[{"author":[{"first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","last_name":"Guseinov"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","oa":1,"date_published":"2020-11-23T00:00:00Z","date_updated":"2025-04-15T07:16:12Z","year":"2020","department":[{"_id":"BeBi"}],"status":"public","date_created":"2020-11-16T10:47:18Z","doi":"10.15479/AT:ISTA:8761","type":"research_data","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","ec_funded":1,"title":"Supplementary data for \"Computational design of cold bent glass façades\"","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8562"}],"link":[{"relation":"software","url":"https://github.com/russelmann/cold-glass-acm"}]},"file":[{"date_updated":"2020-11-16T10:31:29Z","file_name":"mdn_model.tar.gz","checksum":"f5ae57b97017b9f61081032703361233","relation":"main_file","file_size":15378270,"file_id":"8762","date_created":"2020-11-16T10:31:29Z","access_level":"open_access","success":1,"creator":"rguseino","content_type":"application/x-gzip"},{"file_id":"8763","date_created":"2020-11-16T10:43:23Z","success":1,"access_level":"open_access","content_type":"application/x-gzip","creator":"rguseino","date_updated":"2020-11-16T10:43:23Z","file_name":"optimal_panels_data.tar.gz","checksum":"b0d25e04060ee78c585ee2f23542c744","relation":"main_file","file_size":615387734},{"content_type":"text/plain","creator":"rguseino","file_id":"8770","access_level":"open_access","success":1,"date_created":"2020-11-18T10:04:59Z","relation":"main_file","checksum":"69c1dde3434ada86d125e0c2588caf1e","file_size":1228,"date_updated":"2020-11-18T10:04:59Z","file_name":"readme.txt"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["000"],"citation":{"ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>.","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","short":"R. Guseinov, (2020).","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Computational Design of Cold Bent Glass Façades.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>.","ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">https://doi.org/10.15479/AT:ISTA:8761</a>","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">https://doi.org/10.15479/AT:ISTA:8761</a>."},"has_accepted_license":"1","contributor":[{"contributor_type":"researcher","first_name":"Konstantinos","last_name":"Gavriil"},{"orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Ruslan","last_name":"Guseinov"},{"contributor_type":"researcher","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez"},{"contributor_type":"researcher","first_name":"Davide","last_name":"Pellis"},{"last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","first_name":"Paul M","contributor_type":"researcher"},{"last_name":"Rist","first_name":"Florian","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Helmut","last_name":"Pottmann"},{"contributor_type":"researcher","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"}],"_id":"8761","publisher":"Institute of Science and Technology Austria","corr_author":"1","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"day":"23","file_date_updated":"2020-11-18T10:04:59Z"},{"abstract":[{"lang":"eng","text":"This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate."}],"date_created":"2020-11-17T09:35:10Z","intvolume":"        39","quality_controlled":"1","date_published":"2020-05-01T00:00:00Z","year":"2020","issue":"2","oa":1,"_id":"8765","publisher":"Wiley","day":"01","ddc":["000"],"publication":"Computer Graphics Forum","keyword":["Computer Networks and Communications"],"volume":39,"ec_funded":1,"title":"A practical method for animating anisotropic elastoplastic materials","article_type":"original","publication_status":"published","doi":"10.1111/cgf.13914","type":"journal_article","oa_version":"Submitted Version","isi":1,"status":"public","date_updated":"2024-10-22T09:58:14Z","department":[{"_id":"ChWo"}],"author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille","last_name":"Schreck","full_name":"Schreck, Camille"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"article_processing_charge":"No","scopus_import":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"}],"file_date_updated":"2020-11-23T09:05:13Z","citation":{"mla":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>.","ieee":"C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” <i>Computer Graphics Forum</i>, vol. 39, no. 2. Wiley, pp. 89–99, 2020.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99.","ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","chicago":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>.","apa":"Schreck, C., &#38; Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>","ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. 2020;39(2):89-99. doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>"},"has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"8796","date_created":"2020-11-23T09:05:13Z","access_level":"open_access","success":1,"checksum":"7605f605acd84d0942b48bc7a1c2d72e","relation":"main_file","file_size":38969122,"file_name":"2020_poff_revisited.pdf","date_updated":"2020-11-23T09:05:13Z"}],"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176.","page":"89-99","acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["000548709600008"]},"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"month":"05","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"8766","publisher":"Wiley","day":"01","volume":39,"ec_funded":1,"title":"Making procedural water waves boundary-aware","article_type":"original","publication":"Computer Graphics forum","date_created":"2020-11-17T10:47:48Z","intvolume":"        39","abstract":[{"lang":"eng","text":"The “procedural” approach to animating ocean waves is the dominant algorithm for animating larger bodies of water in\r\ninteractive applications as well as in off-line productions — it provides high visual quality with a low computational demand. In this paper, we widen the applicability of procedural water wave animation with an extension that guarantees the satisfaction of boundary conditions imposed by terrain while still approximating physical wave behavior. In combination with a particle system that models wave breaking, foam, and spray, this allows us to naturally model waves interacting with beaches and rocks. Our system is able to animate waves at large scales at interactive frame rates on a commodity PC."}],"quality_controlled":"1","date_published":"2020-12-01T00:00:00Z","year":"2020","issue":"8","citation":{"ama":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. Making procedural water waves boundary-aware. <i>Computer Graphics forum</i>. 2020;39(8):47-54. doi:<a href=\"https://doi.org/10.1111/cgf.14100\">10.1111/cgf.14100</a>","apa":"Jeschke, S., Hafner, C., Chentanez, N., Macklin, M., Müller-Fischer, M., &#38; Wojtan, C. (2020). Making procedural water waves boundary-aware. <i>Computer Graphics Forum</i>. Online Symposium: Wiley. <a href=\"https://doi.org/10.1111/cgf.14100\">https://doi.org/10.1111/cgf.14100</a>","chicago":"Jeschke, Stefan, Christian Hafner, Nuttapong Chentanez, Miles Macklin, Matthias Müller-Fischer, and Chris Wojtan. “Making Procedural Water Waves Boundary-Aware.” <i>Computer Graphics Forum</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/cgf.14100\">https://doi.org/10.1111/cgf.14100</a>.","ieee":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, and C. Wojtan, “Making procedural water waves boundary-aware,” <i>Computer Graphics forum</i>, vol. 39, no. 8. Wiley, pp. 47–54, 2020.","short":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, C. Wojtan, Computer Graphics Forum 39 (2020) 47–54.","ista":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. 2020. Making procedural water waves boundary-aware. Computer Graphics forum. 39(8), 47–54.","mla":"Jeschke, Stefan, et al. “Making Procedural Water Waves Boundary-Aware.” <i>Computer Graphics Forum</i>, vol. 39, no. 8, Wiley, 2020, pp. 47–54, doi:<a href=\"https://doi.org/10.1111/cgf.14100\">10.1111/cgf.14100</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"},{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","month":"12","conference":{"name":"SCA: Symposium on Computer Animation","start_date":"2020-10-06","location":"Online Symposium","end_date":"2020-10-09"},"page":"47-54","external_id":{"isi":["000591780400005"]},"isi":1,"status":"public","publication_status":"published","doi":"10.1111/cgf.14100","type":"journal_article","oa_version":"None","article_processing_charge":"No","author":[{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chentanez, Nuttapong","last_name":"Chentanez","first_name":"Nuttapong"},{"first_name":"Miles","last_name":"Macklin","full_name":"Macklin, Miles"},{"full_name":"Müller-Fischer, Matthias","last_name":"Müller-Fischer","first_name":"Matthias"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"date_updated":"2024-10-22T09:58:15Z","department":[{"_id":"ChWo"},{"_id":"BeBi"}]},{"external_id":{"pmid":["33151935"],"isi":["000591317200004"]},"acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","file":[{"creator":"dernst","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2020-11-18T07:26:10Z","file_id":"8768","file_size":2498594,"relation":"main_file","checksum":"555456dd0e47bcf9e0994bcb95577e88","date_updated":"2020-11-18T07:26:10Z","file_name":"2020_PlosCompBio_Kaveh.pdf"}],"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","scopus_import":"1","file_date_updated":"2020-11-18T07:26:10Z","article_number":"e1008402","has_accepted_license":"1","citation":{"chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., &#38; Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. 2020;16(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>.","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” <i>PLOS Computational Biology</i>, vol. 16, no. 11. Public Library of Science, 2020."},"language":[{"iso":"eng"}],"date_updated":"2025-06-12T07:02:01Z","department":[{"_id":"KrCh"}],"article_processing_charge":"No","author":[{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"full_name":"McAvoy, Alex","last_name":"McAvoy","first_name":"Alex"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"doi":"10.1371/journal.pcbi.1008402","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"publication":"PLOS Computational Biology","volume":16,"article_type":"original","title":"The Moran process on 2-chromatic graphs","_id":"8767","day":"05","publisher":"Public Library of Science","ddc":["000"],"pmid":1,"date_published":"2020-11-05T00:00:00Z","issue":"11","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_created":"2020-11-18T07:20:23Z","abstract":[{"text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring.","lang":"eng"}],"intvolume":"        16","quality_controlled":"1"},{"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"scopus_import":"1","language":[{"iso":"eng"}],"article_number":"144109","citation":{"short":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, R. Seiringer, Physical Review B 102 (2020).","ieee":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, and R. Seiringer, “Quantum impurity model for anyons,” <i>Physical Review B</i>, vol. 102, no. 14. American Physical Society, 2020.","ista":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. 2020. Quantum impurity model for anyons. Physical Review B. 102(14), 144109.","mla":"Yakaboylu, Enderalp, et al. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>, vol. 102, no. 14, 144109, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>.","ama":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. Quantum impurity model for anyons. <i>Physical Review B</i>. 2020;102(14). doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>","apa":"Yakaboylu, E., Ghazaryan, A., Lundholm, D., Rougerie, N., Lemeshko, M., &#38; Seiringer, R. (2020). Quantum impurity model for anyons. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>","chicago":"Yakaboylu, Enderalp, Areg Ghazaryan, D. Lundholm, N. Rougerie, Mikhail Lemeshko, and Robert Seiringer. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>."},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"external_id":{"isi":["000582563300001"],"arxiv":["1912.07890"]},"acknowledgement":"We are grateful to M. Correggi, A. Deuchert, and P. Schmelcher for valuable discussions. We also thank the anonymous referees for helping to clarify a few important points in the experimental realization. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement\r\nNo 754411. D.L. acknowledges financial support from the Goran Gustafsson Foundation (grant no. 1804) and LMU Munich. R.S., M.L., and N.R. gratefully acknowledge financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 694227, No 801770, and No 758620, respectively).","month":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","doi":"10.1103/physrevb.102.144109","publication_status":"published","status":"public","isi":1,"department":[{"_id":"MiLe"},{"_id":"RoSe"}],"date_updated":"2025-04-14T07:26:54Z","author":[{"last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp"},{"last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"D.","full_name":"Lundholm, D.","last_name":"Lundholm"},{"last_name":"Rougerie","full_name":"Rougerie, N.","first_name":"N."},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"article_processing_charge":"No","day":"01","publisher":"American Physical Society","arxiv":1,"_id":"8769","publication":"Physical Review B","title":"Quantum impurity model for anyons","article_type":"original","ec_funded":1,"volume":102,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1912.07890","open_access":"1"}],"intvolume":"       102","date_created":"2020-11-18T07:34:17Z","abstract":[{"lang":"eng","text":"One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas."}],"issue":"14","year":"2020","date_published":"2020-10-01T00:00:00Z","oa":1},{"date_created":"2020-11-25T11:07:25Z","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"doi":"10.5061/dryad.qrfj6q5cn","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"type":"research_data_reference","oa_version":"Published Version","status":"public","date_published":"2020-07-01T00:00:00Z","date_updated":"2025-07-10T11:54:59Z","year":"2020","department":[{"_id":"NiBa"}],"author":[{"last_name":"Perini","full_name":"Perini, Samuel","first_name":"Samuel"},{"first_name":"Marina","full_name":"Rafajlovic, Marina","last_name":"Rafajlovic"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"article_processing_charge":"No","oa":1,"_id":"8809","publisher":"Dryad","license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"01","citation":{"short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","mla":"Perini, Samuel, et al. <i>Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>.","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>"},"has_accepted_license":"1","related_material":{"record":[{"id":"7995","relation":"used_in_publication","status":"public"}]},"month":"07","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina"},{"department":[{"_id":"SiHi"}],"year":"2020","date_updated":"2023-09-12T11:05:28Z","date_published":"2020-11-05T00:00:00Z","oa":1,"article_processing_charge":"No","author":[{"first_name":"Laura","full_name":"Santini, Laura","last_name":"Santini"},{"first_name":"Florian","last_name":"Halbritter","full_name":"Halbritter, Florian"},{"last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian","first_name":"Fabian"},{"first_name":"Toru","full_name":"Suzuki, Toru","last_name":"Suzuki"},{"full_name":"Asami, Maki","last_name":"Asami","first_name":"Maki"},{"last_name":"Ramesmayer","full_name":"Ramesmayer, Julia","first_name":"Julia"},{"first_name":"Xiaoyan","full_name":"Ma, Xiaoyan","last_name":"Ma"},{"last_name":"Lackner","full_name":"Lackner, Andreas","first_name":"Andreas"},{"first_name":"Nick","last_name":"Warr","full_name":"Warr, Nick"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","last_name":"Pauler"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Ernest","last_name":"Laue","full_name":"Laue, Ernest"},{"first_name":"Matthias","last_name":"Farlik","full_name":"Farlik, Matthias"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"first_name":"Andreas","last_name":"Beyer","full_name":"Beyer, Andreas"},{"last_name":"Perry","full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F."},{"first_name":"Martin","full_name":"Leeb, Martin","last_name":"Leeb"}],"oa_version":"Preprint","type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"doi":"10.1101/2020.11.03.366948","date_created":"2020-11-26T07:17:19Z","abstract":[{"lang":"eng","text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation."}],"publication_status":"submitted","status":"public","external_id":{"pmid":["PPR234457 "]},"publication":"bioRxiv","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","publisher":"Cold Spring Harbor Laboratory","_id":"8813","language":[{"iso":"eng"}],"pmid":1,"citation":{"short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","ieee":"L. Santini <i>et al.</i>, “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, <a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>."}},{"contributor":[{"first_name":"Kushagra","contributor_type":"project_member","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal"},{"first_name":"Andrea C","contributor_type":"project_member","id":"340F461A-F248-11E8-B48F-1D18A9856A87","last_name":"Hofmann"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","contributor_type":"project_member","last_name":"Jirovec"},{"last_name":"Prieto Gonzalez","contributor_type":"project_member","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sammak","contributor_type":"project_member","first_name":"Amir"},{"last_name":"Botifoll","first_name":"Marc","contributor_type":"project_member"},{"first_name":"Sara","contributor_type":"project_member","last_name":"Marti-Sanchez"},{"contributor_type":"project_member","first_name":"Menno","last_name":"Veldhorst"},{"last_name":"Arbiol","first_name":"Jordi","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Giordano","last_name":"Scappucci"},{"last_name":"Katsaros","contributor_type":"project_leader","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","ddc":["530"],"citation":{"chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>","ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>","mla":"Katsaros, Georgios. <i>Enhancement of Proximity Induced Superconductivity in Planar Germanium</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>.","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","short":"G. Katsaros, (2020).","ista":"Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>."},"day":"02","file_date_updated":"2020-12-02T10:46:27Z","corr_author":"1","publisher":"Institute of Science and Technology Austria","_id":"8834","title":"Enhancement of proximity induced superconductivity in planar Germanium","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10559"},{"id":"8831","relation":"used_in_publication","status":"public"}]},"file":[{"file_size":898039,"checksum":"898607ac9d7cfbd5c7dd84bcb6d8a924","relation":"main_file","file_name":"Figure1-ICvsVG.hdf5","date_updated":"2020-12-02T10:46:21Z","creator":"gkatsaro","content_type":"application/octet-stream","date_created":"2020-12-02T10:46:21Z","success":1,"access_level":"open_access","file_id":"8836"},{"relation":"main_file","checksum":"f6f5888f8425e82b4dcd5ec3db9162a6","file_size":184971,"date_updated":"2020-12-02T10:46:21Z","file_name":"Figure1-RNvsVG.hdf5","content_type":"application/octet-stream","creator":"gkatsaro","file_id":"8837","success":1,"access_level":"open_access","date_created":"2020-12-02T10:46:21Z"},{"access_level":"open_access","success":1,"date_created":"2020-12-02T10:46:22Z","file_id":"8838","content_type":"application/octet-stream","creator":"gkatsaro","date_updated":"2020-12-02T10:46:22Z","file_name":"Figure2-MAR.hdf5","file_size":2097740,"relation":"main_file","checksum":"63a26c4b0299538610ec58c48c0ab1e3"},{"relation":"main_file","checksum":"4c6795b64b05088606ab7881f801acd7","file_size":911501,"file_name":"Figure3-Fraunhofer.hdf5","date_updated":"2020-12-02T10:46:22Z","content_type":"application/octet-stream","creator":"gkatsaro","file_id":"8839","success":1,"access_level":"open_access","date_created":"2020-12-02T10:46:22Z"},{"content_type":"application/octet-stream","creator":"gkatsaro","access_level":"open_access","success":1,"date_created":"2020-12-02T10:46:22Z","file_id":"8840","file_size":384239,"relation":"main_file","checksum":"6b1b07e8ab0d6c1fead91032bf543818","file_name":"Figure3-ICvsBparallel.hdf5","date_updated":"2020-12-02T10:46:22Z"},{"file_size":942878,"relation":"main_file","checksum":"d825f77f57cbf455a4ac48afeec27f5b","date_updated":"2020-12-02T10:46:22Z","file_name":"Figure3-ICvsBperp.hdf5","content_type":"application/octet-stream","creator":"gkatsaro","success":1,"access_level":"open_access","date_created":"2020-12-02T10:46:22Z","file_id":"8841"},{"file_size":623246,"relation":"main_file","checksum":"ec81afc3697da097a224e9142322243c","file_name":"Figure4-CPR.hdf5","date_updated":"2020-12-02T10:46:22Z","creator":"gkatsaro","content_type":"application/octet-stream","access_level":"open_access","success":1,"date_created":"2020-12-02T10:46:22Z","file_id":"8842"},{"content_type":"application/octet-stream","creator":"gkatsaro","date_created":"2020-12-02T10:46:22Z","access_level":"open_access","success":1,"file_id":"8843","file_size":507164,"checksum":"ca5860a8850a6874312c4ca1d7d41013","relation":"main_file","date_updated":"2020-12-02T10:46:22Z","file_name":"Figure4-SQUID.hdf5"},{"success":1,"access_level":"open_access","date_created":"2020-12-02T10:46:22Z","file_id":"8844","content_type":"text/plain","creator":"gkatsaro","date_updated":"2020-12-02T10:46:22Z","file_name":"Readme.txt","file_size":1573,"relation":"main_file","checksum":"770721205d081c847316d9122c94eb9b"},{"content_type":"application/octet-stream","creator":"gkatsaro","access_level":"open_access","success":1,"date_created":"2020-12-02T10:46:22Z","file_id":"8845","file_size":842702,"relation":"main_file","checksum":"5e2e407ca631fb15b8c3cc51c5dd3bdb","date_updated":"2020-12-02T10:46:22Z","file_name":"Figure 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Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n","lang":"eng"}],"oa":1,"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"article_processing_charge":"No","author":[{"last_name":"Katsaros","full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GeKa"}],"year":"2020","date_updated":"2025-04-15T08:38:16Z","date_published":"2020-12-02T00:00:00Z"},{"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"date_published":"2020-12-01T00:00:00Z","year":"2020","date_created":"2020-12-03T11:47:31Z","intvolume":"       450","abstract":[{"lang":"eng","text":"Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord."}],"quality_controlled":"1","volume":450,"title":"Differential loss of spinal interneurons in a mouse model of ALS","article_type":"original","publication":"Neuroscience","ddc":["570"],"pmid":1,"_id":"8914","publisher":"Elsevier","day":"01","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Alina","full_name":"Salamatina, Alina","last_name":"Salamatina"},{"full_name":"Yang, Jerry H","last_name":"Yang","first_name":"Jerry H"},{"full_name":"Brenner-Morton, Susan","last_name":"Brenner-Morton","first_name":"Susan"},{"full_name":"Bikoff, Jay B ","last_name":"Bikoff","first_name":"Jay B "},{"first_name":"Linjing","last_name":"Fang","full_name":"Fang, Linjing"},{"last_name":"Kintner","full_name":"Kintner, Christopher R","first_name":"Christopher R"},{"full_name":"Jessell, Thomas M","last_name":"Jessell","first_name":"Thomas M"},{"last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger"}],"date_updated":"2024-10-09T21:00:14Z","department":[{"_id":"LoSw"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1016/j.neuroscience.2020.08.011","type":"journal_article","oa_version":"Published Version","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"81-95","file":[{"file_size":4071247,"checksum":"da7413c819e079720669c82451b49294","relation":"main_file","date_updated":"2020-12-03T11:45:26Z","file_name":"2020_Neuroscience_Salamatina.pdf","creator":"dernst","content_type":"application/pdf","date_created":"2020-12-03T11:45:26Z","access_level":"open_access","success":1,"file_id":"8915"}],"acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational scientist, friend and mentor.","external_id":{"pmid":["32858144"],"isi":["000595588700008"]},"publication_identifier":{"issn":["0306-4522"]},"citation":{"chicago":"Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B  Bikoff, Linjing Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>.","apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>","ama":"Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. 2020;450:81-95. doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>","mla":"Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>, vol. 450, Elsevier, 2020, pp. 81–95, doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>.","ista":"Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 450, 81–95.","ieee":"A. Salamatina <i>et al.</i>, “Differential loss of spinal interneurons in a mouse model of ALS,” <i>Neuroscience</i>, vol. 450. Elsevier, pp. 81–95, 2020.","short":"A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner, T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95."},"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2020-12-03T11:45:26Z"},{"quality_controlled":"1","date_created":"2020-12-06T23:01:14Z","abstract":[{"lang":"eng","text":"Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression."}],"intvolume":"        11","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2020","date_published":"2020-11-10T00:00:00Z","pmid":1,"ddc":["580"],"publisher":"Frontiers","day":"10","_id":"8924","title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","article_type":"original","volume":11,"publication":"Frontiers in Plant Science","status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.3389/fpls.2020.586870","author":[{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"full_name":"Dadarou, Despoina","last_name":"Dadarou","first_name":"Despoina"},{"first_name":"Nestoras","last_name":"Kargios","full_name":"Kargios, Nestoras"},{"first_name":"Areti","last_name":"Mallioura","full_name":"Mallioura, Areti"},{"full_name":"Fernandez-Fuentes, Narcis","last_name":"Fernandez-Fuentes","first_name":"Narcis"},{"last_name":"Cavallari","full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"last_name":"Doonan","full_name":"Doonan, John H.","first_name":"John H."}],"article_processing_charge":"No","department":[{"_id":"EvBe"}],"date_updated":"2025-06-12T07:02:22Z","language":[{"iso":"eng"}],"citation":{"apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., &#38; Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>","chicago":"Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>.","ama":"Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>","ieee":"C. Nibau <i>et al.</i>, “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","ista":"Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870.","short":"C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).","mla":"Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>, vol. 11, 586870, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>."},"article_number":"586870","has_accepted_license":"1","file_date_updated":"2020-12-09T09:14:19Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","publication_identifier":{"eissn":["1664-462X"]},"file":[{"relation":"main_file","checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","file_size":1833244,"date_updated":"2020-12-09T09:14:19Z","file_name":"2020_Frontiers_Nibau.pdf","creator":"dernst","content_type":"application/pdf","file_id":"8929","access_level":"open_access","success":1,"date_created":"2020-12-09T09:14:19Z"}],"acknowledgement":"CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna.","external_id":{"pmid":["33240303"],"isi":["000591637000001"]}},{"publisher":"Institute of Science and Technology Austria","corr_author":"1","file_date_updated":"2020-12-09T15:00:19Z","day":"10","_id":"8930","contributor":[{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Gašper"},{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","contributor_type":"supervisor"}],"citation":{"ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","short":"B. Kavcic, (2020).","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","mla":"Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>."},"ddc":["570"],"has_accepted_license":"1","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8997"}]},"file":[{"file_id":"8932","success":1,"access_level":"open_access","date_created":"2020-12-09T15:00:19Z","creator":"bkavcic","content_type":"application/zip","date_updated":"2020-12-09T15:00:19Z","file_name":"PLoSCompBiol2020_datarep.zip","relation":"main_file","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_size":315494370}],"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","oa_version":"Published Version","date_created":"2020-12-09T15:04:02Z","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"doi":"10.15479/AT:ISTA:8930","status":"public","year":"2020","department":[{"_id":"GaTk"}],"date_published":"2020-12-10T00:00:00Z","date_updated":"2025-06-12T06:33:18Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","full_name":"Kavcic, Bor","last_name":"Kavcic"}],"article_processing_charge":"No"},{"publisher":"American Physical Society","arxiv":1,"day":"01","_id":"8944","publication":"Physical Review B","article_type":"original","title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","volume":102,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2."}],"intvolume":"       102","date_created":"2020-12-13T23:01:21Z","main_file_link":[{"url":"https://arxiv.org/abs/2011.04329","open_access":"1"}],"year":"2020","issue":"18","date_published":"2020-11-01T00:00:00Z","oa":1,"scopus_import":"1","language":[{"iso":"eng"}],"citation":{"ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. 2020;102(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>","chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>.","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>.","ieee":"M. Zemlicka <i>et al.</i>, “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” <i>Physical Review B</i>, vol. 102, no. 18. American Physical Society, 2020.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508."},"article_number":"180508","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","external_id":{"isi":["000591509900003"],"arxiv":["2011.04329"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","type":"journal_article","oa_version":"Preprint","publication_status":"published","doi":"10.1103/PhysRevB.102.180508","status":"public","isi":1,"department":[{"_id":"JoFi"}],"date_updated":"2025-07-10T12:01:27Z","article_processing_charge":"No","author":[{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kopčík, M.","last_name":"Kopčík","first_name":"M."},{"full_name":"Szabó, P.","last_name":"Szabó","first_name":"P."},{"last_name":"Samuely","full_name":"Samuely, T.","first_name":"T."},{"first_name":"J.","last_name":"Kačmarčík","full_name":"Kačmarčík, J."},{"last_name":"Neilinger","full_name":"Neilinger, P.","first_name":"P."},{"first_name":"M.","full_name":"Grajcar, M.","last_name":"Grajcar"},{"full_name":"Samuely, P.","last_name":"Samuely","first_name":"P."}]},{"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.3390/cells9122662","status":"public","isi":1,"department":[{"_id":"SiHi"}],"date_updated":"2025-06-12T07:02:43Z","article_processing_charge":"No","author":[{"first_name":"Xuying","last_name":"Zhang","full_name":"Zhang, Xuying"},{"first_name":"Christine V.","last_name":"Mennicke","full_name":"Mennicke, Christine V."},{"first_name":"Guanxi","last_name":"Xiao","full_name":"Xiao, Guanxi"},{"full_name":"Beattie, Robert J","last_name":"Beattie","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753"},{"last_name":"Haider","full_name":"Haider, Mansoor","first_name":"Mansoor"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"H. Troy","full_name":"Ghashghaei, H. Troy","last_name":"Ghashghaei"}],"project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02416"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"}],"file_date_updated":"2020-12-14T08:09:43Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","ieee":"X. Zhang <i>et al.</i>, “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” <i>Cells</i>, vol. 9, no. 12. MDPI, 2020.","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>, vol. 9, no. 12, 2662, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>.","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., &#38; Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>","chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>.","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. 2020;9(12). doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>"},"has_accepted_license":"1","article_number":"2662","publication_identifier":{"issn":["2073-4409"]},"acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"8950","access_level":"open_access","success":1,"date_created":"2020-12-14T08:09:43Z","relation":"main_file","checksum":"5095cbdc728c9a510c5761cf60a8861c","file_size":3504525,"file_name":"2020_Cells_Zhang.pdf","date_updated":"2020-12-14T08:09:43Z"}],"external_id":{"pmid":["33322301"],"isi":["000601787300001"]},"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","abstract":[{"lang":"eng","text":"<jats:p>Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.</jats:p>"}],"date_created":"2020-12-14T08:04:03Z","intvolume":"         9","year":"2020","issue":"12","date_published":"2020-12-11T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publisher":"MDPI","day":"11","_id":"8949","pmid":1,"ddc":["570"],"publication":"Cells","ec_funded":1,"title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","article_type":"original","volume":9},{"type":"research_data","oa_version":"Published Version","date_created":"2020-12-20T10:00:26Z","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"doi":"10.15479/AT:ISTA:8951","status":"public","year":"2020","department":[{"_id":"CaGu"}],"date_published":"2020-12-21T00:00:00Z","date_updated":"2025-06-12T06:36:16Z","oa":1,"author":[{"first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","corr_author":"1","day":"21","file_date_updated":"2020-12-20T22:01:44Z","_id":"8951","contributor":[{"first_name":"Anna A","contributor_type":"project_member","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron"},{"last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","contributor_type":"project_member"},{"last_name":"Caruso Carter","first_name":"Caroline","contributor_type":"project_member"},{"last_name":"Sonnleitner","first_name":"Elisabeth","contributor_type":"project_member"},{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Bor","last_name":"Kavcic"},{"first_name":"Tiago","contributor_type":"project_member","last_name":"Paixão"},{"last_name":"Guet","first_name":"Calin C","contributor_type":"project_manager","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"ddc":["570"],"citation":{"mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","short":"A.A. Nagy-Staron, (2020).","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>"},"has_accepted_license":"1","file":[{"file_size":523,"checksum":"f57862aeee1690c7effd2b1117d40ed1","relation":"main_file","file_name":"readme.txt","date_updated":"2020-12-20T09:52:52Z","creator":"bkavcic","content_type":"text/plain","date_created":"2020-12-20T09:52:52Z","success":1,"access_level":"open_access","file_id":"8952"},{"checksum":"f2c6d5232ec6d551b6993991e8689e9f","relation":"main_file","file_size":379228,"file_name":"GRNs Research depository.gb","date_updated":"2020-12-20T22:01:44Z","creator":"bkavcic","content_type":"application/octet-stream","file_id":"8954","date_created":"2020-12-20T22:01:44Z","access_level":"open_access","success":1}],"keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"related_material":{"record":[{"id":"9283","relation":"used_in_publication","status":"public"}]},"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2020-12-20T23:01:18Z","abstract":[{"lang":"eng","text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies."}],"intvolume":"        11","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-11-26T00:00:00Z","year":"2020","ddc":["570"],"pmid":1,"_id":"8955","day":"26","publisher":"Frontiers","volume":11,"title":"Network physiology of cortico–muscular interactions","article_type":"original","ec_funded":1,"publication":"Frontiers in Physiology","isi":1,"status":"public","doi":"10.3389/fphys.2020.558070","publication_status":"published","oa_version":"Published Version","type":"journal_article","author":[{"last_name":"Rizzo","full_name":"Rizzo, Rossella","first_name":"Rossella"},{"last_name":"Zhang","full_name":"Zhang, Xiyun","first_name":"Xiyun"},{"first_name":"Jilin W.J.L.","full_name":"Wang, Jilin W.J.L.","last_name":"Wang"},{"orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","last_name":"Lombardi"},{"last_name":"Ivanov","full_name":"Ivanov, Plamen Ch","first_name":"Plamen Ch"}],"article_processing_charge":"No","date_updated":"2025-04-14T07:43:50Z","department":[{"_id":"GaTk"}],"article_number":"558070","has_accepted_license":"1","citation":{"ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” <i>Frontiers in Physiology</i>, vol. 11. Frontiers, 2020.","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>, vol. 11, 558070, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., &#38; Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"file_date_updated":"2020-12-21T10:37:50Z","month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000596849400001"],"pmid":["33324233"]},"acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2020-12-21T10:37:50Z","success":1,"access_level":"open_access","file_id":"8961","file_size":13380030,"checksum":"ef9515b28c5619b7126c0f347958bcb3","relation":"main_file","file_name":"2020_Frontiers_Rizzo.pdf","date_updated":"2020-12-21T10:37:50Z"}],"publication_identifier":{"eissn":["1664042X"]}},{"_id":"8957","publisher":"Elsevier","day":"21","pmid":1,"publication":"Developmental Cell","volume":55,"article_type":"original","title":"Apical relaxation during mitotic rounding promotes tension-oriented cell division","abstract":[{"text":"Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation.","lang":"eng"}],"intvolume":"        55","date_created":"2020-12-20T23:01:19Z","quality_controlled":"1","date_published":"2020-12-21T00:00:00Z","year":"2020","issue":"6","scopus_import":"1","corr_author":"1","citation":{"mla":"Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” <i>Developmental Cell</i>, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">10.1016/j.devcel.2020.10.016</a>.","short":"B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706.","ieee":"B. G. Godard <i>et al.</i>, “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” <i>Developmental Cell</i>, vol. 55, no. 6. Elsevier, pp. 695–706, 2020.","ista":"Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706.","chicago":"Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” <i>Developmental Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">https://doi.org/10.1016/j.devcel.2020.10.016</a>.","apa":"Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., &#38; Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">https://doi.org/10.1016/j.devcel.2020.10.016</a>","ama":"Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. <i>Developmental Cell</i>. 2020;55(6):695-706. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">10.1016/j.devcel.2020.10.016</a>"},"language":[{"iso":"eng"}],"page":"695-706","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8).","related_material":{"link":[{"url":"https://ist.ac.at/en/news/relaxing-cell-divisions/","description":"News on IST Homepage","relation":"press_release"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"}],"external_id":{"pmid":["33207225"],"isi":["000600665700008"]},"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","publication_status":"published","doi":"10.1016/j.devcel.2020.10.016","type":"journal_article","oa_version":"None","isi":1,"status":"public","date_updated":"2025-07-10T12:01:28Z","department":[{"_id":"CaHe"}],"author":[{"full_name":"Godard, Benoit G","last_name":"Godard","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G"},{"first_name":"Rémi","last_name":"Dumollard","full_name":"Dumollard, Rémi"},{"full_name":"Munro, Edwin","last_name":"Munro","first_name":"Edwin"},{"last_name":"Chenevert","full_name":"Chenevert, Janet","first_name":"Janet"},{"full_name":"Hebras, Céline","last_name":"Hebras","first_name":"Céline"},{"first_name":"Alex","full_name":"Mcdougall, Alex","last_name":"Mcdougall"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No"},{"publication_identifier":{"issn":["2041-1723"]},"external_id":{"isi":["000603078000003"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"file":[{"file_size":3958727,"checksum":"55d43ea0061cc4027ba45e966e1db8cc","relation":"main_file","file_name":"2020_NatureComm_Faessler.pdf","date_updated":"2020-12-28T08:16:10Z","creator":"dernst","content_type":"application/pdf","date_created":"2020-12-28T08:16:10Z","access_level":"open_access","success":1,"file_id":"8975"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage","relation":"press_release"}]},"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","file_date_updated":"2020-12-28T08:16:10Z","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"M02495","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales"}],"corr_author":"1","scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","article_number":"6437","citation":{"mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>"},"department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"date_updated":"2025-04-15T07:52:12Z","article_processing_charge":"No","author":[{"first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","last_name":"Fäßler"},{"last_name":"Dimchev","full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3904-947X"},{"first_name":"William","full_name":"Wan, William","last_name":"Wan"},{"full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"oa_version":"Published Version","type":"journal_article","doi":"10.1038/s41467-020-20286-x","publication_status":"published","status":"public","isi":1,"publication":"Nature Communications","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"article_type":"original","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","volume":11,"day":"22","publisher":"Springer Nature","_id":"8971","ddc":["570"],"year":"2020","date_published":"2020-12-22T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","date_created":"2020-12-23T08:25:45Z","intvolume":"        11","abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}]},{"ddc":["510"],"_id":"8973","arxiv":1,"publisher":" Institute of Mathematical Statistics","day":"21","volume":25,"ec_funded":1,"article_type":"original","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","publication":"Electronic Journal of Probability","intvolume":"        25","date_created":"2020-12-27T23:01:17Z","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"quality_controlled":"1","oa":1,"date_published":"2020-10-21T00:00:00Z","year":"2020","citation":{"ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>. 2020;25. doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>","apa":"Redig, F., Saada, E., &#38; Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>.","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” <i>Electronic Journal of Probability</i>, vol. 25.  Institute of Mathematical Statistics, 2020.","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>, vol. 25, 138,  Institute of Mathematical Statistics, 2020, doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>."},"article_number":"138","has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2020-12-28T08:24:08Z","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","file":[{"relation":"main_file","checksum":"d75359b9814e78d57c0a481b7cde3751","file_size":696653,"file_name":"2020_ElectronJProbab_Redig.pdf","date_updated":"2020-12-28T08:24:08Z","creator":"dernst","content_type":"application/pdf","file_id":"8976","success":1,"access_level":"open_access","date_created":"2020-12-28T08:24:08Z"}],"external_id":{"isi":["000591737500001"],"arxiv":["1811.01366"]},"publication_identifier":{"eissn":["1083-6489"]},"isi":1,"status":"public","publication_status":"published","doi":"10.1214/20-EJP536","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Frank","full_name":"Redig, Frank","last_name":"Redig"},{"first_name":"Ellen","last_name":"Saada","full_name":"Saada, Ellen"},{"first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico","last_name":"Sau"}],"date_updated":"2025-04-14T07:43:50Z","department":[{"_id":"JaMa"}]},{"isi":1,"status":"public","doi":"10.1073/pnas.2006731117","publication_status":"published","oa_version":"Published Version","type":"journal_article","author":[{"full_name":"Grah, Rok","last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"article_processing_charge":"No","date_updated":"2025-05-14T10:57:50Z","department":[{"_id":"GaTk"}],"has_accepted_license":"1","citation":{"chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>.","apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(50):31614-31622. doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.","short":"R. Grah, B. Zoller, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 31614–31622.","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America. 117(50), 31614–31622."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-01-11T08:37:31Z","project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","external_id":{"pmid":["33268497"],"isi":["000600608300015"]},"page":"31614-31622","acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/","description":"News on IST Homepage","relation":"press_release"}]},"file":[{"relation":"main_file","checksum":"69039cd402a571983aa6cb4815ffa863","file_size":1199247,"file_name":"2020_PNAS_Grah.pdf","date_updated":"2021-01-11T08:37:31Z","creator":"dernst","content_type":"application/pdf","file_id":"9004","access_level":"open_access","success":1,"date_created":"2021-01-11T08:37:31Z"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_created":"2021-01-10T23:01:17Z","abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.","lang":"eng"}],"intvolume":"       117","quality_controlled":"1","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"date_published":"2020-12-15T00:00:00Z","issue":"50","year":"2020","ddc":["570"],"pmid":1,"_id":"9000","day":"15","publisher":"National Academy of Sciences","volume":117,"title":"Nonequilibrium models of optimal enhancer function","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"abstract":[{"text":"Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals.","lang":"eng"}],"date_created":"2021-01-17T23:01:11Z","intvolume":"        95","main_file_link":[{"url":"https://arxiv.org/abs/1906.08463","open_access":"1"}],"quality_controlled":"1","date_published":"2020-12-07T00:00:00Z","year":"2020","issue":"4","oa":1,"_id":"9007","publisher":"European Mathematical Society","arxiv":1,"day":"07","publication":"Commentarii Mathematici Helvetici","volume":95,"article_type":"original","title":"Free rational points on smooth hypersurfaces","publication_status":"published","doi":"10.4171/CMH/499","type":"journal_article","oa_version":"Preprint","isi":1,"status":"public","date_updated":"2025-07-10T12:01:31Z","department":[{"_id":"TiBr"}],"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"},{"last_name":"Sawin","full_name":"Sawin, Will","first_name":"Will"}],"article_processing_charge":"No","scopus_import":"1","citation":{"mla":"Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4, European Mathematical Society, 2020, pp. 635–59, doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>.","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","ieee":"T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4. European Mathematical Society, pp. 635–659, 2020.","ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659.","ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. 2020;95(4):635-659. doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society, 2020. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>.","apa":"Browning, T. D., &#38; Sawin, W. (2020). Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>"},"language":[{"iso":"eng"}],"page":"635-659","external_id":{"arxiv":["1906.08463"],"isi":["000596833300001"]},"publication_identifier":{"eissn":["1420-8946"],"issn":["0010-2571"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12"}]