[{"iso":"eng"}],"year":"2023","page":"5359-5376","publisher":"Usenix","day":"15","has_accepted_license":"1","article_processing_charge":"No","department":[{"_id":"ElKo"}],"date_updated":"2025-04-15T08:16:55Z","publication_status":"published","title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","project":[{"grant_number":"F8512","name":"Security and Privacy by Design for Complex Systems","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"date_published":"2023-08-15T00:00:00Z","abstract":[{"lang":"eng","text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art."}],"quality_controlled":"1","publication_identifier":{"isbn":["9781713879497"]},"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In <i>32nd USENIX Security Symposium</i>, 8:5359–76. Usenix, 2023.","apa":"Das, S., Xiang, Z., Kokoris Kogias, E., &#38; Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In <i>32nd USENIX Security Symposium</i> (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix.","mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” <i>32nd USENIX Security Symposium</i>, vol. 8, Usenix, 2023, pp. 5359–76.","ista":"Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376.","ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: <i>32nd USENIX Security Symposium</i>. Vol 8. Usenix; 2023:5359-5376.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in <i>32nd USENIX Security Symposium</i>, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376."},"publication":"32nd USENIX Security Symposium","file":[{"date_updated":"2023-11-28T09:14:34Z","success":1,"creator":"dernst","access_level":"open_access","file_name":"2023_USENIX_Das.pdf","date_created":"2023-11-28T09:14:34Z","relation":"main_file","content_type":"application/pdf","checksum":"1a730765930138e23c6efd2575872641","file_id":"14621","file_size":704331}],"type":"conference","acknowledgement":"The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.","conference":{"name":"USENIX Security Symposium","end_date":"2023-08-11","start_date":"2023-08-09","location":"Anaheim, CA, United States"}},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","department":[{"_id":"AnSa"}],"article_type":"original","publisher":"Springer Nature","day":"30","page":"1062-1069","year":"2023","language":[{"iso":"eng"}],"ddc":["570"],"_id":"14610","file_date_updated":"2024-07-16T07:41:39Z","oa_version":"Published Version","status":"public","oa":1,"month":"11","author":[{"first_name":"Claudio","full_name":"Bussi, Claudio","last_name":"Bussi"},{"full_name":"Mangiarotti, Agustín","last_name":"Mangiarotti","first_name":"Agustín"},{"first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos"},{"first_name":"Beren","full_name":"Aylan, Beren","last_name":"Aylan"},{"first_name":"Enrica","last_name":"Pellegrino","full_name":"Pellegrino, Enrica"},{"last_name":"Athanasiadi","full_name":"Athanasiadi, Natalia","first_name":"Natalia"},{"first_name":"Antony","full_name":"Fearns, Antony","last_name":"Fearns"},{"full_name":"Rodgers, Angela","last_name":"Rodgers","first_name":"Angela"},{"first_name":"Titus M.","full_name":"Franzmann, Titus M.","last_name":"Franzmann"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela"},{"first_name":"Rumiana","full_name":"Dimova, Rumiana","last_name":"Dimova"},{"last_name":"Gutierrez","full_name":"Gutierrez, Maximiliano G.","first_name":"Maximiliano G."}],"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"}]},"date_created":"2023-11-27T07:56:37Z","doi":"10.1038/s41586-023-06726-w","scopus_import":"1","intvolume":"       623","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.","type":"journal_article","file":[{"success":1,"date_updated":"2024-07-16T07:41:39Z","access_level":"open_access","creator":"dernst","file_name":"2023_Nature_Bussi.pdf","date_created":"2024-07-16T07:41:39Z","relation":"main_file","content_type":"application/pdf","checksum":"b939a19e4c228fbf3beca298ac2ac014","file_id":"17248","file_size":17047711}],"publication":"Nature","citation":{"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>","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.","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>.","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.","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>","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>.","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"quality_controlled":"1","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"}],"title":"Stress granules plug and stabilize damaged endolysosomal membranes","publication_status":"published","date_updated":"2025-09-09T13:30:34Z","external_id":{"isi":["001105882300018"],"pmid":["37968398"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"date_published":"2023-11-30T00:00:00Z"},{"has_accepted_license":"1","type":"research_data","article_processing_charge":"No","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","file":[{"file_id":"14625","file_size":404968272,"content_type":"application/zip","relation":"main_file","checksum":"cd0f13322b5156819ecaebd2bc8e7d12","date_created":"2023-11-28T13:15:26Z","file_name":"panorpaX.zip","success":1,"date_updated":"2023-11-28T13:15:26Z","access_level":"open_access","creator":"clasne"},{"file_size":2625,"file_id":"14634","relation":"main_file","content_type":"text/plain","checksum":"9ff600416577687a737cb3c96dfcb26c","file_name":"panorpa_readme.txt","date_created":"2023-11-30T14:16:59Z","success":1,"date_updated":"2023-11-30T14:16:59Z","creator":"clasne","access_level":"open_access"}],"day":"01","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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>.","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>","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.","short":"C. Lasne, M.N. Elkrewi, (2023).","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>"},"year":"2023","contributor":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","contributor_type":"researcher","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"status":"public","oa_version":"Published Version","_id":"14614","file_date_updated":"2023-11-30T14:16:59Z","ddc":["576"],"oa":1,"corr_author":"1","month":"12","abstract":[{"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.","lang":"eng"}],"author":[{"full_name":"Lasne, Clementine","last_name":"Lasne","orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"}],"date_created":"2023-11-27T16:39:19Z","related_material":{"record":[{"id":"14613","relation":"used_in_publication","status":"public"}]},"date_updated":"2025-09-09T13:33:22Z","doi":"10.15479/AT:ISTA:14614","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","date_published":"2023-12-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"_id":"14616","ddc":["570"],"status":"public","oa_version":"Published Version","month":"09","oa":1,"related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"date_created":"2023-11-28T08:01:53Z","author":[{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"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"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.hx3ffbgkt","open_access":"1"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"date_published":"2023-09-15T00:00:00Z","doi":"10.5061/DRYAD.HX3FFBGKT","title":"The X chromosome of insects likely predates the origin of Class Insecta","date_updated":"2025-09-09T13:32:05Z","department":[{"_id":"BeVi"}],"article_processing_charge":"No","has_accepted_license":"1","type":"research_data_reference","day":"15","publisher":"Dryad","license":"https://creativecommons.org/publicdomain/zero/1.0/","year":"2023","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>","short":"M.A. Toups, B. Vicoso, (2023).","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 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>.","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>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]