[{"abstract":[{"lang":"eng","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."}],"conference":{"end_date":"2023-10-27","location":"Singapore, Singapore","start_date":"2023-10-24","name":"ATVA: Automated Technology for Verification and Analysis"},"title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","date_updated":"2025-09-09T13:20:26Z","page":"357-379","_id":"14559","status":"public","type":"conference","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.1007/978-3-031-45329-8_17","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer Nature","day":"22","date_published":"2023-10-22T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1007/978-3-031-45329-8_17","external_id":{"arxiv":["2210.05304"],"isi":["001456127300017"]},"publication":"21st International Symposium on Automated Technology for Verification and Analysis","date_created":"2023-11-19T23:00:56Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"scopus_import":"1","alternative_title":["LNCS"],"citation":{"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>","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>.","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.","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>.","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>"},"corr_author":"1","arxiv":1,"quality_controlled":"1","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031453281"]},"volume":14215,"ec_funded":1,"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.","author":[{"last_name":"Ansaripour","full_name":"Ansaripour, Matin","first_name":"Matin"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic"}],"publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2210.05304","open_access":"1"}],"intvolume":"     14215","oa_version":"Preprint","month":"10","year":"2023","oa":1,"article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:14562","_id":"14562","status":"public","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"type":"research_data","license":"https://creativecommons.org/licenses/by-sa/4.0/","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\"","abstract":[{"lang":"eng","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"}],"file_date_updated":"2023-11-20T11:49:58Z","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"contributor":[{"contributor_type":"researcher","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian"},{"contributor_type":"researcher","last_name":"Javoor","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","contributor_type":"researcher"},{"first_name":"Hermann","last_name":"Döring","contributor_type":"researcher"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","last_name":"Hofer","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Dimchev","orcid":"0000-0001-8370-6161","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","contributor_type":"researcher"},{"first_name":"Jan","contributor_type":"researcher","last_name":"Faix"},{"contributor_type":"researcher","last_name":"Rottner","first_name":"Klemens"},{"contributor_type":"researcher","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian 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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.","citation":{"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>","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).","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>.","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>"},"corr_author":"1","has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12334"}]},"date_created":"2023-11-20T09:22:33Z","department":[{"_id":"FlSc"}],"oa":1,"year":"2023","article_processing_charge":"No","month":"11","oa_version":"Published Version","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"}],"ddc":["570"]},{"keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"date_published":"2023-11-01T00:00:00Z","day":"01","external_id":{"isi":["001106311000001"]},"isi":1,"fulldoi":"https://doi.org/10.1029/2022ms003391","file":[{"date_updated":"2023-11-20T11:29:16Z","checksum":"e30329dd985559de0ddc7021ca7382b4","file_size":6435697,"creator":"dernst","success":1,"date_created":"2023-11-20T11:29:16Z","relation":"main_file","file_id":"14582","access_level":"open_access","file_name":"2023_JAMES_Khoulder.pdf","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"14564","publisher":"American Geophysical Union","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1029/2022ms003391","title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","file_date_updated":"2023-11-20T11:29:16Z","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"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2025-09-09T13:29:45Z","month":"11","oa_version":"Published Version","issue":"11","intvolume":"        15","article_processing_charge":"Yes","year":"2023","oa":1,"ddc":["550"],"article_type":"original","publication_status":"published","author":[{"first_name":"B.","full_name":"Khouider, B.","last_name":"Khouider"},{"id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"GOSWAMI, BIDYUT B","orcid":"0000-0001-8602-3083","first_name":"BIDYUT B","last_name":"GOSWAMI"},{"last_name":"Phani","full_name":"Phani, R.","first_name":"R."},{"last_name":"Majda","first_name":"A. J.","full_name":"Majda, A. J."}],"publication_identifier":{"eissn":["1942-2466"]},"volume":15,"quality_controlled":"1","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.","article_number":"e2022MS003391","scopus_import":"1","department":[{"_id":"CaMu"}],"date_created":"2023-11-20T09:18:21Z","publication":"Journal of Advances in Modeling Earth Systems","citation":{"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>","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>.","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.","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>.","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.","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>","short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023)."},"has_accepted_license":"1"},{"publisher":"Zenodo","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.5281/ZENODO.8133117","type":"research_data_reference","_id":"14579","status":"public","citation":{"short":"W. Wetzel, (2023).","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>","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","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>.","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>.","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>."},"related_material":{"record":[{"id":"14552","status":"public","relation":"used_in_publication"}]},"date_updated":"2025-09-09T13:23:55Z","department":[{"_id":"NiBa"}],"date_created":"2023-11-20T11:07:45Z","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","abstract":[{"text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n","lang":"eng"}],"article_processing_charge":"No","oa":1,"year":"2023","month":"07","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.5281/ZENODO.8133117","author":[{"full_name":"Wetzel, William","first_name":"William","last_name":"Wetzel"}],"day":"11","date_published":"2023-07-11T00:00:00Z","ddc":["570"]},{"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"date_published":"2023-11-21T00:00:00Z","day":"21","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/at:ista:14587","file":[{"creator":"amarvegg","success":1,"relation":"main_file","date_created":"2023-11-29T09:09:31Z","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","date_updated":"2023-11-29T09:09:31Z","file_size":2881100,"content_type":"application/pdf","file_name":"thesis_Marveggio.pdf","file_id":"14626","access_level":"open_access"},{"relation":"source_file","date_created":"2023-11-29T09:10:19Z","creator":"amarvegg","file_size":10189696,"date_updated":"2024-03-20T12:28:32Z","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","file_name":"Thesis_Marveggio.zip","content_type":"application/zip","access_level":"closed","file_id":"14627"}],"status":"public","_id":"14587","type":"dissertation","project":[{"name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"doi":"10.15479/at:ista:14587","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero."}],"file_date_updated":"2024-03-20T12:28:32Z","title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","date_updated":"2026-04-07T13:28:13Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"228","oa_version":"Published Version","month":"11","oa":1,"year":"2023","degree_awarded":"PhD","article_processing_charge":"No","ddc":["515"],"author":[{"id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice","first_name":"Alice","last_name":"Marveggio"}],"publication_status":"published","OA_place":"publisher","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","first_name":"Julian L"}],"acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","date_created":"2023-11-21T11:41:05Z","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"11842","status":"public","relation":"part_of_dissertation"},{"id":"14597","relation":"part_of_dissertation","status":"public"}]},"citation":{"chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","apa":"Marveggio, A. (2023). <i>Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>","mla":"Marveggio, Alice. <i>Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>.","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria."},"corr_author":"1"},{"abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"file_date_updated":"2023-11-28T08:12:15Z","title":"The X chromosome of insects likely predates the origin of class Insecta","date_updated":"2025-09-09T13:32:06Z","license":"https://creativecommons.org/licenses/by/4.0/","page":"2504-2511","pmid":1,"_id":"14604","status":"public","type":"journal_article","doi":"10.1093/evolut/qpad169","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Oxford University Press","date_published":"2023-11-02T00:00:00Z","day":"02","language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1093/evolut/qpad169","file":[{"access_level":"open_access","file_id":"14618","file_name":"2023_Evolution_Toups.pdf","content_type":"application/pdf","file_size":1399102,"checksum":"b66dc10edae92d38918d534e64dda77c","date_updated":"2023-11-28T08:12:15Z","relation":"main_file","date_created":"2023-11-28T08:12:15Z","success":1,"creator":"dernst"}],"external_id":{"pmid":["37738212"],"isi":["001170341900014"]},"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication":"Evolution","date_created":"2023-11-26T23:00:54Z","scopus_import":"1","department":[{"_id":"BeVi"}],"has_accepted_license":"1","related_material":{"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}],"record":[{"id":"14616","status":"public","relation":"research_data"},{"id":"14617","status":"public","relation":"research_data"}]},"citation":{"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>","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.","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>.","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>","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."},"quality_controlled":"1","publication_identifier":{"eissn":["1558-5646"]},"volume":77,"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.","ddc":["570"],"author":[{"first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"publication_status":"published","article_type":"original","issue":"11","intvolume":"        77","oa_version":"Published Version","month":"11","oa":1,"year":"2023","article_processing_charge":"Yes (in subscription journal)"},{"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.","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"volume":623,"quality_controlled":"1","citation":{"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.","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>","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, vol. 623, Springer Nature, 2023, pp. 1062–69, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>.","short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature 623 (2023) 1062–1069.","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>","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.","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>."},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}],"record":[{"id":"14472","relation":"research_data","status":"public"}]},"has_accepted_license":"1","scopus_import":"1","department":[{"_id":"AnSa"}],"date_created":"2023-11-27T07:56:37Z","publication":"Nature","article_processing_charge":"Yes (via OA deal)","oa":1,"year":"2023","month":"11","intvolume":"       623","oa_version":"Published Version","article_type":"original","publication_status":"published","author":[{"first_name":"Claudio","full_name":"Bussi, Claudio","last_name":"Bussi"},{"last_name":"Mangiarotti","first_name":"Agustín","full_name":"Mangiarotti, Agustín"},{"last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","full_name":"Vanhille-Campos, Christian Eduardo"},{"last_name":"Aylan","first_name":"Beren","full_name":"Aylan, Beren"},{"first_name":"Enrica","full_name":"Pellegrino, Enrica","last_name":"Pellegrino"},{"first_name":"Natalia","full_name":"Athanasiadi, Natalia","last_name":"Athanasiadi"},{"full_name":"Fearns, Antony","first_name":"Antony","last_name":"Fearns"},{"last_name":"Rodgers","first_name":"Angela","full_name":"Rodgers, Angela"},{"last_name":"Franzmann","first_name":"Titus M.","full_name":"Franzmann, Titus M."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Rumiana","full_name":"Dimova, Rumiana","last_name":"Dimova"},{"first_name":"Maximiliano G.","full_name":"Gutierrez, Maximiliano G.","last_name":"Gutierrez"}],"ddc":["570"],"publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/s41586-023-06726-w","type":"journal_article","status":"public","_id":"14610","pmid":1,"page":"1062-1069","date_updated":"2025-09-09T13:30:34Z","title":"Stress granules plug and stabilize damaged endolysosomal membranes","file_date_updated":"2024-07-16T07:41:39Z","abstract":[{"lang":"eng","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."}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"external_id":{"pmid":["37968398"],"isi":["001105882300018"]},"isi":1,"fulldoi":"https://doi.org/10.1038/s41586-023-06726-w","file":[{"file_id":"17248","access_level":"open_access","file_name":"2023_Nature_Bussi.pdf","content_type":"application/pdf","date_updated":"2024-07-16T07:41:39Z","checksum":"b939a19e4c228fbf3beca298ac2ac014","file_size":17047711,"success":1,"creator":"dernst","date_created":"2024-07-16T07:41:39Z","relation":"main_file"}],"language":[{"iso":"eng"}],"day":"30","date_published":"2023-11-30T00:00:00Z"},{"oa_version":"Published Version","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"contributor":[{"last_name":"Elkrewi","contributor_type":"researcher","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"month":"12","article_processing_charge":"No","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"year":"2023","date_published":"2023-12-01T00:00:00Z","day":"01","ddc":["576"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:14614","file":[{"checksum":"cd0f13322b5156819ecaebd2bc8e7d12","date_updated":"2023-11-28T13:15:26Z","file_size":404968272,"creator":"clasne","success":1,"relation":"main_file","date_created":"2023-11-28T13:15:26Z","file_id":"14625","access_level":"open_access","content_type":"application/zip","file_name":"panorpaX.zip"},{"date_created":"2023-11-30T14:16:59Z","relation":"main_file","success":1,"creator":"clasne","file_size":2625,"checksum":"9ff600416577687a737cb3c96dfcb26c","date_updated":"2023-11-30T14:16:59Z","content_type":"text/plain","file_name":"panorpa_readme.txt","access_level":"open_access","file_id":"14634"}],"author":[{"id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","first_name":"Clementine","last_name":"Lasne"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"}],"type":"research_data","status":"public","_id":"14614","doi":"10.15479/AT:ISTA:14614","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-11-30T14:16:59Z","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"department":[{"_id":"BeVi"}],"date_created":"2023-11-27T16:39:19Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14613"}]},"date_updated":"2025-09-09T13:33:22Z","has_accepted_license":"1","corr_author":"1","citation":{"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>.","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.","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>","short":"C. Lasne, M.N. Elkrewi, (2023).","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>","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>.","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>."}},{"citation":{"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>","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","short":"M.A. Toups, B. Vicoso, (2023).","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>.","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>.","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>","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>."},"related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","has_accepted_license":"1","date_updated":"2025-09-09T13:32:05Z","department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","date_created":"2023-11-28T08:01:53Z","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"publisher":"Dryad","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.5061/DRYAD.HX3FFBGKT","type":"research_data_reference","_id":"14616","status":"public","fulldoi":"https://doi.org/10.5061/DRYAD.HX3FFBGKT","author":[{"first_name":"Melissa A","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"day":"15","date_published":"2023-09-15T00:00:00Z","ddc":["570"],"article_processing_charge":"No","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"oa":1,"year":"2023","month":"09","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.hx3ffbgkt","open_access":"1"}]},{"ddc":["570"],"day":"15","date_published":"2023-09-15T00:00:00Z","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"fulldoi":"https://doi.org/10.5281/ZENODO.8138705","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8138705"}],"month":"09","year":"2023","oa":1,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"date_created":"2023-11-28T08:04:03Z","title":"The X chromosome of insects likely predates the origin of Class Insecta","department":[{"_id":"BeVi"}],"has_accepted_license":"1","date_updated":"2025-09-09T13:32:05Z","related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"citation":{"ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","short":"M.A. Toups, B. Vicoso, (2023).","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>."},"_id":"14617","status":"public","other_data_license":"MIT License","type":"research_data_reference","doi":"10.5281/ZENODO.8138705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo"},{"date_created":"2023-11-29T15:02:03Z","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"scopus_import":"1","publication":"ACM Transactions on Graphics","citation":{"apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., &#38; Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>","ieee":"L. Makatura <i>et al.</i>, “Procedural metamaterials: A unified procedural graph for metamaterial design,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","chicago":"Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>.","ista":"Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>","mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>."},"has_accepted_license":"1","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"volume":42,"quality_controlled":"1","article_number":"168","acknowledgement":"The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program.","ddc":["531","006"],"author":[{"last_name":"Makatura","first_name":"Liane","full_name":"Makatura, Liane"},{"last_name":"Wang","full_name":"Wang, Bohan","first_name":"Bohan"},{"first_name":"Yi-Lu","full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","last_name":"Chen"},{"full_name":"Deng, Bolei","first_name":"Bolei","last_name":"Deng"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"}],"publication_status":"published","article_type":"original","month":"10","issue":"5","oa_version":"Published Version","intvolume":"        42","year":"2023","oa":1,"article_processing_charge":"Yes (in subscription journal)","title":"Procedural metamaterials: A unified procedural graph for metamaterial design","abstract":[{"lang":"eng","text":"We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration."}],"file_date_updated":"2023-12-04T08:04:14Z","date_updated":"2025-09-09T13:33:58Z","status":"public","_id":"14628","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Association for Computing Machinery","doi":"10.1145/3605389","day":"01","date_published":"2023-10-01T00:00:00Z","external_id":{"isi":["001086833300007"]},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1145/3605389","file":[{"file_name":"tog-22-0089-File004.zip","content_type":"application/zip","access_level":"open_access","file_id":"14630","date_created":"2023-11-29T15:16:01Z","relation":"main_file","success":1,"creator":"yichen","file_size":95467870,"date_updated":"2023-11-29T15:16:01Z","checksum":"0192f597d7a2ceaf89baddfd6190d4c8"},{"file_name":"tog-22-0089-File005.zip","content_type":"application/zip","access_level":"open_access","file_id":"14631","relation":"main_file","date_created":"2023-11-29T15:16:01Z","creator":"yichen","success":1,"file_size":103731880,"checksum":"7fb024963be81933494f38de191e4710","date_updated":"2023-11-29T15:16:01Z"},{"checksum":"b7d6829ce396e21cac9fae0ec7130a6b","date_updated":"2023-12-04T08:04:14Z","file_size":57067476,"creator":"dernst","success":1,"date_created":"2023-12-04T08:04:14Z","relation":"main_file","file_id":"14638","access_level":"open_access","content_type":"application/pdf","file_name":"2023_ACMToG_Makatura.pdf"}],"isi":1,"keyword":["Computer Graphics and Computer-Aided Design"]},{"article_number":"102","quality_controlled":"1","publication_identifier":{"issn":["1756-994X"]},"volume":15,"extern":"1","has_accepted_license":"1","citation":{"mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>, vol. 15, 102, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>.","ama":"Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. 2023;15. doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>","ista":"Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102.","chicago":"Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>.","short":"S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani, C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra, G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney, N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth, T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A. Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023).","apa":"Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney, G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>","ieee":"S.-J. Lin <i>et al.</i>, “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023."},"publication":"Genome Medicine","date_created":"2023-12-04T08:10:55Z","article_processing_charge":"Yes","year":"2023","oa":1,"intvolume":"        15","oa_version":"Published Version","month":"11","article_type":"original","publication_status":"published","author":[{"last_name":"Lin","full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia"},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"last_name":"Lau","full_name":"Lau, Tracy","first_name":"Tracy"},{"orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin","first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","last_name":"Huang"},{"full_name":"Zaki, Maha S.","first_name":"Maha S.","last_name":"Zaki"},{"full_name":"Aldeen, Huda Shujaa","first_name":"Huda Shujaa","last_name":"Aldeen"},{"first_name":"Ehsan Ghayoor","full_name":"Karimiani, Ehsan Ghayoor","last_name":"Karimiani"},{"last_name":"Rocca","first_name":"Clarissa","full_name":"Rocca, Clarissa"},{"last_name":"Noureldeen","first_name":"Mahmoud M.","full_name":"Noureldeen, Mahmoud M."},{"last_name":"Saad","first_name":"Ahmed K.","full_name":"Saad, Ahmed K."},{"first_name":"Cassidy","full_name":"Petree, Cassidy","last_name":"Petree"},{"last_name":"Bartolomaeus","first_name":"Tobias","full_name":"Bartolomaeus, Tobias"},{"first_name":"Rami","full_name":"Abou Jamra, Rami","last_name":"Abou Jamra"},{"last_name":"Zifarelli","full_name":"Zifarelli, Giovanni","first_name":"Giovanni"},{"first_name":"Aditi","full_name":"Gotkhindikar, Aditi","last_name":"Gotkhindikar"},{"first_name":"Ingrid M.","full_name":"Wentzensen, Ingrid M.","last_name":"Wentzensen"},{"last_name":"Liao","full_name":"Liao, Mingjuan","first_name":"Mingjuan"},{"full_name":"Cork, Emalyn Elise","first_name":"Emalyn Elise","last_name":"Cork"},{"last_name":"Varshney","first_name":"Pratishtha","full_name":"Varshney, Pratishtha"},{"first_name":"Narges","full_name":"Hashemi, Narges","last_name":"Hashemi"},{"last_name":"Mohammadi","full_name":"Mohammadi, Mohammad Hasan","first_name":"Mohammad Hasan"},{"last_name":"Rad","full_name":"Rad, Aboulfazl","first_name":"Aboulfazl"},{"full_name":"Neira, Juanita","first_name":"Juanita","last_name":"Neira"},{"last_name":"Toosi","first_name":"Mehran Beiraghi","full_name":"Toosi, Mehran Beiraghi"},{"full_name":"Knopp, Cordula","first_name":"Cordula","last_name":"Knopp"},{"first_name":"Ingo","full_name":"Kurth, Ingo","last_name":"Kurth"},{"last_name":"Challman","full_name":"Challman, Thomas D.","first_name":"Thomas D."},{"last_name":"Smith","first_name":"Rebecca","full_name":"Smith, Rebecca"},{"last_name":"Abdalla","first_name":"Asmahan","full_name":"Abdalla, Asmahan"},{"last_name":"Haaf","first_name":"Thomas","full_name":"Haaf, Thomas"},{"last_name":"Suri","first_name":"Mohnish","full_name":"Suri, Mohnish"},{"last_name":"Joshi","first_name":"Manali","full_name":"Joshi, Manali"},{"last_name":"Chung","full_name":"Chung, Wendy K.","first_name":"Wendy K."},{"first_name":"Andres","full_name":"Moreno-De-Luca, Andres","last_name":"Moreno-De-Luca"},{"full_name":"Houlden, Henry","first_name":"Henry","last_name":"Houlden"},{"last_name":"Maroofian","full_name":"Maroofian, Reza","first_name":"Reza"},{"full_name":"Varshney, Gaurav K.","first_name":"Gaurav K.","last_name":"Varshney"}],"ddc":["570"],"doi":"10.1186/s13073-023-01258-4","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"14639","date_updated":"2023-12-04T08:17:22Z","file_date_updated":"2023-12-04T08:15:43Z","abstract":[{"lang":"eng","text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”."}],"title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"file":[{"content_type":"application/pdf","file_name":"2023_GenomeMed_Lin.pdf","access_level":"open_access","file_id":"14640","date_created":"2023-12-04T08:15:43Z","relation":"main_file","creator":"dernst","success":1,"file_size":14791081,"checksum":"279efd212005549aba817a487d56d363","date_updated":"2023-12-04T08:15:43Z"}],"fulldoi":"https://doi.org/10.1186/s13073-023-01258-4","language":[{"iso":"eng"}],"day":"23","date_published":"2023-11-23T00:00:00Z"},{"title":"Mechanism of mammalian transcriptional repression by noncoding RNA","file_date_updated":"2023-12-05T10:37:02Z","abstract":[{"lang":"eng","text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression."}],"date_updated":"2025-11-20T10:28:37Z","project":[{"grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","name":"Regulation of mammalian transcription by noncoding RNA"}],"type":"preprint","_id":"14644","status":"public","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:14644","day":"05","date_published":"2023-12-05T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:14644","file":[{"creator":"dernst","success":1,"date_created":"2023-12-05T10:37:02Z","relation":"main_file","date_updated":"2023-12-05T10:37:02Z","checksum":"c45608cb97ee36d7b50ba518db8e07b0","file_size":4892920,"content_type":"application/pdf","file_name":"2023_Tluckova_etal_REx.pdf","file_id":"14646","access_level":"open_access"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"date_created":"2023-12-04T14:51:00Z","corr_author":"1","citation":{"ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","mla":"Tluckova, Katarina, et al. <i>Mechanism of Mammalian Transcriptional Repression by Noncoding RNA</i>. Institute of Science and Technology Austria, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","apa":"Tluckova, K., Testa Salmazo, A. P., &#38; Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>."},"related_material":{"record":[{"status":"public","relation":"later_version","id":"18778"}]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","ddc":["572"],"publication_status":"draft","author":[{"last_name":"Tluckova","first_name":"Katarina","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P","full_name":"Testa Salmazo, Anita P"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky"}],"month":"12","oa_version":"Submitted Version","article_processing_charge":"No","year":"2023","oa":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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"keyword":["General Physics and Astronomy"],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.21468/scipostphys.15.6.232","file":[{"file_id":"14669","access_level":"open_access","content_type":"application/pdf","file_name":"2023_SciPostPhysics_Volosniev.pdf","date_updated":"2023-12-11T07:42:04Z","checksum":"e664372a1fe9d628a9bb1d135ebab7d8","file_size":3543541,"creator":"dernst","success":1,"relation":"main_file","date_created":"2023-12-11T07:42:04Z"}],"isi":1,"external_id":{"isi":["001121864100003"],"arxiv":["2305.17969"]},"date_published":"2023-12-07T00:00:00Z","day":"07","doi":"10.21468/scipostphys.15.6.232","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"SciPost Foundation","status":"public","_id":"14650","project":[{"grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"type":"journal_article","date_updated":"2025-09-09T13:34:34Z","abstract":[{"lang":"eng","text":"We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures."}],"file_date_updated":"2023-12-11T07:42:04Z","title":"Non-equilibrium dynamics of dipolar polarons","oa":1,"year":"2023","article_processing_charge":"No","issue":"6","oa_version":"Published Version","intvolume":"        15","month":"12","author":[{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luis","full_name":"Santos, Luis","last_name":"Santos"},{"full_name":"Peña Ardila, Luisllu A.","first_name":"Luisllu A.","last_name":"Peña Ardila"}],"publication_status":"published","article_type":"original","ddc":["530"],"article_number":"232","acknowledgement":"We thank Lauriane Chomaz for useful discussions and comments on the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No. M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948 (the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967 and FOR2247.","quality_controlled":"1","arxiv":1,"volume":15,"publication_identifier":{"issn":["2542-4653"]},"ec_funded":1,"has_accepted_license":"1","citation":{"short":"A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15 (2023).","apa":"Volosniev, A., Bighin, G., Santos, L., &#38; Peña Ardila, L. A. (2023). Non-equilibrium dynamics of dipolar polarons. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">https://doi.org/10.21468/scipostphys.15.6.232</a>","ieee":"A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium dynamics of dipolar polarons,” <i>SciPost Physics</i>, vol. 15, no. 6. SciPost Foundation, 2023.","chicago":"Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila. “Non-Equilibrium Dynamics of Dipolar Polarons.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">https://doi.org/10.21468/scipostphys.15.6.232</a>.","ista":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 15(6), 232.","ama":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of dipolar polarons. <i>SciPost Physics</i>. 2023;15(6). doi:<a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">10.21468/scipostphys.15.6.232</a>","mla":"Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” <i>SciPost Physics</i>, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">10.21468/scipostphys.15.6.232</a>."},"corr_author":"1","publication":"SciPost Physics","date_created":"2023-12-10T13:03:07Z","scopus_import":"1","department":[{"_id":"MiLe"}]},{"page":"96","date_updated":"2026-04-07T13:28:30Z","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","file_date_updated":"2023-12-14T08:58:18Z","abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:14651","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"type":"dissertation","status":"public","_id":"14651","fulldoi":"https://doi.org/10.15479/at:ista:14651","file":[{"file_id":"14684","access_level":"open_access","file_name":"Phd_Thesis_LA.pdf","content_type":"application/pdf","date_updated":"2023-12-13T15:37:55Z","checksum":"520bdb61e95e66070e02824947d2c5fa","file_size":34101468,"creator":"larathoo","success":1,"relation":"main_file","date_created":"2023-12-13T15:37:55Z"},{"date_created":"2023-12-13T15:42:23Z","relation":"source_file","creator":"larathoo","file_size":31052872,"checksum":"d8e59afd0817c98fba2564a264508e5c","date_updated":"2023-12-14T08:58:18Z","content_type":"application/zip","file_name":"Phd_Thesis_LA.zip","access_level":"closed","file_id":"14685"},{"creator":"larathoo","relation":"supplementary_material","date_created":"2023-12-11T19:24:59Z","checksum":"9a778c949932286f4519e1f1fca2820d","date_updated":"2023-12-14T08:58:18Z","file_size":10713896,"content_type":"application/zip","file_name":"Supplementary_Materials.zip","file_id":"14681","access_level":"closed"}],"language":[{"iso":"eng"}],"day":"12","date_published":"2023-12-12T00:00:00Z","corr_author":"1","citation":{"ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","mla":"Arathoon, Louise S. <i>Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","apa":"Arathoon, L. S. (2023). <i>Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>."},"related_material":{"record":[{"id":"11411","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2023-12-11T19:30:37Z","supervisor":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"OA_place":"publisher","publication_status":"published","author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon"}],"ddc":["570"],"degree_awarded":"PhD","article_processing_charge":"No","oa":1,"year":"2023","month":"12","oa_version":"Published Version"},{"volume":15,"ec_funded":1,"publication_identifier":{"eissn":["1942-2466"]},"quality_controlled":"1","article_number":"e2023MS003726","acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. CJM gratefully acknowledges funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). YLH and SCS were supported by the Australian Research Council (FL150100035). The authors thank Brian Mapes, David Fuchs and Siwon Song for stimulating and helpful discussions. MC warmly thanks the LMD team in Paris for their assistance with the LMDZ model. We thank the two anonymous reviewers for their constructive comments that greatly improved this manuscript.","date_created":"2023-12-10T23:00:57Z","department":[{"_id":"CaMu"}],"scopus_import":"1","publication":"Journal of Advances in Modeling Earth Systems","citation":{"ista":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Assessing memory in convection schemes using idealized tests. Journal of Advances in Modeling Earth Systems. 15(12), e2023MS003726.","ama":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Assessing memory in convection schemes using idealized tests. <i>Journal of Advances in Modeling Earth Systems</i>. 2023;15(12). doi:<a href=\"https://doi.org/10.1029/2023MS003726\">10.1029/2023MS003726</a>","mla":"Hwong, Yi-Ling, et al. “Assessing Memory in Convection Schemes Using Idealized Tests.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 12, e2023MS003726, Wiley, 2023, doi:<a href=\"https://doi.org/10.1029/2023MS003726\">10.1029/2023MS003726</a>.","ieee":"Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Assessing memory in convection schemes using idealized tests,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 12. Wiley, 2023.","apa":"Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., &#38; Sherwood, S. C. (2023). Assessing memory in convection schemes using idealized tests. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2023MS003726\">https://doi.org/10.1029/2023MS003726</a>","short":"Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, Journal of Advances in Modeling Earth Systems 15 (2023).","chicago":"Hwong, Yi-Ling, M. Colin, Philipp Aglas, Caroline J Muller, and S. C. Sherwood. “Assessing Memory in Convection Schemes Using Idealized Tests.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2023. <a href=\"https://doi.org/10.1029/2023MS003726\">https://doi.org/10.1029/2023MS003726</a>."},"corr_author":"1","has_accepted_license":"1","related_material":{"record":[{"id":"14991","relation":"research_data","status":"public"}]},"month":"12","intvolume":"        15","issue":"12","oa_version":"Published Version","year":"2023","oa":1,"article_processing_charge":"Yes","ddc":["550"],"author":[{"orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","last_name":"Hwong"},{"full_name":"Colin, M.","first_name":"M.","last_name":"Colin"},{"last_name":"Aglas","full_name":"Aglas, Philipp","first_name":"Philipp","id":"02eace56-97fc-11ee-b81a-f0939ca85a77"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller"},{"full_name":"Sherwood, S. C.","first_name":"S. C.","last_name":"Sherwood"}],"publication_status":"published","article_type":"original","_id":"14654","status":"public","project":[{"grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Wiley","doi":"10.1029/2023MS003726","title":"Assessing memory in convection schemes using idealized tests","abstract":[{"text":"Two assumptions commonly applied in convection schemes—the diagnostic and quasi-equilibrium assumptions—imply that convective activity (e.g., convective precipitation) is controlled only by the large-scale (macrostate) environment at the time. In contrast, numerical experiments indicate a “memory” or dependence of convection also on its own previous activity whereby subgrid-scale (microstate) structures boost but are also boosted by convection. In this study we investigated this memory by comparing single-column model behavior in two idealized tests previously executed by a cloud-resolving model (CRM). Conventional convection schemes that employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks implied by the CRM. Analysis of this failure suggests that it is because the CRM supports a linear (or superlinear) dependence of the subgrid structure growth rate on the precipitation rate, while the org scheme assumes a sublinear dependence. Among varying versions of the org scheme, the growth rate of the org variable representing subgrid structure is strongly associated with memory strength. These results demonstrate the importance of parameterizing convective memory, and the ability of idealized tests to reveal shortcomings of convection schemes and constrain model structural assumptions.","lang":"eng"}],"file_date_updated":"2023-12-11T08:08:44Z","date_updated":"2025-09-09T13:35:40Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"01","date_published":"2023-12-01T00:00:00Z","external_id":{"isi":["001110801100001"]},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1029/2023MS003726","file":[{"success":1,"creator":"dernst","date_created":"2023-12-11T08:08:44Z","relation":"main_file","checksum":"4d060b293da3d203de8769e398edf711","date_updated":"2023-12-11T08:08:44Z","file_size":2783677,"file_name":"2023_JAMES_Hwong.pdf","content_type":"application/pdf","file_id":"14670","access_level":"open_access"}],"isi":1},{"corr_author":"1","citation":{"short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","apa":"Sorichetti, V., &#38; Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” <i>Physical Review Letters</i>, vol. 131, no. 22. American Physical Society, 2023.","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>.","ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401.","ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. 2023;131(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>","mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>."},"scopus_import":"1","department":[{"_id":"AnSa"}],"date_created":"2023-12-10T23:00:57Z","publication":"Physical Review Letters","acknowledgement":"The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066).","article_number":"228401","volume":131,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"arxiv":1,"quality_controlled":"1","publication_status":"published","article_type":"original","author":[{"last_name":"Sorichetti","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","full_name":"Sorichetti, Valerio","orcid":"0000-0002-9645-6576","first_name":"Valerio"},{"last_name":"Lenz","full_name":"Lenz, Martin","first_name":"Martin"}],"article_processing_charge":"No","oa":1,"year":"2023","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.03088"}],"intvolume":"       131","oa_version":"Preprint","issue":"22","pmid":1,"date_updated":"2025-09-09T13:35:06Z","title":"Transverse fluctuations control the assembly of semiflexible filaments","abstract":[{"text":"The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.","lang":"eng"}],"publisher":"American Physical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1103/PhysRevLett.131.228401","type":"journal_article","_id":"14655","status":"public","external_id":{"arxiv":["2303.03088"],"isi":["001163810200008"],"pmid":["38101392"]},"fulldoi":"https://doi.org/10.1103/PhysRevLett.131.228401","isi":1,"language":[{"iso":"eng"}],"day":"01","date_published":"2023-12-01T00:00:00Z"},{"date_updated":"2025-04-14T07:54:54Z","title":"Spin-charge correlations in finite one-dimensional multiband Fermi systems","file_date_updated":"2023-12-11T10:49:07Z","abstract":[{"lang":"eng","text":"We investigate spin-charge separation of a spin-\r\n1\r\n2\r\n Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom."}],"publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevResearch.5.043039","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413"}],"type":"journal_article","_id":"14658","status":"public","external_id":{"arxiv":["2305.09529"]},"file":[{"date_created":"2023-12-11T10:49:07Z","relation":"main_file","creator":"dernst","success":1,"file_size":2362158,"date_updated":"2023-12-11T10:49:07Z","checksum":"ee31c0d0de5d1b65591990ae6705a601","content_type":"application/pdf","file_name":"2023_PhysReviewResearch_Becker.pdf","access_level":"open_access","file_id":"14672"}],"fulldoi":"https://doi.org/10.1103/PhysRevResearch.5.043039","language":[{"iso":"eng"}],"day":"12","date_published":"2023-10-12T00:00:00Z","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","citation":{"ama":"Becker JM, Koutentakis G, Schmelcher P. Spin-charge correlations in finite one-dimensional multiband Fermi systems. <i>Physical Review Research</i>. 2023;5(4). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">10.1103/PhysRevResearch.5.043039</a>","mla":"Becker, J. M., et al. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” <i>Physical Review Research</i>, vol. 5, no. 4, 043039, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">10.1103/PhysRevResearch.5.043039</a>.","ista":"Becker JM, Koutentakis G, Schmelcher P. 2023. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 5(4), 043039.","chicago":"Becker, J. M., Georgios Koutentakis, and P. Schmelcher. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” <i>Physical Review Research</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">https://doi.org/10.1103/PhysRevResearch.5.043039</a>.","apa":"Becker, J. M., Koutentakis, G., &#38; Schmelcher, P. (2023). Spin-charge correlations in finite one-dimensional multiband Fermi systems. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">https://doi.org/10.1103/PhysRevResearch.5.043039</a>","ieee":"J. M. Becker, G. Koutentakis, and P. Schmelcher, “Spin-charge correlations in finite one-dimensional multiband Fermi systems,” <i>Physical Review Research</i>, vol. 5, no. 4. American Physical Society, 2023.","short":"J.M. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 5 (2023)."},"has_accepted_license":"1","scopus_import":"1","department":[{"_id":"MiLe"}],"date_created":"2023-12-10T23:00:58Z","publication":"Physical Review Research","acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG)-EXC 2056-Project ID No. 390715994. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","article_number":"043039","ec_funded":1,"volume":5,"publication_identifier":{"issn":["2643-1564"]},"arxiv":1,"quality_controlled":"1","article_type":"original","publication_status":"published","author":[{"first_name":"J. M.","full_name":"Becker, J. M.","last_name":"Becker"},{"full_name":"Koutentakis, Georgios","first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis"},{"full_name":"Schmelcher, P.","first_name":"P.","last_name":"Schmelcher"}],"ddc":["530"],"article_processing_charge":"Yes","oa":1,"year":"2023","month":"10","intvolume":"         5","issue":"4","oa_version":"Published Version"},{"title":"Local cooling and drying induced by Himalayan glaciers under global warming","abstract":[{"text":"Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment.","lang":"eng"}],"file_date_updated":"2023-12-11T10:11:19Z","date_updated":"2025-09-09T13:36:16Z","page":"1120-1127","status":"public","_id":"14659","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer Nature","doi":"10.1038/s41561-023-01331-y","day":"04","date_published":"2023-12-04T00:00:00Z","external_id":{"isi":["001112839700003"]},"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1038/s41561-023-01331-y","file":[{"creator":"dernst","success":1,"date_created":"2023-12-11T10:11:19Z","relation":"main_file","checksum":"d5ae0d17069eebc6f454c8608cf83e21","date_updated":"2023-12-11T10:11:19Z","file_size":6072603,"content_type":"application/pdf","file_name":"2023_NatureGeoscience_Salerno.pdf","file_id":"14671","access_level":"open_access"}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_created":"2023-12-10T23:00:58Z","scopus_import":"1","department":[{"_id":"FrPe"}],"publication":"Nature Geoscience","citation":{"ista":"Salerno F, Guyennon N, Yang K, Shaw T, Lin C, Colombo N, Romano E, Gruber S, Bolch T, Alessandri A, Cristofanelli P, Putero D, Diolaiuti G, Tartari G, Verza G, Thakuri S, Balsamo G, Miles ES, Pellicciotti F. 2023. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 16, 1120–1127.","ama":"Salerno F, Guyennon N, Yang K, et al. Local cooling and drying induced by Himalayan glaciers under global warming. <i>Nature Geoscience</i>. 2023;16:1120-1127. doi:<a href=\"https://doi.org/10.1038/s41561-023-01331-y\">10.1038/s41561-023-01331-y</a>","mla":"Salerno, Franco, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” <i>Nature Geoscience</i>, vol. 16, Springer Nature, 2023, pp. 1120–27, doi:<a href=\"https://doi.org/10.1038/s41561-023-01331-y\">10.1038/s41561-023-01331-y</a>.","ieee":"F. Salerno <i>et al.</i>, “Local cooling and drying induced by Himalayan glaciers under global warming,” <i>Nature Geoscience</i>, vol. 16. Springer Nature, pp. 1120–1127, 2023.","apa":"Salerno, F., Guyennon, N., Yang, K., Shaw, T., Lin, C., Colombo, N., … Pellicciotti, F. (2023). Local cooling and drying induced by Himalayan glaciers under global warming. <i>Nature Geoscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41561-023-01331-y\">https://doi.org/10.1038/s41561-023-01331-y</a>","short":"F. Salerno, N. Guyennon, K. Yang, T. Shaw, C. Lin, N. Colombo, E. Romano, S. Gruber, T. Bolch, A. Alessandri, P. Cristofanelli, D. Putero, G. Diolaiuti, G. Tartari, G. Verza, S. Thakuri, G. Balsamo, E.S. Miles, F. Pellicciotti, Nature Geoscience 16 (2023) 1120–1127.","chicago":"Salerno, Franco, Nicolas Guyennon, Kun Yang, Thomas Shaw, Changgui Lin, Nicola Colombo, Emanuele Romano, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” <i>Nature Geoscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41561-023-01331-y\">https://doi.org/10.1038/s41561-023-01331-y</a>."},"has_accepted_license":"1","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/wind-of-climate-change/","relation":"press_release"}]},"volume":16,"publication_identifier":{"eissn":["1752-0908"],"issn":["1752-0894"]},"OA_place":"publisher","quality_controlled":"1","OA_type":"hybrid","acknowledgement":"This work was carried out within the framework of the EV-K2-CNR and Nepal Academy of Science and Technology. K.Y. was supported by the Second Tibetan Plateau Scientific Expedition and Research Program (grant no. 2019QZKK0206). N.C. was supported by the project NODES, which has received funding from the MUR–M4C2 1.5 of PNRR funded by the European Union - NextGeneration EU (Grant agreement no. ECS00000036). T.E.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant no. 101026058. F.P. has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant no. 772751, RAVEN, ‘Rapid mass losses of debris-covered glaciers in High Mountain Asia’ and has been supported by the SNSF grant ‘High-elevation precipitation in High Mountain Asia’ (grant no. 183633). A.A. was supported by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 101004156 (CONFESS project) and by the European Union’s Horizon Europe research and innovation program under grant agreement no. 101081193 (OptimESM project). We thank H. Wehrli for valuable comments and suggestions and J. Giannitrapani for the graphic support. We thank A. Da Polenza and K. Bista of EV-K2-CNR for believing that studying the high elevations is relevant for the whole globe.","ddc":["550"],"author":[{"last_name":"Salerno","first_name":"Franco","full_name":"Salerno, Franco"},{"last_name":"Guyennon","first_name":"Nicolas","full_name":"Guyennon, Nicolas"},{"last_name":"Yang","first_name":"Kun","full_name":"Yang, Kun"},{"last_name":"Shaw","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","full_name":"Shaw, Thomas","orcid":"0000-0001-7640-6152","first_name":"Thomas"},{"last_name":"Lin","first_name":"Changgui","full_name":"Lin, Changgui"},{"full_name":"Colombo, Nicola","first_name":"Nicola","last_name":"Colombo"},{"last_name":"Romano","full_name":"Romano, Emanuele","first_name":"Emanuele"},{"last_name":"Gruber","first_name":"Stephan","full_name":"Gruber, Stephan"},{"last_name":"Bolch","first_name":"Tobias","full_name":"Bolch, Tobias"},{"first_name":"Andrea","full_name":"Alessandri, Andrea","last_name":"Alessandri"},{"last_name":"Cristofanelli","first_name":"Paolo","full_name":"Cristofanelli, Paolo"},{"last_name":"Putero","first_name":"Davide","full_name":"Putero, Davide"},{"last_name":"Diolaiuti","full_name":"Diolaiuti, Guglielmina","first_name":"Guglielmina"},{"last_name":"Tartari","first_name":"Gianni","full_name":"Tartari, Gianni"},{"full_name":"Verza, Gianpietro","first_name":"Gianpietro","last_name":"Verza"},{"first_name":"Sudeep","full_name":"Thakuri, Sudeep","last_name":"Thakuri"},{"full_name":"Balsamo, Gianpaolo","first_name":"Gianpaolo","last_name":"Balsamo"},{"last_name":"Miles","first_name":"Evan S.","full_name":"Miles, Evan S."},{"orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti"}],"publication_status":"published","article_type":"original","month":"12","APC_amount":"4800 EUR","intvolume":"        16","oa_version":"Published Version","oa":1,"year":"2023","article_processing_charge":"Yes (in subscription journal)"},{"quality_controlled":"1","arxiv":1,"volume":30,"publication_identifier":{"issn":["0944-6532"],"eissn":["2363-6394"]},"citation":{"ama":"Carioni M, Fischer JL, Schlömerkemper A. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. <i>Journal of Convex Analysis</i>. 2023;30(1):217-247.","mla":"Carioni, Marcello, et al. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” <i>Journal of Convex Analysis</i>, vol. 30, no. 1, Heldermann Verlag, 2023, pp. 217–47.","ista":"Carioni M, Fischer JL, Schlömerkemper A. 2023. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. 30(1), 217–247.","chicago":"Carioni, Marcello, Julian L Fischer, and Anja Schlömerkemper. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” <i>Journal of Convex Analysis</i>. Heldermann Verlag, 2023.","apa":"Carioni, M., Fischer, J. L., &#38; Schlömerkemper, A. (2023). External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. <i>Journal of Convex Analysis</i>. Heldermann Verlag.","ieee":"M. Carioni, J. L. Fischer, and A. Schlömerkemper, “External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development,” <i>Journal of Convex Analysis</i>, vol. 30, no. 1. Heldermann Verlag, pp. 217–247, 2023.","short":"M. Carioni, J.L. Fischer, A. Schlömerkemper, Journal of Convex Analysis 30 (2023) 217–247."},"corr_author":"1","publication":"Journal of Convex Analysis","date_created":"2023-12-10T23:00:59Z","scopus_import":"1","department":[{"_id":"JuFi"}],"oa":1,"year":"2023","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1811.09857","open_access":"1"}],"issue":"1","intvolume":"        30","oa_version":"Preprint","month":"01","author":[{"last_name":"Carioni","full_name":"Carioni, Marcello","first_name":"Marcello"},{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlömerkemper","first_name":"Anja","full_name":"Schlömerkemper, Anja"}],"article_type":"original","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Heldermann Verlag","status":"public","_id":"14661","type":"journal_article","page":"217-247","date_updated":"2024-10-09T21:07:35Z","abstract":[{"lang":"eng","text":"This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are \"close to\" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit."}],"title":"External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["001115503400013"],"arxiv":["1811.09857"]},"date_published":"2023-01-01T00:00:00Z","day":"01"}]