[{"day":"22","month":"10","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"intvolume":"     14215","publication_status":"published","date_published":"2023-10-22T00:00:00Z","author":[{"last_name":"Ansaripour","first_name":"Matin","full_name":"Ansaripour, Matin"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","doi":"10.1007/978-3-031-45329-8_17","date_updated":"2025-07-14T09:09:59Z","alternative_title":["LNCS"],"scopus_import":"1","quality_controlled":"1","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2023-10-27","location":"Singapore, Singapore","start_date":"2023-10-24"},"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.","status":"public","citation":{"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>.","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.","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>","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>","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>.","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.","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."},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031453281"]},"volume":14215,"page":"357-379","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"14559","year":"2023","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."}],"publication":"21st International Symposium on Automated Technology for Verification and Analysis","title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer Nature","ec_funded":1,"date_created":"2023-11-19T23:00:56Z","oa_version":"None"},{"month":"11","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 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KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"date_published":"2023-11-21T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"file_date_updated":"2023-11-20T11:49:58Z","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.","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>.","short":"F.K. Schur, (2023).","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","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>"},"oa":1,"acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","status":"public","year":"2023","has_accepted_license":"1","_id":"14562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","contributor":[{"orcid":"0000-0001-7149-769X","last_name":"Fäßler","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"last_name":"Javoor","first_name":"Manjunath","contributor_type":"researcher","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Julia","orcid":"0000-0002-3616-8580","last_name":"Datler","contributor_type":"researcher","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hermann","last_name":"Döring","contributor_type":"researcher"},{"contributor_type":"researcher","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","last_name":"Hofer"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Faix","first_name":"Jan","contributor_type":"researcher"},{"first_name":"Klemens","last_name":"Rottner","contributor_type":"researcher"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"date_created":"2023-11-20T09:22:33Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","department":[{"_id":"FlSc"}]},{"oa":1,"status":"public","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_type":"original","issue":"11","citation":{"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>","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>","ista":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.","mla":"Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2022ms003391\">10.1029/2022ms003391</a>.","short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023)."},"publication_identifier":{"eissn":["1942-2466"]},"volume":15,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14564","has_accepted_license":"1","year":"2023","abstract":[{"lang":"eng","text":"Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized."}],"title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","department":[{"_id":"CaMu"}],"publication":"Journal of Advances in Modeling Earth Systems","publisher":"American Geophysical Union","oa_version":"Published Version","date_created":"2023-11-20T09:18:21Z","day":"01","ddc":["550"],"language":[{"iso":"eng"}],"month":"11","intvolume":"        15","publication_status":"published","file":[{"date_updated":"2023-11-20T11:29:16Z","file_id":"14582","file_size":6435697,"file_name":"2023_JAMES_Khoulder.pdf","checksum":"e30329dd985559de0ddc7021ca7382b4","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-11-20T11:29:16Z"}],"date_published":"2023-11-01T00:00:00Z","author":[{"full_name":"Khouider, B.","last_name":"Khouider","first_name":"B."},{"full_name":"GOSWAMI, BIDYUT B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"BIDYUT B","orcid":"0000-0001-8602-3083","last_name":"GOSWAMI"},{"full_name":"Phani, R.","first_name":"R.","last_name":"Phani"},{"full_name":"Majda, A. J.","first_name":"A. J.","last_name":"Majda"}],"doi":"10.1029/2022ms003391","date_updated":"2023-11-28T12:04:42Z","article_processing_charge":"Yes","scopus_import":"1","keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"quality_controlled":"1","file_date_updated":"2023-11-20T11:29:16Z","article_number":"e2022MS003391","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"}},{"department":[{"_id":"NiBa"}],"title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","publisher":"Zenodo","date_created":"2023-11-20T11:07:45Z","oa_version":"Published Version","date_published":"2023-07-11T00:00:00Z","author":[{"last_name":"Wetzel","first_name":"William","full_name":"Wetzel, William"}],"article_processing_charge":"No","doi":"10.5281/ZENODO.8133117","date_updated":"2023-11-20T11:17:33Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14552"}]},"abstract":[{"lang":"eng","text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"_id":"14579","year":"2023","status":"public","oa":1,"ddc":["570"],"day":"11","citation":{"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>.","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>","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>","short":"W. Wetzel, (2023).","mla":"Wetzel, William. <i>HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>.","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>."},"month":"07"},{"oa_version":"Published Version","ec_funded":1,"date_created":"2023-11-21T11:41:05Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","abstract":[{"text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.","lang":"eng"}],"year":"2023","has_accepted_license":"1","_id":"14587","supervisor":[{"full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X"}],"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"228","publication_identifier":{"issn":["2663 - 337X"]},"citation":{"ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","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>.","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>.","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.","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."},"oa":1,"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).","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"file_date_updated":"2023-11-29T09:28:30Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"11842","status":"public","relation":"part_of_dissertation"},{"id":"14597","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/at:ista:14587","date_updated":"2023-11-30T13:25:03Z","article_processing_charge":"No","date_published":"2023-11-21T00:00:00Z","author":[{"full_name":"Marveggio, Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","first_name":"Alice","last_name":"Marveggio"}],"publication_status":"published","file":[{"file_size":2881100,"file_name":"thesis_Marveggio.pdf","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","file_id":"14626","date_updated":"2023-11-29T09:09:31Z","content_type":"application/pdf","success":1,"date_created":"2023-11-29T09:09:31Z","relation":"main_file","creator":"amarvegg","access_level":"open_access"},{"date_updated":"2023-11-29T09:28:30Z","file_id":"14627","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","file_name":"Thesis_Marveggio.zip","file_size":10189696,"access_level":"open_access","creator":"amarvegg","relation":"source_file","date_created":"2023-11-29T09:10:19Z","content_type":"application/zip"}],"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","name":"Bridging Scales in Random Materials","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"11","day":"21","ddc":["515"]},{"citation":{"chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>.","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” <i>bioRxiv</i>. .","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, <a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>."},"month":"10","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"language":[{"iso":"eng"}],"status":"public","oa":1,"day":"10","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2","open_access":"1"}],"_id":"14591","year":"2023","publication_status":"submitted","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"date_published":"2023-10-10T00:00:00Z","author":[{"first_name":"Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"full_name":"Nagel, Marie-Kristin","last_name":"Nagel","first_name":"Marie-Kristin"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"first_name":"Annamaria","last_name":"Hlavata","full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Isono, Erika","last_name":"Isono","first_name":"Erika"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14510"}]},"doi":"10.1101/2023.10.09.561523","date_updated":"2023-12-01T13:51:06Z","date_created":"2023-11-22T10:17:49Z","ec_funded":1,"oa_version":"Preprint","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication":"bioRxiv","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}]},{"ddc":["530","540"],"day":"14","month":"11","language":[{"iso":"eng"}],"file":[{"date_updated":"2023-11-28T08:39:06Z","file_id":"14620","file_size":6276059,"file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","checksum":"f668ee0d07096eef81159d05bc27aabc","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-11-28T08:39:06Z"}],"publication_status":"published","intvolume":"       159","article_processing_charge":"Yes (in subscription journal)","date_updated":"2023-11-28T08:39:23Z","doi":"10.1063/5.0173341","related_material":{"record":[{"status":"public","relation":"research_data","id":"14619"}]},"date_published":"2023-11-14T00:00:00Z","author":[{"full_name":"Reinhardt, Aleks","last_name":"Reinhardt","first_name":"Aleks"},{"full_name":"Chew, Pin Yu","first_name":"Pin Yu","last_name":"Chew"},{"last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"}],"quality_controlled":"1","scopus_import":"1","article_number":"184110","file_date_updated":"2023-11-28T08:39:06Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"18","external_id":{"arxiv":["2308.10886"]},"article_type":"original","status":"public","oa":1,"acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"citation":{"ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110.","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>.","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. 2023;159(18). doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>","apa":"Reinhardt, A., Chew, P. Y., &#38; Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>.","ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” <i>Journal of Chemical Physics</i>, vol. 159, no. 18. AIP Publishing, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":159,"has_accepted_license":"1","year":"2023","_id":"14603","arxiv":1,"abstract":[{"lang":"eng","text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances."}],"publisher":"AIP Publishing","publication":"Journal of Chemical Physics","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","department":[{"_id":"BiCh"}],"date_created":"2023-11-26T23:00:54Z","oa_version":"Published Version"},{"page":"2504-2511","volume":77,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14604","has_accepted_license":"1","year":"2023","oa":1,"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.","status":"public","external_id":{"pmid":["37738212"]},"article_type":"original","issue":"11","citation":{"ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","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>.","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","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>","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>.","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."},"publication_identifier":{"eissn":["1558-5646"]},"department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of class Insecta","publication":"Evolution","publisher":"Oxford University Press","oa_version":"Published Version","date_created":"2023-11-26T23:00:54Z","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."}],"intvolume":"        77","publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2023-11-28T08:12:15Z","success":1,"file_id":"14618","date_updated":"2023-11-28T08:12:15Z","file_size":1399102,"checksum":"b66dc10edae92d38918d534e64dda77c","file_name":"2023_Evolution_Toups.pdf"}],"pmid":1,"day":"02","ddc":["570"],"language":[{"iso":"eng"}],"month":"11","file_date_updated":"2023-11-28T08:12:15Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-11-02T00:00:00Z","doi":"10.1093/evolut/qpad169","date_updated":"2023-11-28T08:25:28Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"14616"},{"relation":"research_data","status":"public","id":"14617"}],"link":[{"relation":"software","url":"https://git.ista.ac.at/bvicoso/veryoldx"}]},"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","quality_controlled":"1"},{"language":[{"iso":"eng"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"month":"11","day":"01","intvolume":"       108","publication_status":"published","scopus_import":"1","quality_controlled":"1","date_published":"2023-11-01T00:00:00Z","author":[{"full_name":"Ouyang, Niuchang","first_name":"Niuchang","last_name":"Ouyang"},{"first_name":"Zezhu","last_name":"Zeng","full_name":"Zeng, Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7"},{"full_name":"Wang, Chen","last_name":"Wang","first_name":"Chen"},{"last_name":"Wang","first_name":"Qi","full_name":"Wang, Qi"},{"last_name":"Chen","first_name":"Yue","full_name":"Chen, Yue"}],"date_updated":"2023-11-28T07:48:55Z","doi":"10.1103/PhysRevB.108.174302","article_processing_charge":"No","article_number":"174302","citation":{"ieee":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),” <i>Physical Review B</i>, vol. 108, no. 17. American Physical Society, 2023.","chicago":"Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>.","apa":"Ouyang, N., Zeng, Z., Wang, C., Wang, Q., &#38; Chen, Y. (2023). Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>","ama":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. 2023;108(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>","ista":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 108(17), 174302.","short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).","mla":"Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>, vol. 108, no. 17, 174302, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>."},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (Grants No. 17318122 and No. 17306721). The authors are grateful for the research computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","status":"public","article_type":"original","issue":"17","_id":"14605","year":"2023","volume":108,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments.","lang":"eng"}],"oa_version":"None","date_created":"2023-11-26T23:00:54Z","ec_funded":1,"title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","department":[{"_id":"BiCh"}],"publication":"Physical Review B","publisher":"American Physical Society"},{"date_created":"2023-11-26T23:00:55Z","oa_version":"Published Version","publication":"32nd USENIX Security Symposium","title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","department":[{"_id":"ElKo"}],"publisher":"Usenix","abstract":[{"text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art.","lang":"eng"}],"_id":"14609","year":"2023","has_accepted_license":"1","volume":8,"page":"5359-5376","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","citation":{"apa":"Das, S., Xiang, Z., Kokoris Kogias, E., &#38; Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In <i>32nd USENIX Security Symposium</i> (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in <i>32nd USENIX Security Symposium</i>, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In <i>32nd USENIX Security Symposium</i>, 8:5359–76. Usenix, 2023.","mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” <i>32nd USENIX Security Symposium</i>, vol. 8, Usenix, 2023, pp. 5359–76.","ista":"Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376.","short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376.","ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: <i>32nd USENIX Security Symposium</i>. Vol 8. Usenix; 2023:5359-5376."},"publication_identifier":{"isbn":["9781713879497"]},"oa":1,"status":"public","acknowledgement":"The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.","conference":{"location":"Anaheim, CA, United States","start_date":"2023-08-09","name":"USENIX Security Symposium","end_date":"2023-08-11"},"file_date_updated":"2023-11-28T09:14:34Z","scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Sourav","last_name":"Das","full_name":"Das, Sourav"},{"first_name":"Zhuolun","last_name":"Xiang","full_name":"Xiang, Zhuolun"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"first_name":"Ling","last_name":"Ren","full_name":"Ren, Ling"}],"date_published":"2023-08-15T00:00:00Z","article_processing_charge":"No","date_updated":"2023-11-28T09:17:38Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1389"}],"intvolume":"         8","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-11-28T09:14:34Z","file_id":"14621","date_updated":"2023-11-28T09:14:34Z","file_size":704331,"file_name":"2023_USENIX_Das.pdf","checksum":"1a730765930138e23c6efd2575872641"}],"publication_status":"published","month":"08","project":[{"name":"Secure Network and Hardware for Efficient Blockchains","grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"language":[{"iso":"eng"}],"ddc":["000"],"day":"15"},{"author":[{"last_name":"Bussi","first_name":"Claudio","full_name":"Bussi, Claudio"},{"full_name":"Mangiarotti, Agustín","last_name":"Mangiarotti","first_name":"Agustín"},{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo"},{"last_name":"Aylan","first_name":"Beren","full_name":"Aylan, Beren"},{"full_name":"Pellegrino, Enrica","first_name":"Enrica","last_name":"Pellegrino"},{"full_name":"Athanasiadi, Natalia","last_name":"Athanasiadi","first_name":"Natalia"},{"first_name":"Antony","last_name":"Fearns","full_name":"Fearns, Antony"},{"last_name":"Rodgers","first_name":"Angela","full_name":"Rodgers, Angela"},{"last_name":"Franzmann","first_name":"Titus M.","full_name":"Franzmann, Titus M."},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"first_name":"Maximiliano G.","last_name":"Gutierrez","full_name":"Gutierrez, Maximiliano G."}],"date_published":"2023-11-15T00:00:00Z","article_processing_charge":"Yes (via OA deal)","doi":"10.1038/s41586-023-06726-w","date_updated":"2023-11-27T09:05:08Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}],"record":[{"id":"14472","status":"public","relation":"research_data"}]},"keyword":["Multidisciplinary"],"quality_controlled":"1","pmid":1,"day":"15","month":"11","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1038/s41586-023-06726-w","open_access":"1"}],"publication_status":"epub_ahead","abstract":[{"lang":"eng","text":"<jats:title>Abstract</jats:title><jats:p>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.</jats:p>"}],"publication":"Nature","department":[{"_id":"AnSa"}],"title":"Stress granules plug and stabilize damaged endolysosomal membranes","publisher":"Springer Nature","date_created":"2023-11-27T07:56:37Z","oa_version":"Published Version","status":"public","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.","oa":1,"article_type":"original","external_id":{"pmid":["37968398"]},"citation":{"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>. Springer Nature, 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>.","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.","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, Springer Nature, 2023, 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 (2023).","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>"},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14610","year":"2023"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"msad245","file_date_updated":"2024-01-02T11:39:38Z","quality_controlled":"1","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","doi":"10.1093/molbev/msad245","date_updated":"2024-02-21T12:18:35Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"14614"}],"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage","relation":"press_release"}]},"date_published":"2023-12-01T00:00:00Z","author":[{"id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","last_name":"Lasne","first_name":"Clementine"},{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380"},{"first_name":"Lorena Alexandra","orcid":"0000-0002-1253-6297","last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"file":[{"file_id":"14727","date_updated":"2024-01-02T11:39:38Z","file_size":8623505,"file_name":"2023_MolecularBioEvo_Lasne.pdf","checksum":"47c1c72fb499f26ea52d216b242208c8","relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2024-01-02T11:39:38Z"}],"publication_status":"published","intvolume":"        40","month":"12","language":[{"iso":"eng"}],"project":[{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"},{"grant_number":"ESP39 49461","name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3"}],"ddc":["570"],"day":"01","pmid":1,"date_created":"2023-11-27T16:14:37Z","oa_version":"Published Version","publisher":"Oxford University Press","publication":"Molecular Biology and Evolution","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","department":[{"_id":"BeVi"}],"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 a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). 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 two 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."}],"year":"2023","has_accepted_license":"1","_id":"14613","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":40,"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"citation":{"short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>."},"issue":"12","article_type":"original","external_id":{"pmid":["37988296"]},"status":"public","oa":1,"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10)."},{"status":"public","oa":1,"day":"01","ddc":["576"],"citation":{"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>","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","mla":"Lasne, Clementine, and Marwan N. Elkrewi. <i>The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","short":"C. Lasne, M.N. Elkrewi, (2023).","chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>.","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>"},"month":"12","contributor":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","contributor_type":"researcher","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14614","year":"2023","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","creator":"clasne","content_type":"application/zip","success":1,"date_created":"2023-11-28T13:15:26Z","file_id":"14625","date_updated":"2023-11-28T13:15:26Z","file_size":404968272,"file_name":"panorpaX.zip","checksum":"cd0f13322b5156819ecaebd2bc8e7d12"},{"content_type":"text/plain","date_created":"2023-11-30T14:16:59Z","success":1,"relation":"main_file","access_level":"open_access","creator":"clasne","file_size":2625,"checksum":"9ff600416577687a737cb3c96dfcb26c","file_name":"panorpa_readme.txt","date_updated":"2023-11-30T14:16:59Z","file_id":"14634"}],"author":[{"first_name":"Clementine","last_name":"Lasne","orcid":"0000-0002-1197-8616","full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","first_name":"Marwan N"}],"date_published":"2023-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14614","date_updated":"2024-02-21T12:18:35Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14613"}]},"article_processing_charge":"No","abstract":[{"text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"keyword":["Panorpa","scorpionfly","genome","transcriptome"],"department":[{"_id":"BeVi"}],"file_date_updated":"2023-11-30T14:16:59Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_created":"2023-11-27T16:39:19Z"},{"year":"2023","has_accepted_license":"1","_id":"14616","main_file_link":[{"url":"https://doi.org/10.5061/dryad.hx3ffbgkt","open_access":"1"}],"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"09","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>","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>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>.","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Dryad, 2023, doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>.","short":"M.A. Toups, B. Vicoso, (2023).","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>"},"day":"15","ddc":["570"],"oa":1,"status":"public","oa_version":"Published Version","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"date_created":"2023-11-28T08:01:53Z","publisher":"Dryad","title":"The X chromosome of insects likely predates the origin of Class Insecta","department":[{"_id":"BeVi"}],"abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"related_material":{"record":[{"id":"14604","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-11-28T08:17:31Z","doi":"10.5061/DRYAD.HX3FFBGKT","article_processing_charge":"No","author":[{"first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-09-15T00:00:00Z"},{"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","other_data_license":"MIT License","year":"2023","has_accepted_license":"1","_id":"14617","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8138705","open_access":"1"}],"day":"15","ddc":["570"],"oa":1,"status":"public","month":"09","citation":{"ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>","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>.","short":"M.A. Toups, B. Vicoso, (2023).","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","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>.","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>"},"publisher":"Zenodo","department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","oa_version":"Published Version","date_created":"2023-11-28T08:04:03Z","related_material":{"record":[{"id":"14604","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.8138705","date_updated":"2023-11-28T08:25:28Z","article_processing_charge":"No","date_published":"2023-09-15T00:00:00Z","author":[{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"}],"abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}]},{"abstract":[{"text":"Data underlying the publication \"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals\" (DOI https://doi.org/10.1063/5.0173341).","lang":"eng"}],"related_material":{"record":[{"id":"14603","relation":"used_in_publication","status":"public"}]},"doi":"10.5281/ZENODO.8398094","date_updated":"2023-11-28T08:39:22Z","article_processing_charge":"No","author":[{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"date_published":"2023-10-02T00:00:00Z","oa_version":"Published Version","date_created":"2023-11-28T08:32:18Z","publisher":"Zenodo","title":"BingqingCheng/solubility: V1.0","department":[{"_id":"BiCh"}],"month":"10","citation":{"mla":"Cheng, Bingqing. <i>BingqingCheng/Solubility: V1.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","short":"B. Cheng, (2023).","ama":"Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>","apa":"Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>","chicago":"Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>.","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023."},"day":"02","ddc":["530"],"status":"public","oa":1,"has_accepted_license":"1","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8398094"}],"_id":"14619","type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2023-11-28T10:58:13Z","ec_funded":1,"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","publisher":"Institute of Science and Technology Austria","_id":"14622","supervisor":[{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"}],"year":"2023","has_accepted_license":"1","page":"142","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","citation":{"apa":"Sack, S. (2023). <i>Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>.","mla":"Sack, Stefan. <i>Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>"},"publication_identifier":{"issn":["2663 - 337X"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"file_date_updated":"2023-12-01T11:10:46Z","degree_awarded":"PhD","date_published":"2023-11-30T00:00:00Z","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan"}],"article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11471"},{"id":"13125","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9760"}]},"alternative_title":["ISTA Thesis"],"date_updated":"2023-12-13T14:47:25Z","doi":"10.15479/at:ista:14622","file":[{"relation":"main_file","creator":"ssack","access_level":"closed","content_type":"application/pdf","embargo_to":"open_access","date_created":"2023-11-30T15:53:10Z","file_id":"14635","embargo":"2024-11-30","date_updated":"2023-12-01T11:10:46Z","file_size":11947523,"file_name":"PhD_Thesis.pdf","checksum":"068fd3570506ec42b2faa390de784bc4"},{"access_level":"closed","creator":"ssack","relation":"source_file","date_created":"2023-11-30T15:54:11Z","content_type":"application/zip","date_updated":"2023-12-01T11:10:46Z","file_id":"14636","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_name":"PhD Thesis (1).zip","file_size":18422964}],"publication_status":"published","month":"11","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"},{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"language":[{"iso":"eng"}],"ddc":["530"],"day":"30"},{"article_type":"original","issue":"5","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.","status":"public","oa":1,"publication_identifier":{"issn":["0730-0301","1557-7368"]},"citation":{"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>","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.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","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>.","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.","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>.","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>"},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":42,"has_accepted_license":"1","year":"2023","_id":"14628","abstract":[{"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.","lang":"eng"}],"publisher":"Association for Computing Machinery","title":"Procedural metamaterials: A unified procedural graph for metamaterial design","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"publication":"ACM Transactions on Graphics","oa_version":"Published Version","date_created":"2023-11-29T15:02:03Z","day":"01","ddc":["531","006"],"project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"language":[{"iso":"eng"}],"month":"10","publication_status":"published","file":[{"file_size":95467870,"file_name":"tog-22-0089-File004.zip","checksum":"0192f597d7a2ceaf89baddfd6190d4c8","file_id":"14630","date_updated":"2023-11-29T15:16:01Z","content_type":"application/zip","success":1,"date_created":"2023-11-29T15:16:01Z","relation":"main_file","access_level":"open_access","creator":"yichen"},{"success":1,"date_created":"2023-11-29T15:16:01Z","content_type":"application/zip","creator":"yichen","access_level":"open_access","relation":"main_file","file_name":"tog-22-0089-File005.zip","checksum":"7fb024963be81933494f38de191e4710","file_size":103731880,"file_id":"14631","date_updated":"2023-11-29T15:16:01Z"},{"date_updated":"2023-12-04T08:04:14Z","file_id":"14638","file_size":57067476,"checksum":"b7d6829ce396e21cac9fae0ec7130a6b","file_name":"2023_ACMToG_Makatura.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2023-12-04T08:04:14Z","success":1}],"intvolume":"        42","date_updated":"2023-12-04T08:09:05Z","doi":"10.1145/3605389","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Makatura, Liane","first_name":"Liane","last_name":"Makatura"},{"first_name":"Bohan","last_name":"Wang","full_name":"Wang, Bohan"},{"full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","first_name":"Yi-Lu","last_name":"Chen"},{"first_name":"Bolei","last_name":"Deng","full_name":"Deng, Bolei"},{"first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"}],"date_published":"2023-10-01T00:00:00Z","quality_controlled":"1","keyword":["Computer Graphics and Computer-Aided Design"],"article_number":"168","file_date_updated":"2023-12-04T08:04:14Z"},{"publication_identifier":{"issn":["2663 - 337X"]},"citation":{"chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). <i>Adaptive mutation in E. coli modulated by luxS</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>","mla":"Hennessey-Wesen, Mike. <i>Adaptive Mutation in E. Coli Modulated by LuxS</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria."},"status":"public","has_accepted_license":"1","year":"2023","supervisor":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"_id":"14641","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","page":"104","ec_funded":1,"date_created":"2023-12-04T13:17:37Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","title":"Adaptive mutation in E. coli modulated by luxS","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"month":"11","language":[{"iso":"eng"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ddc":["570"],"day":"30","file":[{"date_created":"2023-12-06T13:13:26Z","content_type":"application/vnd.oasis.opendocument.text","creator":"mhenness","access_level":"closed","relation":"source_file","file_name":"mike_thesis_v06-12-2023.odt","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","file_size":46405919,"file_id":"14648","date_updated":"2023-12-06T13:13:26Z"},{"date_created":"2023-12-06T13:14:15Z","embargo_to":"open_access","content_type":"application/pdf","creator":"mhenness","access_level":"closed","relation":"main_file","checksum":"f5203a61eddaf35235bbc51904d73982","file_name":"mike_thesis_v06-12-2023.pdf","file_size":21282155,"embargo":"2024-11-30","file_id":"14649","date_updated":"2023-12-06T13:14:15Z"}],"publication_status":"published","degree_awarded":"PhD","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"article_processing_charge":"No","doi":"10.15479/at:ista:14641","date_updated":"2023-12-07T14:12:25Z","alternative_title":["ISTA Thesis"],"date_published":"2023-11-30T00:00:00Z","author":[{"last_name":"Hennessey-Wesen","first_name":"Mike","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"file_date_updated":"2023-12-06T13:14:15Z"},{"title":"Mechanism of mammalian transcriptional repression by noncoding RNA","file_date_updated":"2023-12-05T10:37:02Z","department":[{"_id":"CaBe"}],"publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"oa_version":"Submitted Version","date_created":"2023-12-04T14:51:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"author":[{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","full_name":"Tluckova, Katarina","last_name":"Tluckova","first_name":"Katarina"},{"last_name":"Testa Salmazo","first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","first_name":"Carrie A"}],"date_published":"2023-12-05T00:00:00Z","doi":"10.15479/AT:ISTA:14644","date_updated":"2023-12-05T10:37:28Z","article_processing_charge":"No","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."}],"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14644","publication_status":"submitted","has_accepted_license":"1","year":"2023","file":[{"success":1,"date_created":"2023-12-05T10:37:02Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","file_name":"2023_Tluckova_etal_REx.pdf","checksum":"c45608cb97ee36d7b50ba518db8e07b0","file_size":4892920,"date_updated":"2023-12-05T10:37:02Z","file_id":"14646"}],"status":"public","oa":1,"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).","day":"05","ddc":["572"],"citation":{"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>.","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","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>"},"language":[{"iso":"eng"}],"project":[{"_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185"}],"month":"12"}]