[{"acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"day":"13","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","year":"2024","date_published":"2024-02-13T00:00:00Z","doi":"10.1073/pnas.2220075121","date_created":"2024-02-18T23:01:00Z","article_number":"e2220075121","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121","mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121."},"title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","author":[{"last_name":"Curk","orcid":"0000-0001-6160-9766","full_name":"Curk, Samo","first_name":"Samo","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"}],"article_processing_charge":"Yes","external_id":{"pmid":["38335256"]},"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor."}],"month":"02","intvolume":" 121","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"15026","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","file_size":7699487,"date_updated":"2024-02-26T08:20:00Z","creator":"dernst","file_name":"2024_PNAS_Curk.pdf","date_created":"2024-02-26T08:20:00Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","issue":"7","volume":121,"related_material":{"record":[{"relation":"research_data","id":"15027","status":"public"}]},"ec_funded":1,"_id":"15001","status":"public","article_type":"original","type":"journal_article","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"},"ddc":["570"],"date_updated":"2024-02-26T08:45:56Z","department":[{"_id":"AnSa"}],"file_date_updated":"2024-02-26T08:20:00Z"},{"article_number":"050401","article_processing_charge":"No","external_id":{"arxiv":["2201.10220"]},"author":[{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","first_name":"Elena","full_name":"Petrova, Elena","last_name":"Petrova"},{"first_name":"Egor S.","full_name":"Tiunov, Egor S.","last_name":"Tiunov"},{"full_name":"Bañuls, Mari Carmen","last_name":"Bañuls","first_name":"Mari Carmen"},{"first_name":"Aleksey K.","last_name":"Fedorov","full_name":"Fedorov, Aleksey K."}],"title":"Fractal states of the Schwinger model","citation":{"ista":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. 2024. Fractal states of the Schwinger model. Physical Review Letters. 132(5), 050401.","chicago":"Petrova, Elena, Egor S. Tiunov, Mari Carmen Bañuls, and Aleksey K. Fedorov. “Fractal States of the Schwinger Model.” Physical Review Letters. American Physical Society, 2024. https://doi.org/10.1103/PhysRevLett.132.050401.","short":"E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters 132 (2024).","ieee":"E. Petrova, E. S. Tiunov, M. C. Bañuls, and A. K. Fedorov, “Fractal states of the Schwinger model,” Physical Review Letters, vol. 132, no. 5. American Physical Society, 2024.","ama":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. Fractal states of the Schwinger model. Physical Review Letters. 2024;132(5). doi:10.1103/PhysRevLett.132.050401","apa":"Petrova, E., Tiunov, E. S., Bañuls, M. C., & Fedorov, A. K. (2024). Fractal states of the Schwinger model. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.132.050401","mla":"Petrova, Elena, et al. “Fractal States of the Schwinger Model.” Physical Review Letters, vol. 132, no. 5, 050401, American Physical Society, 2024, doi:10.1103/PhysRevLett.132.050401."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We thank A. Bargov, I. Khaymovich, and V. Tiunova for fruitful discussions and for useful comments. M. C. B. thanks S. Kühn for discussions about the phase structure of the model. A. K. F. thanks V. Gritsev and A. Garkun for insightful comments. E. V. P., E. S. T., and A. K. F. are\r\nsupported by the RSF Grant No. 20-42-05002 (studying the fractal Ansatz) and the Roadmap on Quantum Computing (Contract No. 868-1.3-15/15-2021, October 5, 2021; calculating on GS energies). A. K. F. thanks the Priority 2030 program at the NIST “MISIS” under the project No. K1-2022-027. M. C. B. was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868.","date_created":"2024-02-18T23:01:00Z","doi":"10.1103/PhysRevLett.132.050401","date_published":"2024-01-30T00:00:00Z","year":"2024","publication":"Physical Review Letters","day":"30","type":"journal_article","article_type":"original","status":"public","_id":"15002","department":[{"_id":"MaSe"}],"date_updated":"2024-02-26T08:03:31Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.10220","open_access":"1"}],"scopus_import":"1","intvolume":" 132","month":"01","abstract":[{"lang":"eng","text":"The lattice Schwinger model, the discrete version of QED in \r\n1\r\n+\r\n1\r\n dimensions, is a well-studied test bench for lattice gauge theories. Here, we study the fractal properties of this model. We reveal the self-similarity of the ground state, which allows us to develop a recurrent procedure for finding the ground-state wave functions and predicting ground-state energies. We present the results of recurrently calculating ground-state wave functions using the fractal Ansatz and automized software package for fractal image processing. In certain parameter regimes, just a few terms are enough for our recurrent procedure to predict ground-state energies close to the exact ones for several hundreds of sites. Our findings pave the way to understanding the complexity of calculating many-body wave functions in terms of their fractal properties as well as finding new links between condensed matter and high-energy lattice models."}],"oa_version":"Preprint","volume":132,"issue":"5","publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"language":[{"iso":"eng"}]},{"author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","last_name":"Agresti","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"external_id":{"arxiv":["2206.00230"]},"article_processing_charge":"No","title":"The critical variational setting for stochastic evolution equations","citation":{"mla":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields, Springer Nature, 2024, doi:10.1007/s00440-023-01249-x.","short":"A. Agresti, M. Veraar, Probability Theory and Related Fields (2024).","ieee":"A. Agresti and M. Veraar, “The critical variational setting for stochastic evolution equations,” Probability Theory and Related Fields. Springer Nature, 2024.","apa":"Agresti, A., & Veraar, M. (2024). The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01249-x","ama":"Agresti A, Veraar M. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. 2024. doi:10.1007/s00440-023-01249-x","chicago":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields. Springer Nature, 2024. https://doi.org/10.1007/s00440-023-01249-x.","ista":"Agresti A, Veraar M. 2024. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"doi":"10.1007/s00440-023-01249-x","date_published":"2024-02-02T00:00:00Z","date_created":"2023-02-02T10:45:15Z","year":"2024","day":"02","publication":"Probability Theory and Related Fields","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819) . The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","department":[{"_id":"JuFi"}],"date_updated":"2024-02-26T09:39:07Z","article_type":"original","type":"journal_article","status":"public","_id":"12485","ec_funded":1,"publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s00440-023-01249-x","open_access":"1"}],"month":"02","abstract":[{"lang":"eng","text":"In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation."}],"oa_version":"Preprint"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. \r\nIn this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth."}],"month":"01","intvolume":" 287","scopus_import":"1","alternative_title":["LIPIcs"],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"b89716aae6a5599f187897e39de1e53a","file_id":"15030","file_size":1054754,"date_updated":"2024-02-26T10:10:48Z","creator":"dernst","file_name":"2024_LIPICs_Goranci.pdf","date_created":"2024-02-26T10:10:48Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773096"]},"publication_status":"published","volume":287,"ec_funded":1,"_id":"15008","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2024-01-30","location":"Berkeley, CA, United States","end_date":"2024-02-02","name":"ITCS: Innovations in Theoretical Computer Science Conference"},"ddc":["000"],"date_updated":"2024-02-26T10:12:19Z","file_date_updated":"2024-02-26T10:10:48Z","department":[{"_id":"MoHe"}],"acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets), 2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398 and a Sloan Research Fellowship.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"day":"24","publication":"15th Innovations in Theoretical Computer Science Conference","has_accepted_license":"1","year":"2024","doi":"10.4230/LIPIcs.ITCS.2024.55","date_published":"2024-01-24T00:00:00Z","date_created":"2024-02-18T23:01:02Z","article_number":"55","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures"},{"grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Goranci, Gramoz, Monika H Henzinger, Harald Räcke, Sushant Sachdeva, and A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” In 15th Innovations in Theoretical Computer Science Conference, Vol. 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.55.","ista":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science Conference, LIPIcs, vol. 287, 55.","mla":"Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” 15th Innovations in Theoretical Computer Science Conference, vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ITCS.2024.55.","ama":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. Electrical flows for polylogarithmic competitive oblivious routing. In: 15th Innovations in Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ITCS.2024.55","apa":"Goranci, G., Henzinger, M. H., Räcke, H., Sachdeva, S., & Sricharan, A. R. (2024). Electrical flows for polylogarithmic competitive oblivious routing. In 15th Innovations in Theoretical Computer Science Conference (Vol. 287). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.55","ieee":"G. Goranci, M. H. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical flows for polylogarithmic competitive oblivious routing,” in 15th Innovations in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287.","short":"G. Goranci, M.H. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024."},"title":"Electrical flows for polylogarithmic competitive oblivious routing","author":[{"full_name":"Goranci, Gramoz","last_name":"Goranci","first_name":"Gramoz"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"first_name":"Harald","full_name":"Räcke, Harald","last_name":"Räcke"},{"first_name":"Sushant","full_name":"Sachdeva, Sushant","last_name":"Sachdeva"},{"first_name":"A. R.","full_name":"Sricharan, A. R.","last_name":"Sricharan"}],"external_id":{"arxiv":["2303.02491"]},"article_processing_charge":"No"},{"volume":286,"language":[{"iso":"eng"}],"file":[{"file_name":"2024_LIPICs_Alpos.pdf","date_created":"2024-02-26T10:16:57Z","file_size":1505994,"date_updated":"2024-02-26T10:16:57Z","creator":"dernst","success":1,"checksum":"2993e810a45e8c8056106834b07aea92","file_id":"15031","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773089"]},"intvolume":" 286","month":"01","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"Traditional blockchains grant the miner of a block full control not only over which transactions but also their order. This constitutes a major flaw discovered with the introduction of decentralized finance and allows miners to perform MEV attacks. In this paper, we address the issue of sandwich attacks by providing a construction that takes as input a blockchain protocol and outputs a new blockchain protocol with the same security but in which sandwich attacks are not profitable. Furthermore, our protocol is fully decentralized with no trusted third parties or heavy cryptography primitives and carries a linear increase in latency and minimum computation overhead.","lang":"eng"}],"department":[{"_id":"KrPi"}],"file_date_updated":"2024-02-26T10:16:57Z","ddc":["000"],"date_updated":"2024-02-26T10:18:18Z","status":"public","conference":{"name":"OPODIS: Conference on Principles of Distributed Systems","end_date":"2023-12-08","location":"Tokyo, Japan","start_date":"2023-12-06"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"15007","date_created":"2024-02-18T23:01:02Z","doi":"10.4230/LIPIcs.OPODIS.2023.12","date_published":"2024-01-18T00:00:00Z","publication":"27th International Conference on Principles of Distributed Systems","day":"18","year":"2024","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"We would like to thank Krzysztof Pietrzak and Jovana Mićić for useful discussions. This work has been funded by the Swiss National Science Foundation (SNSF) under grant agreement Nr. 200021_188443 (Advanced Consensus Protocols).\r\n","title":"Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks","article_processing_charge":"No","external_id":{"arxiv":["2307.02954"]},"author":[{"first_name":"Orestis","last_name":"Alpos","full_name":"Alpos, Orestis"},{"first_name":"Ignacio","last_name":"Amores-Sesar","full_name":"Amores-Sesar, Ignacio"},{"first_name":"Christian","last_name":"Cachin","full_name":"Cachin, Christian"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Alpos, Orestis, et al. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” 27th International Conference on Principles of Distributed Systems, vol. 286, 12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.12.","ama":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.12","apa":"Alpos, O., Amores-Sesar, I., Cachin, C., & Yeo, M. X. (2024). Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12","ieee":"O. Alpos, I. Amores-Sesar, C. Cachin, and M. X. Yeo, “Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","short":"O. Alpos, I. Amores-Sesar, C. Cachin, M.X. Yeo, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Alpos, Orestis, Ignacio Amores-Sesar, Christian Cachin, and Michelle X Yeo. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12.","ista":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. 2024. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 12."},"article_number":"12"},{"title":"Experimental evaluation of fully dynamic k-means via coresets","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","first_name":"David","last_name":"Saulpic","full_name":"Saulpic, David"},{"full_name":"Sidl, Leonhard","last_name":"Sidl","id":"8b563fd0-b441-11ee-9101-a3891c61efa6","first_name":"Leonhard"}],"external_id":{"arxiv":["2310.18034"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Henzinger, Monika H, David Saulpic, and Leonhard Sidl. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, 220–33. Society for Industrial & Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977929.17.","ista":"Henzinger MH, Saulpic D, Sidl L. 2024. Experimental evaluation of fully dynamic k-means via coresets. 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. ALENEX: Workshop on Algorithm Engineering and Experiments, 220–233.","mla":"Henzinger, Monika H., et al. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–33, doi:10.1137/1.9781611977929.17.","apa":"Henzinger, M. H., Saulpic, D., & Sidl, L. (2024). Experimental evaluation of fully dynamic k-means via coresets. In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments (pp. 220–233). Alexandria, VA, United States: Society for Industrial & Applied Mathematics. https://doi.org/10.1137/1.9781611977929.17","ama":"Henzinger MH, Saulpic D, Sidl L. Experimental evaluation of fully dynamic k-means via coresets. In: 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. Society for Industrial & Applied Mathematics; 2024:220-233. doi:10.1137/1.9781611977929.17","short":"M.H. Henzinger, D. Saulpic, L. Sidl, in:, 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–233.","ieee":"M. H. Henzinger, D. Saulpic, and L. Sidl, “Experimental evaluation of fully dynamic k-means via coresets,” in 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Alexandria, VA, United States, 2024, pp. 220–233."},"project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"date_published":"2024-01-04T00:00:00Z","doi":"10.1137/1.9781611977929.17","date_created":"2024-01-09T16:22:47Z","page":"220-233","day":"04","publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","year":"2024","quality_controlled":"1","publisher":"Society for Industrial & Applied Mathematics","oa":1,"acknowledgement":"This project has received funding from the Euro-pean Research Council (ERC) under the EuropeanUnion’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The De-sign of Modern Fully Dynamic Data Structures (Mo-DynStruct)” and the Austrian Science Fund (FWF)project Z 422-N, project “Static and Dynamic Hierar-chical Graph Decompositions”, I 5982-N, and project“Fast Algorithms for a Reactive Network Layer (Re-actNet)”, P 33775-N, with additional funding from thenetidee SCIENCE Stiftung, 2020–2024.D. Sauplic has received funding from the Euro-pean Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreementNo 101034413.","department":[{"_id":"MoHe"}],"date_updated":"2024-02-26T09:51:31Z","status":"public","type":"conference","conference":{"start_date":"2024-01-07","end_date":"2024-01-08","location":"Alexandria, VA, United States","name":"ALENEX: Workshop on Algorithm Engineering and Experiments"},"_id":"14769","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781611977929"]},"publication_status":"published","month":"01","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.18034"}],"oa_version":"Preprint","abstract":[{"text":"For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution.","lang":"eng"}]},{"_id":"15009","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2024-02-26T09:59:30Z","file_date_updated":"2024-02-26T09:54:59Z","department":[{"_id":"BeVi"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"intvolume":" 16","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"106a40f10443b2e7ba66749844ebbdf1","file_id":"15029","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-02-26T09:54:59Z","file_name":"2024_GBE_Bett.pdf","date_updated":"2024-02-26T09:54:59Z","file_size":5213306,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1759-6653"]},"related_material":{"record":[{"id":"14705","status":"public","relation":"research_data"}]},"volume":16,"issue":"1","article_number":"evae006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006.","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.","apa":"Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/evae006","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024."},"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","article_processing_charge":"Yes","external_id":{"pmid":["38245839"]},"author":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K","last_name":"Bett"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"}],"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","publication":"Genome Biology and Evolution","day":"20","year":"2024","has_accepted_license":"1","date_created":"2024-02-18T23:01:02Z","date_published":"2024-01-20T00:00:00Z","doi":"10.1093/gbe/evae006"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We thank Bretislav Friedrich, Marjan Mirahmadi, Artem Volosniev, and Burkhard Schmidt for insightful discussions. M.L. acknowledges support by the European Research Council (ERC) under Starting Grant No. 801770 (ANGULON).","date_created":"2024-02-18T23:01:01Z","date_published":"2024-02-01T00:00:00Z","doi":"10.1103/PhysRevA.109.023101","year":"2024","publication":"Physical Review A","day":"01","project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"article_number":"023101","external_id":{"arxiv":["2307.07256"]},"article_processing_charge":"No","author":[{"full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"title":"Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics","citation":{"chicago":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.023101.","ista":"Karle V, Lemeshko M. 2024. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 109(2), 023101.","mla":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A, vol. 109, no. 2, 023101, American Physical Society, 2024, doi:10.1103/PhysRevA.109.023101.","short":"V. Karle, M. Lemeshko, Physical Review A 109 (2024).","ieee":"V. Karle and M. Lemeshko, “Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics,” Physical Review A, vol. 109, no. 2. American Physical Society, 2024.","ama":"Karle V, Lemeshko M. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 2024;109(2). doi:10.1103/PhysRevA.109.023101","apa":"Karle, V., & Lemeshko, M. (2024). Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.023101"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.07256"}],"scopus_import":"1","intvolume":" 109","month":"02","abstract":[{"lang":"eng","text":"The impulsive limit (the “sudden approximation”) has been widely employed to describe the interaction between molecules and short, far-off-resonant laser pulses. This approximation assumes that the timescale of the laser-molecule interaction is significantly shorter than the internal rotational period of the molecule, resulting in the rotational motion being instantaneously “frozen” during the interaction. This simplified description of the laser-molecule interaction is incorporated in various theoretical models predicting rotational dynamics of molecules driven by short laser pulses. In this theoretical work, we develop an effective theory for ultrashort laser pulses by examining the full time-evolution operator and solving the time-dependent Schrödinger equation at the operator level. Our findings reveal a critical angular momentum, lcrit, at which the impulsive limit breaks down. In other words, the validity of the sudden approximation depends not only on the pulse duration but also on its intensity, since the latter determines how many angular momentum states are populated. We explore both ultrashort multicycle (Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce distinct effective potentials. We discuss the limitations of the impulsive limit and propose a method that rescales the effective matrix elements, enabling an improved and more accurate description of laser-molecule interactions."}],"oa_version":"Preprint","ec_funded":1,"volume":109,"issue":"2","publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"15004","department":[{"_id":"MiLe"}],"date_updated":"2024-02-26T09:45:20Z"},{"date_updated":"2024-02-26T09:59:29Z","citation":{"chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705.","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","short":"M.N. Elkrewi, (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"}],"article_processing_charge":"No","file_date_updated":"2023-12-22T14:14:06Z","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"_id":"14705","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"has_accepted_license":"1","year":"2024","day":"02","file":[{"file_id":"14707","checksum":"bdaf1392867786634ec5466d528c36ca","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/plain","date_created":"2023-12-22T13:54:21Z","file_name":"readme.txt.txt","creator":"melkrewi","date_updated":"2023-12-22T13:54:21Z","file_size":847},{"success":1,"checksum":"973e1cbdab923a71709782177980829f","file_id":"14708","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"data_artemia_franciscana_genome.zip","date_created":"2023-12-22T14:14:06Z","creator":"melkrewi","file_size":343632753,"date_updated":"2023-12-22T14:14:06Z"}],"related_material":{"record":[{"relation":"used_in_publication","id":"15009","status":"public"}]},"date_published":"2024-01-02T00:00:00Z","doi":"10.15479/AT:ISTA:14705","date_created":"2023-12-22T13:40:48Z","contributor":[{"last_name":"Bett","contributor_type":"researcher","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"},{"last_name":"Macon","first_name":"Ariana","contributor_type":"project_member","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"},{"contributor_type":"researcher","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"}],"abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"01"},{"main_file_link":[{"url":"https://doi.org/10.1016/j.mssp.2024.108231","open_access":"1"}],"intvolume":" 174","month":"02","abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"oa_version":"Published Version","volume":174,"issue":"5","publication_status":"epub_ahead","publication_identifier":{"issn":["1369-8001"]},"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"status":"public","_id":"15018","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"date_updated":"2024-02-26T10:36:35Z","ddc":["530"],"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","date_created":"2024-02-22T14:10:40Z","doi":"10.1016/j.mssp.2024.108231","date_published":"2024-02-20T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Materials Science in Semiconductor Processing","day":"20","project":[{"name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"}],"article_number":"108231","article_processing_charge":"No","author":[{"last_name":"Shimura","full_name":"Shimura, Yosuke","first_name":"Yosuke"},{"last_name":"Godfrin","full_name":"Godfrin, Clement","first_name":"Clement"},{"last_name":"Hikavyy","full_name":"Hikavyy, Andriy","first_name":"Andriy"},{"first_name":"Roy","full_name":"Li, Roy","last_name":"Li"},{"last_name":"Aguilera Servin","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"},{"last_name":"Favia","full_name":"Favia, Paola","first_name":"Paola"},{"last_name":"Han","full_name":"Han, Han","first_name":"Han"},{"first_name":"Danny","full_name":"Wan, Danny","last_name":"Wan"},{"first_name":"Kristiaan","full_name":"de Greve, Kristiaan","last_name":"de Greve"},{"last_name":"Loo","full_name":"Loo, Roger","first_name":"Roger"}],"title":"Compressively strained epitaxial Ge layers for quantum computing applications","citation":{"ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231.","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. Elsevier. https://doi.org/10.1016/j.mssp.2024.108231","ieee":"Y. Shimura et al., “Compressively strained epitaxial Ge layers for quantum computing applications,” Materials Science in Semiconductor Processing, vol. 174, no. 5. Elsevier, 2024.","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing, vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 234","month":"01","main_file_link":[{"url":"https://proceedings.mlr.press/v234/kurtic24a","open_access":"1"}],"scopus_import":"1","alternative_title":["PMLR"],"oa_version":"Preprint","abstract":[{"text":"Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach.","lang":"eng"}],"volume":234,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2640-3498"]},"status":"public","conference":{"start_date":"2024-01-03","end_date":"2024-01-06","location":"Hongkong, China","name":"CPAL: Conference on Parsimony and Learning"},"type":"conference","_id":"15011","department":[{"_id":"DaAl"}],"date_updated":"2024-02-26T10:30:52Z","oa":1,"quality_controlled":"1","publisher":"ML Research Press","date_created":"2024-02-18T23:01:03Z","date_published":"2024-01-08T00:00:00Z","page":"542-553","publication":"Proceedings of Machine Learning Research","day":"08","year":"2024","title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","external_id":{"arxiv":["2312.13547"]},"article_processing_charge":"No","author":[{"full_name":"Kurtic, Eldar","last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"first_name":"Torsten","full_name":"Hoefler, Torsten","last_name":"Hoefler"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” In Proceedings of Machine Learning Research, 234:542–53. ML Research Press, 2024.","ista":"Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234, 542–553.","mla":"Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” Proceedings of Machine Learning Research, vol. 234, ML Research Press, 2024, pp. 542–53.","ama":"Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In: Proceedings of Machine Learning Research. Vol 234. ML Research Press; 2024:542-553.","apa":"Kurtic, E., Hoefler, T., & Alistarh, D.-A. (2024). How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In Proceedings of Machine Learning Research (Vol. 234, pp. 542–553). Hongkong, China: ML Research Press.","ieee":"E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in Proceedings of Machine Learning Research, Hongkong, China, 2024, vol. 234, pp. 542–553.","short":"E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning Research, ML Research Press, 2024, pp. 542–553."}},{"publication":"Journal of Chemical Physics","day":"14","year":"2024","has_accepted_license":"1","date_created":"2024-02-25T23:00:55Z","date_published":"2024-02-14T00:00:00Z","doi":"10.1063/5.0188215","acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215.","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215."},"title":"Correlation-induced viscous dissipation in concentrated electrolytes","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2311.11784"],"pmid":["38349632"]},"author":[{"last_name":"Robin","full_name":"Robin, Paul","orcid":"0000-0002-5728-9189","first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d"}],"article_number":"064503","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"language":[{"iso":"eng"}],"file":[{"checksum":"0a5e0ae70849bce674466fc054390ec0","file_id":"15034","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-02-27T08:12:52Z","file_name":"2024_JourChemicalPhysics_Robin.pdf","creator":"dernst","date_updated":"2024-02-27T08:12:52Z","file_size":5452738}],"publication_status":"published","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"ec_funded":1,"volume":160,"issue":"6","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions.","lang":"eng"}],"intvolume":" 160","month":"02","scopus_import":"1","ddc":["540"],"date_updated":"2024-02-27T08:16:06Z","file_date_updated":"2024-02-27T08:12:52Z","department":[{"_id":"EdHa"}],"_id":"15024","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"},{"department":[{"_id":"LaEr"}],"date_updated":"2024-02-27T08:29:05Z","status":"public","type":"journal_article","article_type":"original","_id":"15025","ec_funded":1,"issue":"1B","volume":34,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1050-5164"]},"intvolume":" 34","month":"02","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.12206","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble."}],"title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","article_processing_charge":"No","external_id":{"arxiv":["2208.12206"]},"author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"id":"b0cc634c-d549-11ee-96c8-87338c7ad808","first_name":"Benjamin","orcid":"0000-0003-2625-495X","full_name":"McKenna, Benjamin","last_name":"McKenna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Erdös, L., & McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AAP2000","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 2024;34(1B):1623-1662. doi:10.1214/23-AAP2000","short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” Annals of Applied Probability, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:10.1214/23-AAP2000.","ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.","chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/23-AAP2000."},"project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"date_created":"2024-02-25T23:00:56Z","date_published":"2024-02-01T00:00:00Z","doi":"10.1214/23-AAP2000","page":"1623-1662","publication":"Annals of Applied Probability","day":"01","year":"2024","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation."},{"_id":"15033","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","date_updated":"2024-02-28T12:29:43Z","ddc":["580"],"department":[{"_id":"JiFr"}],"abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68993","open_access":"1"}],"intvolume":" 13","month":"02","publication_status":"epub_ahead","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":13,"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"citation":{"ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993","apa":"Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68993","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife Sciences Publications, 2024.","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.68993.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.68993."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","full_name":"Matijevic, Ivana","last_name":"Matijevic"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","year":"2024","has_accepted_license":"1","publication":"eLife","day":"21","date_created":"2024-02-27T07:10:11Z","date_published":"2024-02-21T00:00:00Z","doi":"10.7554/elife.68993"},{"_id":"14479","type":"journal_article","article_type":"original","status":"public","date_updated":"2024-03-04T07:14:41Z","department":[{"_id":"SyCr"}],"abstract":[{"text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.","lang":"eng"}],"pmid":1,"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.26.564092"}],"month":"02","intvolume":" 34","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":34,"citation":{"apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6. doi:10.1016/j.cub.2024.01.017","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ieee":"E. Csata et al., “Fungal infection alters collective nutritional intake of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:10.1016/j.cub.2024.01.017.","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Eniko","last_name":"Csata","full_name":"Csata, Eniko"},{"first_name":"Alfonso","last_name":"Perez-Escudero","full_name":"Perez-Escudero, Alfonso"},{"first_name":"Emmanuel","full_name":"Laury, Emmanuel","last_name":"Laury"},{"full_name":"Leitner, Hanna","last_name":"Leitner","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna"},{"first_name":"Gerard","last_name":"Latil","full_name":"Latil, Gerard"},{"first_name":"Juerge","full_name":"Heinze, Juerge","last_name":"Heinze"},{"first_name":"Stephen","full_name":"Simpson, Stephen","last_name":"Simpson"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dussutour","full_name":"Dussutour, Audrey","first_name":"Audrey"}],"article_processing_charge":"No","external_id":{"pmid":["38307022"]},"title":"Fungal infection alters collective nutritional intake of ant colonies","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","publisher":"Elsevier","quality_controlled":"1","oa":1,"year":"2024","day":"26","publication":"Current Biology","page":"902-909.e6","doi":"10.1016/j.cub.2024.01.017","date_published":"2024-02-26T00:00:00Z","date_created":"2023-10-31T13:30:20Z"},{"ddc":["530"],"date_updated":"2024-03-04T07:08:16Z","file_date_updated":"2024-03-04T07:07:10Z","department":[{"_id":"MiLe"}],"_id":"15045","keyword":["Atomic and Molecular Physics","and Optics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"file_size":436712,"date_updated":"2024-03-04T07:07:10Z","creator":"dernst","file_name":"2024_FewBodySys_Varshney.pdf","date_created":"2024-03-04T07:07:10Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"15049","checksum":"c4e08cc7bc756da69b1b36fda7bb92fb"}],"publication_status":"published","publication_identifier":{"issn":["1432-5411"]},"volume":65,"oa_version":"Published Version","abstract":[{"text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport.","lang":"eng"}],"intvolume":" 65","month":"02","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems. Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.","apa":"Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. Springer Nature. https://doi.org/10.1007/s00601-024-01880-x","ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer Nature, 2024.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024, doi:10.1007/s00601-024-01880-x."},"title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2401.08454"]},"author":[{"last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"article_number":"12","publication":"Few-Body Systems","day":"17","year":"2024","has_accepted_license":"1","date_created":"2024-03-01T11:39:33Z","doi":"10.1007/s00601-024-01880-x","date_published":"2024-02-17T00:00:00Z","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","date_published":"2024-02-13T00:00:00Z","doi":"10.1103/physrevresearch.6.013158","date_created":"2024-03-04T07:42:52Z","day":"13","publication":"Physical Review Research","has_accepted_license":"1","year":"2024","article_number":"013158","title":"Multipurpose platform for analog quantum simulation","author":[{"last_name":"Jin","full_name":"Jin, Shuwei","first_name":"Shuwei"},{"full_name":"Dai, Kunlun","last_name":"Dai","first_name":"Kunlun"},{"first_name":"Joris","full_name":"Verstraten, Joris","last_name":"Verstraten"},{"first_name":"Maxime","last_name":"Dixmerias","full_name":"Dixmerias, Maxime"},{"full_name":"Al Hyder, Ragheed","last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed"},{"first_name":"Christophe","full_name":"Salomon, Christophe","last_name":"Salomon"},{"full_name":"Peaudecerf, Bruno","last_name":"Peaudecerf","first_name":"Bruno"},{"first_name":"Tim","last_name":"de Jongh","full_name":"de Jongh, Tim"},{"last_name":"Yefsah","full_name":"Yefsah, Tarik","first_name":"Tarik"}],"external_id":{"arxiv":["2304.08433"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013158.","ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158","ieee":"S. Jin et al., “Multipurpose platform for analog quantum simulation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158."},"month":"02","intvolume":" 6","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator.","lang":"eng"}],"issue":"1","volume":6,"file":[{"creator":"dernst","date_updated":"2024-03-04T07:53:08Z","file_size":4025988,"date_created":"2024-03-04T07:53:08Z","file_name":"2024_PhysicalReviewResearch_Jin.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15054","checksum":"ba2ae3e3a011f8897d3803c9366a67e2","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","status":"public","keyword":["General Physics and Astronomy"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"15053","file_date_updated":"2024-03-04T07:53:08Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2024-03-04T07:55:29Z"},{"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","article_processing_charge":"Yes (via OA deal)","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","last_name":"Schauer"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. The Company of Biologists. https://doi.org/10.1242/dev.202316","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18."},"oa":1,"publisher":"The Company of Biologists","quality_controlled":"1","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","date_created":"2024-03-03T23:00:50Z","date_published":"2024-02-01T00:00:00Z","doi":"10.1242/dev.202316","page":"1-18","publication":"Development","day":"01","year":"2024","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"15048","department":[{"_id":"CaHe"},{"_id":"Bio"}],"file_date_updated":"2024-03-04T07:24:43Z","ddc":["570"],"date_updated":"2024-03-04T07:28:25Z","intvolume":" 151","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"volume":151,"related_material":{"record":[{"relation":"research_data","status":"public","id":"14926"}]},"issue":"4","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","creator":"dernst","file_size":14839986,"date_updated":"2024-03-04T07:24:43Z","file_name":"2024_Development_Schauer.pdf","date_created":"2024-03-04T07:24:43Z"}],"publication_status":"published","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]}},{"file":[{"checksum":"df7f358ae19a176cf710c0a802ce31b1","file_id":"14927","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","date_created":"2024-02-02T14:40:31Z","file_name":"README.md","creator":"rhauschild","date_updated":"2024-02-02T14:40:31Z","file_size":736},{"creator":"rhauschild","file_size":3543,"date_updated":"2024-02-02T14:40:31Z","file_name":"Supplementary_file_1.zip","date_created":"2024-02-02T14:40:31Z","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"checksum":"10194cc11619eccd8f4b24472e465b7f","file_id":"14928"}],"day":"02","year":"2024","has_accepted_license":"1","license":"https://opensource.org/licenses/MIT","date_created":"2024-02-02T14:42:26Z","doi":"10.15479/AT:ISTA:14926","date_published":"2024-02-02T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"15048","status":"public"}]},"month":"02","oa":1,"publisher":"ISTA","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-04T07:28:25Z","citation":{"chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” ISTA, 2024. https://doi.org/10.15479/AT:ISTA:14926.","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, ISTA, 10.15479/AT:ISTA:14926.","mla":"Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. ISTA, 2024, doi:10.15479/AT:ISTA:14926.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. ISTA. https://doi.org/10.15479/AT:ISTA:14926","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024.","short":"R. Hauschild, (2024)."},"file_date_updated":"2024-02-02T14:40:31Z","department":[{"_id":"Bio"}],"title":"Matlab script for analysis of clone dispersal","author":[{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"}],"_id":"14926","status":"public","tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"type":"software"},{"_id":"15047","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["550"],"date_updated":"2024-03-05T09:26:47Z","department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-04T07:34:00Z","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling.","lang":"eng"}],"intvolume":" 10","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"15051","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-03-04T07:34:00Z","file_name":"2024_ScienceAdv_Bao.pdf","creator":"dernst","date_updated":"2024-03-04T07:34:00Z","file_size":800926}],"publication_status":"published","publication_identifier":{"eissn":["2375-2548"]},"ec_funded":1,"volume":10,"issue":"8","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/"}]},"article_number":"eadj6801","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801.","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801.","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” Science Advances, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 2024;10(8). doi:10.1126/sciadv.adj6801","apa":"Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801"},"title":"Intensification of daily tropical precipitation extremes from more organized convection","article_processing_charge":"Yes","external_id":{"pmid":["38394192"]},"author":[{"full_name":"Bao, Jiawei","last_name":"Bao","first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"},{"full_name":"Stevens, Bjorn","last_name":"Stevens","first_name":"Bjorn"},{"last_name":"Kluft","full_name":"Kluft, Lukas","first_name":"Lukas"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller"}],"acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","publication":"Science Advances","day":"23","year":"2024","has_accepted_license":"1","date_created":"2024-03-03T23:00:50Z","doi":"10.1126/sciadv.adj6801","date_published":"2024-02-23T00:00:00Z"},{"project":[{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"title":"Multipotent progenitors instruct ontogeny of the superior colliculus","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["38096816"]},"author":[{"last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"first_name":"Thomas","last_name":"Krausgruber","full_name":"Krausgruber, Thomas"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"first_name":"Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","full_name":"Schrammel, Martin","last_name":"Schrammel"},{"full_name":"Özgen, Natalie Y","last_name":"Özgen","first_name":"Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090"},{"last_name":"Ivec","full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","first_name":"Alexis"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009","ieee":"G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","date_created":"2023-04-27T09:41:48Z","doi":"10.1016/j.neuron.2023.11.009","date_published":"2024-01-17T00:00:00Z","page":"230-246.e11","publication":"Neuron","day":"17","year":"2024","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"12875","department":[{"_id":"SiHi"},{"_id":"RySh"}],"file_date_updated":"2024-02-06T13:56:15Z","ddc":["570"],"date_updated":"2024-03-05T09:43:02Z","intvolume":" 112","month":"01","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny."}],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","description":"News on ISTA Website"}]},"volume":112,"issue":"2","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-02-06T13:56:15Z","file_size":5942467,"date_created":"2024-02-06T13:56:15Z","file_name":"2024_Neuron_Cheung.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14944","checksum":"32b3788f7085cf44a84108d8faaff3ce","success":1}],"publication_status":"published","publication_identifier":{"issn":["0896-6273"]}},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","doi":"10.1038/s41594-023-01201-6","date_published":"2024-02-05T00:00:00Z","date_created":"2024-02-12T09:59:45Z","has_accepted_license":"1","year":"2024","day":"05","publication":"Nature Structural & Molecular Biology","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"last_name":"Hansen","full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse"},{"first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","full_name":"Thader, Andreas"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","full_name":"Bauer, Lukas W","last_name":"Bauer"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38316877"]},"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","citation":{"chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41594-023-01201-6"}],"month":"02","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses."}],"oa_version":"Published Version","pmid":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release","description":"News on ISTA Website"}]},"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Molecular Biology","Structural Biology"],"_id":"14979","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"date_updated":"2024-03-05T09:27:47Z","ddc":["570"]},{"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/"}]},"oa_version":"Published Version","abstract":[{"text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"month":"01","main_file_link":[{"url":"https://doi.org/10.1038/s41567-023-02302-1","open_access":"1"}],"scopus_import":"1","date_updated":"2024-03-05T09:33:38Z","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"_id":"14846","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"Nature Physics","day":"09","year":"2024","has_accepted_license":"1","date_created":"2024-01-21T23:00:57Z","date_published":"2024-01-09T00:00:00Z","doi":"10.1038/s41567-023-02302-1","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1.","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024."},"title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia"},{"first_name":"Rushikesh","last_name":"Shinde","full_name":"Shinde, Rushikesh"},{"orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","first_name":"Madison"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo"},{"id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","first_name":"Gregory","full_name":"Szep, Gregory","last_name":"Szep"},{"last_name":"Steccari","full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene"},{"id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","first_name":"David","last_name":"Labrousse Arias","full_name":"Labrousse Arias, David"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Andrew","last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew"},{"first_name":"Raphaël","full_name":"Voituriez, Raphaël","last_name":"Voituriez"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"project":[{"_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601"}]},{"citation":{"ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik"}],"article_processing_charge":"No","title":"Genetic information and biological optimization","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"has_accepted_license":"1","year":"2024","day":"23","page":"158","doi":"10.15479/at:ista:15020","date_published":"2024-02-23T00:00:00Z","date_created":"2024-02-23T14:02:04Z","publisher":"Institute of Science and Technology Austria","oa":1,"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"date_updated":"2024-03-06T14:22:52Z","ddc":["576","519"],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2024-02-23T14:20:16Z","_id":"15020","type":"dissertation","status":"public","keyword":["Theoretical biology","Optimality","Evolution","Information"],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_created":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","date_updated":"2024-02-23T13:50:53Z","file_size":7102089,"creator":"mhledik","file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"date_created":"2024-02-23T13:50:54Z","file_name":"hledik thesis source.zip","date_updated":"2024-02-23T14:20:16Z","file_size":14014790,"creator":"mhledik","file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7553","status":"public"},{"id":"12081","status":"public","relation":"part_of_dissertation"},{"id":"7606","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"02"},{"date_updated":"2024-03-12T12:19:12Z","department":[{"_id":"EvBe"}],"_id":"14842","status":"public","type":"other_academic_publication","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1879-0445"]},"volume":34,"issue":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability."}],"intvolume":" 34","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2023.11.039"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039.","short":"E. Benková, Eva Benkova, Elsevier, 2024.","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","ama":"Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039","apa":"Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp. R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039","mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039."},"title":"Eva Benkova","article_processing_charge":"No","author":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publication":"Current Biology","day":"08","year":"2024","date_created":"2024-01-21T23:00:56Z","date_published":"2024-01-08T00:00:00Z","doi":"10.1016/j.cub.2023.11.039","page":"R3-R5","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"department":[{"_id":"RySh"},{"_id":"PeJo"}],"file_date_updated":"2024-03-12T13:42:42Z","date_updated":"2024-03-12T13:44:18Z","ddc":["570"],"article_type":"original","type":"journal_article","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"},"status":"public","_id":"15084","volume":121,"issue":"8","related_material":{"record":[{"id":"13173","status":"public","relation":"research_data"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","description":"News on ISTA Website"}]},"ec_funded":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","file":[{"creator":"dernst","file_size":13648221,"date_updated":"2024-03-12T13:42:42Z","file_name":"2024_PNAS_Koppensteiner.pdf","date_created":"2024-03-12T13:42:42Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15110","checksum":"b25b2a057c266ff317a48b0d54d6fc8a"}],"language":[{"iso":"eng"}],"month":"02","intvolume":" 121","abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Published Version","pmid":1,"author":[{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep"},{"full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal","first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","last_name":"Le Monnier"},{"id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2","first_name":"Utsa","last_name":"Roy","full_name":"Roy, Utsa"},{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"last_name":"Sadakata","full_name":"Sadakata, Tetsushi","first_name":"Tetsushi"},{"full_name":"Sanbo, Makoto","last_name":"Sanbo","first_name":"Makoto"},{"full_name":"Hirabayashi, Masumi","last_name":"Hirabayashi","first_name":"Masumi"},{"first_name":"JeongSeop","last_name":"Rhee","full_name":"Rhee, JeongSeop"},{"full_name":"Brose, Nils","last_name":"Brose","first_name":"Nils"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38346189"]},"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","citation":{"ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 121(8), e2301449121.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 2024;121(8). doi:10.1073/pnas.2301449121","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no. 8. Proceedings of the National Academy of Sciences, 2024.","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121 (2024).","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e2301449121","doi":"10.1073/pnas.2301449121","date_published":"2024-02-20T00:00:00Z","date_created":"2024-03-05T09:23:55Z","has_accepted_license":"1","year":"2024","day":"20","publication":"Proceedings of the National Academy of Sciences","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support."},{"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"e2315558121","author":[{"first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","last_name":"Hübner","full_name":"Hübner, Valentin"},{"last_name":"Staab","full_name":"Staab, Manuel","first_name":"Manuel"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Maria","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"external_id":{"pmid":["38408249"]},"article_processing_charge":"Yes (in subscription journal)","title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","citation":{"ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 121(10), e2315558121.","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National Academy of Sciences, 2024.","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences 121 (2024).","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences, vol. 121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","doi":"10.1073/pnas.2315558121","date_published":"2024-03-05T00:00:00Z","date_created":"2024-03-05T09:18:49Z","has_accepted_license":"1","year":"2024","day":"05","publication":"Proceedings of the National Academy of Sciences","type":"journal_article","article_type":"original","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"},"status":"public","_id":"15083","file_date_updated":"2024-03-12T13:12:22Z","department":[{"_id":"KrCh"}],"date_updated":"2024-03-12T13:29:25Z","ddc":["000"],"month":"03","intvolume":" 121","abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation."}],"pmid":1,"oa_version":"Published Version","volume":121,"related_material":{"record":[{"relation":"research_data","id":"15108","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","relation":"press_release","description":"News on ISTA Website"}]},"issue":"10","ec_funded":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15109","checksum":"068520e3efd4d008bb9177e8aedb7d22","creator":"dernst","file_size":2203220,"date_updated":"2024-03-12T13:12:22Z","file_name":"2024_PNAS_Huebner.pdf","date_created":"2024-03-12T13:12:22Z"}],"language":[{"iso":"eng"}]},{"status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"15108","department":[{"_id":"KrCh"}],"title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","author":[{"id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","full_name":"Hübner, Valentin","last_name":"Hübner"},{"first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","short":"V. Hübner, M. Kleshnina, (2024).","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167."},"date_updated":"2024-03-12T13:29:26Z","month":"02","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://10.5281/zenodo.10639167","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below."}],"date_published":"2024-02-09T00:00:00Z","doi":"10.5281/ZENODO.10639167","related_material":{"record":[{"id":"15083","status":"public","relation":"used_in_publication"}]},"date_created":"2024-03-12T13:02:58Z","day":"09","has_accepted_license":"1","year":"2024"},{"file":[{"creator":"dernst","file_size":13364601,"date_updated":"2024-03-13T08:59:21Z","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","date_created":"2024-03-13T08:59:21Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"270d2340402729b0532f7072ea914cae","file_id":"15111"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"publication_status":"published","issue":"4","volume":17,"oa_version":"Published Version","abstract":[{"text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study.","lang":"eng"}],"month":"02","intvolume":" 17","scopus_import":"1","ddc":["550"],"date_updated":"2024-03-13T09:01:20Z","file_date_updated":"2024-03-13T08:59:21Z","department":[{"_id":"CaMu"}],"_id":"15097","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"22","publication":"Geoscientific Model Development","has_accepted_license":"1","year":"2024","date_published":"2024-02-22T00:00:00Z","doi":"10.5194/gmd-17-1563-2024","date_created":"2024-03-10T23:00:53Z","page":"1563-1584","acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","publisher":"European Geosciences Union","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.","ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024."},"title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","author":[{"full_name":"Schmidt, Hauke","last_name":"Schmidt","first_name":"Hauke"},{"last_name":"Rast","full_name":"Rast, Sebastian","first_name":"Sebastian"},{"full_name":"Bao, Jiawei","last_name":"Bao","first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"},{"full_name":"Cassim, Amrit","last_name":"Cassim","first_name":"Amrit"},{"full_name":"Fang, Shih Wei","last_name":"Fang","first_name":"Shih Wei"},{"first_name":"Diego","full_name":"Jimenez-De La Cuesta, Diego","last_name":"Jimenez-De La Cuesta"},{"first_name":"Paul","last_name":"Keil","full_name":"Keil, Paul"},{"first_name":"Lukas","full_name":"Kluft, Lukas","last_name":"Kluft"},{"first_name":"Clarissa","full_name":"Kroll, Clarissa","last_name":"Kroll"},{"first_name":"Theresa","full_name":"Lang, Theresa","last_name":"Lang"},{"last_name":"Niemeier","full_name":"Niemeier, Ulrike","first_name":"Ulrike"},{"full_name":"Schneidereit, Andrea","last_name":"Schneidereit","first_name":"Andrea"},{"full_name":"Williams, Andrew I.L.","last_name":"Williams","first_name":"Andrew I.L."},{"first_name":"Bjorn","last_name":"Stevens","full_name":"Stevens, Bjorn"}],"article_processing_charge":"Yes (via OA deal)"},{"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"article_number":"2203.02015","external_id":{"arxiv":["2203.02015"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Naskręcki, Bartosz","last_name":"Naskręcki","first_name":"Bartosz"},{"orcid":"0000-0002-0854-0306","full_name":"Verzobio, Matteo","last_name":"Verzobio","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","first_name":"Matteo"}],"title":"Common valuations of division polynomials","citation":{"ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.","chicago":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.","ieee":"B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024.","short":"B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2024).","apa":"Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2024.7","ama":"Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7","mla":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015, Cambridge University Press, 2024, doi:10.1017/prm.2024.7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","acknowledgement":"Silverman, and Paul Voutier for the comments on the earlier version of this paper. The first author acknowledges the support by Dioscuri programme initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. The second author has been supported by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in arithmetic’ and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","date_created":"2023-01-16T11:45:22Z","date_published":"2024-02-26T00:00:00Z","doi":"10.1017/prm.2024.7","year":"2024","has_accepted_license":"1","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","day":"26","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"status":"public","_id":"12311","department":[{"_id":"TiBr"}],"date_updated":"2024-03-13T11:55:21Z","ddc":["510"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/prm.2024.7"}],"scopus_import":"1","month":"02","abstract":[{"text":"In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"publication_status":"epub_ahead","publication_identifier":{"eissn":["1473-7124"],"issn":["0308-2105"]},"language":[{"iso":"eng"}]},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tig.2024.01.002"}],"month":"02","abstract":[{"lang":"eng","text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems."}],"pmid":1,"oa_version":"Published Version","publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"15099","department":[{"_id":"NiBa"}],"date_updated":"2024-03-13T12:08:57Z","ddc":["570"],"publisher":"Cell Press","quality_controlled":"1","oa":1,"acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","date_published":"2024-02-22T00:00:00Z","doi":"10.1016/j.tig.2024.01.002","date_created":"2024-03-10T23:00:54Z","has_accepted_license":"1","year":"2024","day":"22","publication":"Trends in Genetics","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38395682"]},"title":"Diverse pathways to speciation revealed by marine snails","citation":{"mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024).","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002.","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","article_type":"original","type":"journal_article","_id":"15098","department":[{"_id":"JuFi"}],"date_updated":"2024-03-13T12:20:23Z","month":"02","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-024-02812-0"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force."}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0025-5831"],"eissn":["1432-1807"]},"publication_status":"epub_ahead","project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","author":[{"orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti","first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72"},{"last_name":"Luongo","full_name":"Luongo, Eliseo","first_name":"Eliseo"}],"external_id":{"arxiv":["2306.11081"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Agresti, E. Luongo, Mathematische Annalen (2024).","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen. Springer Nature, 2024.","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0","ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024. doi:10.1007/s00208-024-02812-0","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, Springer Nature, 2024, doi:10.1007/s00208-024-02812-0.","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen.","chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","date_published":"2024-02-27T00:00:00Z","doi":"10.1007/s00208-024-02812-0","date_created":"2024-03-10T23:00:54Z","day":"27","publication":"Mathematische Annalen","year":"2024"},{"article_number":"013223","project":[{"name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 6(1), 013223.","chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.","ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","apa":"Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013223","mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223."},"title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","external_id":{"arxiv":["2307.14427"]},"article_processing_charge":"Yes","author":[{"full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"},{"first_name":"Daniel J.","full_name":"Egger, Daniel J.","last_name":"Egger"}],"acknowledgement":"S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and S. Woerner for fruitful discussions.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review Research","day":"01","year":"2024","has_accepted_license":"1","date_created":"2024-03-17T23:00:59Z","date_published":"2024-03-01T00:00:00Z","doi":"10.1103/PhysRevResearch.6.013223","_id":"15122","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["530"],"date_updated":"2024-03-19T07:24:03Z","department":[{"_id":"MaSe"}],"file_date_updated":"2024-03-19T07:16:38Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA."}],"intvolume":" 6","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15123","checksum":"274c9f1b15b3547a10a03f39e4ccc582","success":1,"creator":"dernst","date_updated":"2024-03-19T07:16:38Z","file_size":2777593,"date_created":"2024-03-19T07:16:38Z","file_name":"2024_PhysicalReviewResearch_Sack.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"volume":6,"issue":"1"},{"date_created":"2024-03-17T23:00:58Z","date_published":"2024-02-01T00:00:00Z","doi":"10.1214/22-AIHP1333","page":"413-430","publication":"Annales de l'institut Henri Poincare Probability and Statistics","day":"01","year":"2024","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","acknowledgement":"The first author has been partially supported by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO). The authors thank the anonymous referees and Max Sauerbrey for careful reading and helpful suggestions.","title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions","article_processing_charge":"No","external_id":{"arxiv":["2106.01274"]},"author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","last_name":"Agresti","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio"},{"first_name":"Mark","full_name":"Veraar, Mark","last_name":"Veraar"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/22-AIHP1333.","ista":"Agresti A, Veraar M. 2024. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 60(1), 413–430.","mla":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1, Institute of Mathematical Statistics, 2024, pp. 413–30, doi:10.1214/22-AIHP1333.","ieee":"A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions,” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1. Institute of Mathematical Statistics, pp. 413–430, 2024.","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430.","apa":"Agresti, A., & Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1333","ama":"Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 2024;60(1):413-430. doi:10.1214/22-AIHP1333"},"issue":"1","volume":60,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0246-0203"]},"intvolume":" 60","month":"02","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness.","lang":"eng"}],"department":[{"_id":"JuFi"}],"date_updated":"2024-03-19T08:14:17Z","status":"public","article_type":"original","type":"journal_article","_id":"15119"},{"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"article_number":"e2316284121","title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","author":[{"last_name":"Habig","full_name":"Habig, Michael","first_name":"Michael"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"first_name":"Judith","full_name":"Müller, Judith","last_name":"Müller"},{"first_name":"Eva H.","last_name":"Stukenbrock","full_name":"Stukenbrock, Eva H."},{"full_name":"Leitner, Hanna","last_name":"Leitner","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"external_id":{"pmid":["38442176"]},"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2316284121.","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2316284121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121.","short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., & Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2316284121"},"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","oa":1,"acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","doi":"10.1073/pnas.2316284121","date_published":"2024-03-12T00:00:00Z","date_created":"2023-10-31T13:30:00Z","day":"12","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","year":"2024","status":"public","type":"journal_article","article_type":"original","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"},"_id":"14478","department":[{"_id":"SyCr"}],"file_date_updated":"2024-03-19T09:02:57Z","ddc":["570"],"date_updated":"2024-03-19T09:07:20Z","month":"03","intvolume":" 121","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens."}],"issue":"11","volume":121,"ec_funded":1,"file":[{"date_created":"2024-03-19T09:02:57Z","file_name":"2024_PNAS_Habig.pdf","date_updated":"2024-03-19T09:02:57Z","file_size":5750361,"creator":"dernst","file_id":"15124","checksum":"f5e871db617b682edc71fcd08670dc81","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","date_created":"2021-09-27T10:48:23Z","doi":"10.1007/s10107-024-02064-5","date_published":"2024-03-07T00:00:00Z","publication":"Mathematical Programming","day":"07","year":"2024","has_accepted_license":"1","article_number":"2109.10203","title":"Generalized minimum 0-extension problem and discrete convexity","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2109.10203"]},"author":[{"last_name":"Dvorak","full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X","first_name":"Martin","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5.","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5.","ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203."},"month":"03","scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n","lang":"eng"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","file_id":"10046","file_size":603672,"date_updated":"2021-09-27T10:54:51Z","creator":"mdvorak","file_name":"Generalized-0-Ext.pdf","date_created":"2021-09-27T10:54:51Z"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"10045","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"file_date_updated":"2021-09-27T10:54:51Z","ddc":["004"],"date_updated":"2024-03-19T08:20:31Z"},{"publication":"Mathematical Programming","day":"06","year":"2024","date_created":"2024-03-17T23:00:58Z","doi":"10.1007/s10107-024-02066-3","date_published":"2024-03-06T00:00:00Z","acknowledgement":"The first author thanks Chandra Chekuri for useful discussions about this paper. This work was done in part at the University of Vienna. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Zheng, D. W., & Henzinger, M. H. (2024). Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02066-3","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. 2024. doi:10.1007/s10107-024-02066-3","short":"D.W. Zheng, M.H. Henzinger, Mathematical Programming (2024).","ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” Mathematical Programming. Springer Nature, 2024.","mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming, Springer Nature, 2024, doi:10.1007/s10107-024-02066-3.","ista":"Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming.","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02066-3."},"title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","article_processing_charge":"No","external_id":{"arxiv":["2301.09217"]},"author":[{"first_name":"Da Wei","last_name":"Zheng","full_name":"Zheng, Da Wei"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1436-4646"],"issn":["0025-5610"]},"ec_funded":1,"related_material":{"record":[{"id":"13236","status":"public","relation":"earlier_version"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges."}],"month":"03","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.09217","open_access":"1"}],"scopus_import":"1","date_updated":"2024-03-19T08:32:32Z","department":[{"_id":"MoHe"}],"_id":"15121","status":"public","article_type":"original","type":"journal_article"},{"citation":{"ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121.","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121","ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38451946"]},"author":[{"full_name":"Giubertoni, Giulia","last_name":"Giubertoni","first_name":"Giulia"},{"full_name":"Feng, Liru","last_name":"Feng","first_name":"Liru"},{"first_name":"Kevin","full_name":"Klein, Kevin","last_name":"Klein"},{"last_name":"Giannetti","full_name":"Giannetti, Guido","first_name":"Guido"},{"first_name":"Luco","full_name":"Rutten, Luco","last_name":"Rutten"},{"full_name":"Choi, Yeji","last_name":"Choi","first_name":"Yeji"},{"first_name":"Anouk","last_name":"Van Der Net","full_name":"Van Der Net, Anouk"},{"first_name":"Gerard","last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard"},{"first_name":"Federico","full_name":"Caporaletti, Federico","last_name":"Caporaletti"},{"first_name":"Dimitra","full_name":"Micha, Dimitra","last_name":"Micha"},{"full_name":"Hunger, Johannes","last_name":"Hunger","first_name":"Johannes"},{"last_name":"Deblais","full_name":"Deblais, Antoine","first_name":"Antoine"},{"first_name":"Daniel","last_name":"Bonn","full_name":"Bonn, Daniel"},{"last_name":"Sommerdijk","full_name":"Sommerdijk, Nico","first_name":"Nico"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Ilie, Ioana M.","last_name":"Ilie","first_name":"Ioana M."},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."},{"first_name":"Sander","full_name":"Woutersen, Sander","last_name":"Woutersen"}],"title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","article_number":"e2313162121","year":"2024","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"12","date_created":"2024-03-17T23:00:57Z","doi":"10.1073/pnas.2313162121","date_published":"2024-03-12T00:00:00Z","acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","oa":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2024-03-19T11:41:32Z","ddc":["550"],"department":[{"_id":"AnSa"}],"file_date_updated":"2024-03-19T10:22:42Z","_id":"15116","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":12952586,"date_updated":"2024-03-19T10:22:42Z","file_name":"2024_PNAS_Giubertoni.pdf","date_created":"2024-03-19T10:22:42Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15125","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05"}],"related_material":{"record":[{"id":"15126","status":"public","relation":"research_data"}]},"issue":"11","volume":121,"abstract":[{"lang":"eng","text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 121","month":"03"},{"oa_version":"Published Version","abstract":[{"text":"This zip file contains data, and analysis for the paper \"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration\".","lang":"eng"}],"month":"02","publisher":"Figshare","main_file_link":[{"url":"https://doi.org/10.21942/UVA.24829896","open_access":"1"}],"oa":1,"day":"14","has_accepted_license":"1","year":"2024","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15116"}]},"date_published":"2024-02-14T00:00:00Z","doi":"10.21942/UVA.24829896","date_created":"2024-03-19T10:47:16Z","_id":"15126","status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"citation":{"mla":"Giubertoni, G., and S. Woutersen. Dataset Collagen Self Assembly in H2O and D2O. Figshare, 2024, doi:10.21942/UVA.24829896.","ieee":"G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024.","short":"G. Giubertoni, S. Woutersen, (2024).","apa":"Giubertoni, G., & Woutersen, S. (2024). Dataset Collagen Self Assembly in H2O and D2O. Figshare. https://doi.org/10.21942/UVA.24829896","ama":"Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024. doi:10.21942/UVA.24829896","chicago":"Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. https://doi.org/10.21942/UVA.24829896.","ista":"Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and D2O, Figshare, 10.21942/UVA.24829896."},"date_updated":"2024-03-19T11:41:33Z","title":"Dataset Collagen Self Assembly in H2O and D2O","author":[{"last_name":"Giubertoni","full_name":"Giubertoni, G.","first_name":"G."},{"first_name":"S.","last_name":"Woutersen","full_name":"Woutersen, S."}],"article_processing_charge":"No"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094."},"title":"Persistence and Morse theory for discrete geometric structures","article_processing_charge":"No","author":[{"last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I4887","name":"Discretization in Geometry and Dynamics","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"day":"08","year":"2024","has_accepted_license":"1","date_created":"2024-03-08T15:28:10Z","date_published":"2024-03-08T00:00:00Z","doi":"10.15479/at:ista:15094","page":"108","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["514","500","516"],"date_updated":"2024-03-20T09:36:57Z","supervisor":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2024-03-14T14:14:35Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"_id":"15094","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"creator":"scultrer","file_size":4106872,"date_updated":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","date_created":"2024-03-14T08:55:07Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15112","checksum":"1e468bfa42a7dcf04d89f4dadc621c87"},{"file_id":"15113","checksum":"bcbd213490f5a7e68855a092bbce93f1","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2024-03-14T08:56:24Z","file_name":"Thesis (1).zip","creator":"scultrer","date_updated":"2024-03-14T14:14:35Z","file_size":4746234}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11660"},{"relation":"part_of_dissertation","id":"11658","status":"public"},{"relation":"part_of_dissertation","id":"13182","status":"public"},{"status":"public","id":"15090","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"15091"},{"status":"public","id":"15093","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n"}],"month":"03","alternative_title":["ISTA Thesis"]},{"_id":"15093","type":"conference","conference":{"end_date":"2024-01-10","location":"Alexandria, VA, USA","start_date":"2024-01-07","name":"SODA: Symposium on Discrete Algorigthms"},"status":"public","date_updated":"2024-03-20T09:36:56Z","department":[{"_id":"HeEd"},{"_id":"MoHe"}],"abstract":[{"lang":"eng","text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2311.01115"}],"month":"01","publication_identifier":{"eisbn":["9781611977912"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"15094","status":"public"}]},"ec_funded":1,"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "}],"citation":{"ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Lara","full_name":"Ost, Lara","last_name":"Ost"}],"external_id":{"arxiv":["2311.01115"]},"article_processing_charge":"No","title":"Dynamically maintaining the persistent homology of time series","editor":[{"first_name":"David P.","last_name":"Woodruff","full_name":"Woodruff, David P."}],"acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","oa":1,"year":"2024","day":"04","publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","page":"243 - 295","doi":"10.1137/1.9781611977912.11","date_published":"2024-01-04T00:00:00Z","date_created":"2024-03-08T10:27:39Z"},{"date_created":"2024-03-08T10:13:59Z","date_published":"2024-02-07T00:00:00Z","related_material":{"record":[{"status":"public","id":"15094","relation":"dissertation_contains"}]},"publication":"arXiv","language":[{"iso":"eng"}],"day":"07","publication_status":"submitted","year":"2024","month":"02","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided."}],"title":"Chromatic alpha complexes","department":[{"_id":"HeEd"}],"article_processing_charge":"No","external_id":{"arxiv":["2212.03128"]},"author":[{"orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","first_name":"Ondrej","last_name":"Draganov","full_name":"Draganov, Ondrej"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128."},"date_updated":"2024-03-20T09:36:56Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","article_number":"2212.03128","_id":"15091"},{"department":[{"_id":"TiVo"}],"date_updated":"2024-03-25T07:04:05Z","type":"journal_article","article_type":"original","status":"public","_id":"15171","ec_funded":1,"publication_status":"epub_ahead","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-024-01597-4"}],"scopus_import":"1","month":"03","abstract":[{"lang":"eng","text":"The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena."}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."},{"last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks","citation":{"chicago":"Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.","ista":"Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience.","mla":"Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4.","short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024).","ieee":"E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks,” Nature Neuroscience. Springer Nature, 2024.","apa":"Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4","ama":"Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. 2024. doi:10.1038/s41593-024-01597-4"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"date_created":"2024-03-24T23:01:00Z","date_published":"2024-03-20T00:00:00Z","doi":"10.1038/s41593-024-01597-4","year":"2024","publication":"Nature Neuroscience","day":"20","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank C. Currin, B. Podlaski and the members of the Vogels group for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. Open access funding provided by University of Basel."},{"article_processing_charge":"Yes","external_id":{"arxiv":["2309.05714"]},"author":[{"first_name":"Jenny E.","full_name":"Greene, Jenny E.","last_name":"Greene"},{"last_name":"Labbe","full_name":"Labbe, Ivo","first_name":"Ivo"},{"last_name":"Goulding","full_name":"Goulding, Andy D.","first_name":"Andy D."},{"last_name":"Furtak","full_name":"Furtak, Lukas J.","first_name":"Lukas J."},{"first_name":"Iryna","last_name":"Chemerynska","full_name":"Chemerynska, Iryna"},{"full_name":"Kokorev, Vasily","last_name":"Kokorev","first_name":"Vasily"},{"first_name":"Pratika","full_name":"Dayal, Pratika","last_name":"Dayal"},{"first_name":"Marta","last_name":"Volonteri","full_name":"Volonteri, Marta"},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."},{"last_name":"Wang","full_name":"Wang, Bingjie","first_name":"Bingjie"},{"full_name":"Setton, David J.","last_name":"Setton","first_name":"David J."},{"first_name":"Adam J.","full_name":"Burgasser, Adam J.","last_name":"Burgasser"},{"last_name":"Bezanson","full_name":"Bezanson, Rachel","first_name":"Rachel"},{"last_name":"Atek","full_name":"Atek, Hakim","first_name":"Hakim"},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"last_name":"Cutler","full_name":"Cutler, Sam E.","first_name":"Sam E."},{"last_name":"Feldmann","full_name":"Feldmann, Robert","first_name":"Robert"},{"last_name":"Fujimoto","full_name":"Fujimoto, Seiji","first_name":"Seiji"},{"first_name":"Karl","last_name":"Glazebrook","full_name":"Glazebrook, Karl"},{"first_name":"Anna","last_name":"De Graaff","full_name":"De Graaff, Anna"},{"full_name":"Khullar, Gourav","last_name":"Khullar","first_name":"Gourav"},{"full_name":"Leja, Joel","last_name":"Leja","first_name":"Joel"},{"full_name":"Marchesini, Danilo","last_name":"Marchesini","first_name":"Danilo"},{"first_name":"Michael V.","full_name":"Maseda, Michael V.","last_name":"Maseda"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"last_name":"Miller","full_name":"Miller, Tim B.","first_name":"Tim B."},{"first_name":"Rohan P.","full_name":"Naidu, Rohan P.","last_name":"Naidu"},{"first_name":"Themiya","last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya"},{"first_name":"Pascal A.","full_name":"Oesch, Pascal A.","last_name":"Oesch"},{"full_name":"Pan, Richard","last_name":"Pan","first_name":"Richard"},{"first_name":"Casey","full_name":"Papovich, Casey","last_name":"Papovich"},{"first_name":"Sedona H.","last_name":"Price","full_name":"Price, Sedona H."},{"last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter","first_name":"Pieter"},{"full_name":"Weaver, John R.","last_name":"Weaver","first_name":"John R."},{"full_name":"Whitaker, Katherine E.","last_name":"Whitaker","first_name":"Katherine E."},{"last_name":"Zitrin","full_name":"Zitrin, Adi","first_name":"Adi"}],"title":"UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5","citation":{"mla":"Greene, Jenny E., et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal, vol. 964, 39, IOP Publishing, 2024, doi:10.3847/1538-4357/ad1e5f.","ieee":"J. E. Greene et al., “UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5,” Astrophysical Journal, vol. 964. IOP Publishing, 2024.","short":"J.E. Greene, I. Labbe, A.D. Goulding, L.J. Furtak, I. Chemerynska, V. Kokorev, P. Dayal, M. Volonteri, C.C. Williams, B. Wang, D.J. Setton, A.J. Burgasser, R. Bezanson, H. Atek, G. Brammer, S.E. Cutler, R. Feldmann, S. Fujimoto, K. Glazebrook, A. De Graaff, G. Khullar, J. Leja, D. Marchesini, M.V. Maseda, J.J. Matthee, T.B. Miller, R.P. Naidu, T. Nanayakkara, P.A. Oesch, R. Pan, C. Papovich, S.H. Price, P. Van Dokkum, J.R. Weaver, K.E. Whitaker, A. Zitrin, Astrophysical Journal 964 (2024).","ama":"Greene JE, Labbe I, Goulding AD, et al. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 2024;964. doi:10.3847/1538-4357/ad1e5f","apa":"Greene, J. E., Labbe, I., Goulding, A. D., Furtak, L. J., Chemerynska, I., Kokorev, V., … Zitrin, A. (2024). UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad1e5f","chicago":"Greene, Jenny E., Ivo Labbe, Andy D. Goulding, Lukas J. Furtak, Iryna Chemerynska, Vasily Kokorev, Pratika Dayal, et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad1e5f.","ista":"Greene JE, Labbe I, Goulding AD, Furtak LJ, Chemerynska I, Kokorev V, Dayal P, Volonteri M, Williams CC, Wang B, Setton DJ, Burgasser AJ, Bezanson R, Atek H, Brammer G, Cutler SE, Feldmann R, Fujimoto S, Glazebrook K, De Graaff A, Khullar G, Leja J, Marchesini D, Maseda MV, Matthee JJ, Miller TB, Naidu RP, Nanayakkara T, Oesch PA, Pan R, Papovich C, Price SH, Van Dokkum P, Weaver JR, Whitaker KE, Zitrin A. 2024. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 964, 39."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"39","date_created":"2024-03-24T23:00:59Z","doi":"10.3847/1538-4357/ad1e5f","date_published":"2024-03-01T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Astrophysical Journal","day":"01","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","acknowledgement":"J.E.G. and A.D.G acknowledge support from NSF/AAG grant No. 1007094, and J.E.G. also acknowledges support from NSF/AAG grant No. 1007052. A.Z. acknowledges support by grant No. 2020750 from the United States-Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (\"ODIN\") and from the European Commission's and University of Groningen's CO-FUND Rosalind Franklin program. K.G. and T.N. acknowledge support from Australian Research Council Laureate Fellowship FL180100060. H.A. and I.C. acknowledge support from CNES, focused on the JWST mission, and the Programme National Cosmology and Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, cofunded by CEA and CNES. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. B.W. acknowledges support from JWST-GO-02561.022-A. A.J.B. acknowledges funding support from NASA/ADAP grant 21-ADAP21-0187. Support for this work was provided by The Brinson Foundation through a Brinson Prize Fellowship grant. R.P.N. acknowledges support for this work provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. C.P. thanks Marsha and Ralph Schilling for the generous support of this research.","file_date_updated":"2024-03-25T08:02:43Z","department":[{"_id":"JoMa"}],"date_updated":"2024-03-25T08:04:13Z","ddc":["550"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"15170","volume":964,"publication_status":"published","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-03-25T08:02:43Z","file_size":2700137,"date_created":"2024-03-25T08:02:43Z","file_name":"2024_AstrophysicalJourn_Greene.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"389a880e176799d5c062ea7cb82d08c9","file_id":"15176","success":1}],"scopus_import":"1","intvolume":" 964","month":"03","abstract":[{"lang":"eng","text":"The James Webb Space Telescope is revealing a new population of dust-reddened broad-line active galactic nuclei (AGN) at redshifts z ≳ 5. Here we present deep NIRSpec/Prism spectroscopy from the Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam ObserVations before the Epoch of Reionization (UNCOVER) of 15 AGN candidates selected to be compact, with red continua in the rest-frame optical but with blue slopes in the UV. From NIRCam photometry alone, they could have been dominated by dusty star formation or an AGN. Here we show that the majority of the compact red sources in UNCOVER are dust-reddened AGN: 60% show definitive evidence for broad-line Hα with a FWHM > 2000 km s −1, 20% of the current data are inconclusive, and 20% are brown dwarf stars. We propose an updated photometric criterion to select red z > 5 AGN that excludes brown dwarfs and is expected to yield >80% AGN. Remarkably, among all zphot > 5 galaxies with F277W – F444W > 1 in UNCOVER at least 33% are AGN regardless of compactness, climbing to at least 80% AGN for sources with F277W – F444W > 1.6. The confirmed AGN have black hole masses of 107–109M⊙. While their UV luminosities (−16 > MUV > −20 AB mag) are low compared to UV-selected AGN at these epochs, consistent with percent-level scattered AGN light or low levels of unobscured star formation, the inferred bolometric luminosities are typical of 107–109M⊙ black holes radiating at ∼10%–40% the Eddington limit. The number densities are surprisingly high at ∼10−5 Mpc−3 mag−1, 100 times more common than the faintest UV-selected quasars, while accounting for ∼1% of the UV-selected galaxies. While their UV faintness suggests they may not contribute strongly to reionization, their ubiquity poses challenges to models of black hole growth."}],"oa_version":"Published Version"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Clermont-Ferrand, France","end_date":"2024-03-14","start_date":"2024-03-12","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"type":"conference","status":"public","_id":"15168","department":[{"_id":"UlWa"}],"file_date_updated":"2024-03-25T07:44:30Z","date_updated":"2024-03-25T07:45:54Z","ddc":["510"],"alternative_title":["LIPIcs"],"scopus_import":"1","intvolume":" 289","month":"03","abstract":[{"text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, … , k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring). Here, we investigate the complexity of approximating the \"linearly ordered chromatic number\" of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023).","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":289,"publication_status":"published","publication_identifier":{"isbn":["9783959773119"],"eissn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"checksum":"0524d4189fd1ed08989546511343edf3","file_id":"15175","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-03-25T07:44:30Z","file_name":"2024_LIPICs_Filakovsky.pdf","creator":"dernst","date_updated":"2024-03-25T07:44:30Z","file_size":927290}],"project":[{"grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"article_number":"34","external_id":{"arxiv":["2312.12981"]},"article_processing_charge":"No","author":[{"id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","full_name":"Filakovský, Marek","last_name":"Filakovský"},{"first_name":"Tamio Vesa","full_name":"Nakajima, Tamio Vesa","last_name":"Nakajima"},{"full_name":"Opršal, Jakub","orcid":"0000-0003-1245-3456","last_name":"Opršal","id":"ec596741-c539-11ec-b829-c79322a91242","first_name":"Jakub"},{"last_name":"Tasinato","full_name":"Tasinato, Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","first_name":"Gianluca"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","citation":{"ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In: 41st International Symposium on Theoretical Aspects of Computer Science. Vol 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.STACS.2024.34","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., & Wagner, U. (2024). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In 41st International Symposium on Theoretical Aspects of Computer Science (Vol. 289). Clermont-Ferrand, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2024.34","short":"M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, in:, 41st International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ieee":"M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” in 41st International Symposium on Theoretical Aspects of Computer Science, Clermont-Ferrand, France, 2024, vol. 289.","mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” 41st International Symposium on Theoretical Aspects of Computer Science, vol. 289, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.STACS.2024.34.","ista":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2024. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. 41st International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 289, 34.","chicago":"Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” In 41st International Symposium on Theoretical Aspects of Computer Science, Vol. 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.STACS.2024.34."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","acknowledgement":"Marek Filakovský: This research was supported by Charles University (project PRIMUS/\r\n21/SCI/014), the Austrian Science Fund (FWF project P31312-N35), and MSCAfellow5_MUNI\r\n(CZ.02.01.01/00/22_010/0003229). Tamio-Vesa Nakajima: This research was funded by UKRI EP/X024431/1 and by a Clarendon Fund Scholarship. All data is provided in full in the results section of this paper. Jakub Opršal: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Uli Wagner: This research was supported by the Austrian Science Fund (FWF project P31312-N35).","date_created":"2024-03-24T23:00:59Z","date_published":"2024-03-01T00:00:00Z","doi":"10.4230/LIPIcs.STACS.2024.34","year":"2024","has_accepted_license":"1","publication":"41st International Symposium on Theoretical Aspects of Computer Science","day":"01"},{"_id":"15164","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2024-03-25T08:31:01Z","ddc":["610"],"department":[{"_id":"PreCl"}],"file_date_updated":"2024-03-25T08:29:52Z","abstract":[{"text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 126","publication_identifier":{"eissn":["1873-4030"],"issn":["1350-4533"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"974acbf2731e7382dcf5920ac762e551","file_id":"15177","creator":"dernst","file_size":10039402,"date_updated":"2024-03-25T08:29:52Z","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","date_created":"2024-03-25T08:29:52Z"}],"language":[{"iso":"eng"}],"volume":126,"article_number":"104143","citation":{"mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024.","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143.","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Silva-Henao","full_name":"Silva-Henao, Juan D.","first_name":"Juan D."},{"last_name":"Schober","full_name":"Schober, Sophie","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie"},{"full_name":"Pahr, Dieter H.","last_name":"Pahr","first_name":"Dieter H."},{"first_name":"Andreas G.","full_name":"Reisinger, Andreas G.","last_name":"Reisinger"}],"article_processing_charge":"Yes (in subscription journal)","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2024","day":"01","publication":"Medical Engineering and Physics","date_published":"2024-04-01T00:00:00Z","doi":"10.1016/j.medengphy.2024.104143","date_created":"2024-03-24T23:00:58Z"},{"acknowledgement":"We thank Félix Werner and Kris Van Houcke for interesting discussions.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"year":"2024","day":"19","publication":"Physical Review A","date_published":"2024-03-19T00:00:00Z","doi":"10.1103/PhysRevA.109.033315","date_created":"2024-03-24T23:00:59Z","article_number":"033315","citation":{"chicago":"Al Hyder, Ragheed, F. Chevy, and X. Leyronas. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.033315.","ista":"Al Hyder R, Chevy F, Leyronas X. 2024. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 109(3), 033315.","mla":"Al Hyder, Ragheed, et al. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A, vol. 109, no. 3, 033315, American Physical Society, 2024, doi:10.1103/PhysRevA.109.033315.","short":"R. Al Hyder, F. Chevy, X. Leyronas, Physical Review A 109 (2024).","ieee":"R. Al Hyder, F. Chevy, and X. Leyronas, “Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy,” Physical Review A, vol. 109, no. 3. American Physical Society, 2024.","ama":"Al Hyder R, Chevy F, Leyronas X. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 2024;109(3). doi:10.1103/PhysRevA.109.033315","apa":"Al Hyder, R., Chevy, F., & Leyronas, X. (2024). Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.033315"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed"},{"full_name":"Chevy, F.","last_name":"Chevy","first_name":"F."},{"last_name":"Leyronas","full_name":"Leyronas, X.","first_name":"X."}],"article_processing_charge":"No","external_id":{"arxiv":["2311.14536"]},"title":"Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy","abstract":[{"lang":"eng","text":"We perform a diagrammatic analysis of the energy of a mobile impurity immersed in a strongly interacting two-component Fermi gas to second order in the impurity-bath interaction. These corrections demonstrate divergent behavior in the limit of large impurity momentum. We show the fundamental processes responsible for these logarithmically divergent terms. We study the problem in the general case without any assumptions regarding the fermion-fermion interactions in the bath. We show that the divergent term can be summed up to all orders in the Fermi-Fermi interaction and that the resulting expression is equivalent to the one obtained in the few-body calculation. Finally, we provide a perturbative calculation to the second order in the Fermi-Fermi interaction, and we show the diagrams responsible for these terms."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2311.14536"}],"month":"03","intvolume":" 109","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":109,"issue":"3","_id":"15167","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-25T07:36:55Z","department":[{"_id":"MiLe"}]},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"For some k∈Z≥0∪{∞}, we call a linear forest k-bounded if each of its components has at most k edges. We will say a (k,ℓ)-bounded linear forest decomposition of a graph G is a partition of E(G) into the edge sets of two linear forests Fk,Fℓ where Fk is k-bounded and Fℓ is ℓ-bounded. We show that the problem of deciding whether a given graph has such a decomposition is NP-complete if both k and ℓ are at least 2, NP-complete if k≥9 and ℓ=1, and is in P for (k,ℓ)=(2,1). Before this, the only known NP-complete cases were the (2,2) and (3,3) cases. Our hardness result answers a question of Bermond et al. from 1984. We also show that planar graphs of girth at least nine decompose into a linear forest and a matching, which in particular is stronger than 3-edge-colouring such graphs."}],"intvolume":" 347","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.11615"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0012-365X"]},"volume":347,"issue":"6","_id":"15163","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-03-25T08:09:43Z","department":[{"_id":"MaKw"}],"acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them.","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Discrete Mathematics","day":"19","year":"2024","date_created":"2024-03-24T23:00:58Z","date_published":"2024-03-19T00:00:00Z","doi":"10.1016/j.disc.2024.113962","article_number":"113962","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Campbell R, Hörsch F, Moore B. 2024. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 347(6), 113962.","chicago":"Campbell, Rutger, Florian Hörsch, and Benjamin Moore. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.disc.2024.113962.","apa":"Campbell, R., Hörsch, F., & Moore, B. (2024). Decompositions into two linear forests of bounded lengths. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2024.113962","ama":"Campbell R, Hörsch F, Moore B. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 2024;347(6). doi:10.1016/j.disc.2024.113962","short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024).","ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” Discrete Mathematics, vol. 347, no. 6. Elsevier, 2024.","mla":"Campbell, Rutger, et al. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics, vol. 347, no. 6, 113962, Elsevier, 2024, doi:10.1016/j.disc.2024.113962."},"title":"Decompositions into two linear forests of bounded lengths","external_id":{"arxiv":["2301.11615"]},"article_processing_charge":"No","author":[{"first_name":"Rutger","full_name":"Campbell, Rutger","last_name":"Campbell"},{"full_name":"Hörsch, Florian","last_name":"Hörsch","first_name":"Florian"},{"first_name":"Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","last_name":"Moore","full_name":"Moore, Benjamin"}]},{"ddc":["550"],"date_updated":"2024-03-25T09:37:27Z","file_date_updated":"2024-03-25T09:31:58Z","department":[{"_id":"JoMa"}],"_id":"15180","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"date_created":"2024-03-25T09:31:58Z","file_name":"2024_AstrophysicalJourn_Matthee.pdf","creator":"dernst","date_updated":"2024-03-25T09:31:58Z","file_size":6047536,"file_id":"15184","checksum":"dc7af4694f9f94a551417ab49fa43edf","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"volume":963,"issue":"2","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Characterizing the prevalence and properties of faint active galactic nuclei (AGNs) in the early Universe is key for understanding the formation of supermassive black holes (SMBHs) and determining their role in cosmic reionization. We perform a spectroscopic search for broad Hα emitters at z ≈ 4–6 using deep JWST/NIRCam imaging and wide field slitless spectroscopy from the EIGER and FRESCO surveys. We identify 20 Hα lines at z = 4.2–5.5 that have broad components with line widths from ∼1200–3700 km s−1, contributing ∼30%–90% of the total line flux. We interpret these broad components as being powered by accretion onto SMBHs with implied masses ∼107–8M⊙. In the UV luminosity range MUV,AGN+host = −21 to −18, we measure number densities of ≈10−5 cMpc−3. This is an order of magnitude higher than expected from extrapolating quasar UV luminosity functions (LFs). Yet, such AGN are found in only <1% of star-forming galaxies at z ∼ 5. The number density discrepancy is much lower when compared to the broad Hα LF. The SMBH mass function agrees with large cosmological simulations. In two objects, we detect complex Hα profiles that we tentatively interpret as caused by absorption signatures from dense gas fueling SMBH growth and outflows. We may be witnessing early AGN feedback that will clear dust-free pathways through which more massive blue quasars are seen. We uncover a strong correlation between reddening and the fraction of total galaxy luminosity arising from faint AGN. This implies that early SMBH growth is highly obscured and that faint AGN are only minor contributors to cosmic reionization."}],"intvolume":" 963","month":"03","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Matthee JJ, Naidu RP, Brammer G, Chisholm J, Eilers A-C, Goulding A, Greene J, Kashino D, Labbe I, Lilly SJ, Mackenzie R, Oesch PA, Weibel A, Wuyts S, Xiao M, Bordoloi R, Bouwens R, van Dokkum P, Illingworth G, Kramarenko I, Maseda MV, Mason C, Meyer RA, Nelson EJ, Reddy NA, Shivaei I, Simcoe RA, Yue M. 2024. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 963(2), 129.","chicago":"Matthee, Jorryt J, Rohan P. Naidu, Gabriel Brammer, John Chisholm, Anna-Christina Eilers, Andy Goulding, Jenny Greene, et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad2345.","apa":"Matthee, J. J., Naidu, R. P., Brammer, G., Chisholm, J., Eilers, A.-C., Goulding, A., … Yue, M. (2024). Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad2345","ama":"Matthee JJ, Naidu RP, Brammer G, et al. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 2024;963(2). doi:10.3847/1538-4357/ad2345","ieee":"J. J. Matthee et al., “Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys,” The Astrophysical Journal, vol. 963, no. 2. American Astronomical Society, 2024.","short":"J.J. Matthee, R.P. Naidu, G. Brammer, J. Chisholm, A.-C. Eilers, A. Goulding, J. Greene, D. Kashino, I. Labbe, S.J. Lilly, R. Mackenzie, P.A. Oesch, A. Weibel, S. Wuyts, M. Xiao, R. Bordoloi, R. Bouwens, P. van Dokkum, G. Illingworth, I. Kramarenko, M.V. Maseda, C. Mason, R.A. Meyer, E.J. Nelson, N.A. Reddy, I. Shivaei, R.A. Simcoe, M. Yue, The Astrophysical Journal 963 (2024).","mla":"Matthee, Jorryt J., et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal, vol. 963, no. 2, 129, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad2345."},"title":"Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys","article_processing_charge":"Yes","author":[{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X"},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"full_name":"Chisholm, John","last_name":"Chisholm","first_name":"John"},{"first_name":"Anna-Christina","last_name":"Eilers","full_name":"Eilers, Anna-Christina"},{"first_name":"Andy","full_name":"Goulding, Andy","last_name":"Goulding"},{"last_name":"Greene","full_name":"Greene, Jenny","first_name":"Jenny"},{"first_name":"Daichi","last_name":"Kashino","full_name":"Kashino, Daichi"},{"first_name":"Ivo","last_name":"Labbe","full_name":"Labbe, Ivo"},{"first_name":"Simon J.","last_name":"Lilly","full_name":"Lilly, Simon J."},{"last_name":"Mackenzie","full_name":"Mackenzie, Ruari","first_name":"Ruari"},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"full_name":"Weibel, Andrea","last_name":"Weibel","first_name":"Andrea"},{"first_name":"Stijn","full_name":"Wuyts, Stijn","last_name":"Wuyts"},{"first_name":"Mengyuan","full_name":"Xiao, Mengyuan","last_name":"Xiao"},{"full_name":"Bordoloi, Rongmon","last_name":"Bordoloi","first_name":"Rongmon"},{"last_name":"Bouwens","full_name":"Bouwens, Rychard","first_name":"Rychard"},{"last_name":"van Dokkum","full_name":"van Dokkum, Pieter","first_name":"Pieter"},{"last_name":"Illingworth","full_name":"Illingworth, Garth","first_name":"Garth"},{"full_name":"Kramarenko, Ivan","last_name":"Kramarenko","first_name":"Ivan"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"first_name":"Charlotte","last_name":"Mason","full_name":"Mason, Charlotte"},{"last_name":"Meyer","full_name":"Meyer, Romain A.","first_name":"Romain A."},{"first_name":"Erica J.","last_name":"Nelson","full_name":"Nelson, Erica J."},{"first_name":"Naveen A.","last_name":"Reddy","full_name":"Reddy, Naveen A."},{"first_name":"Irene","full_name":"Shivaei, Irene","last_name":"Shivaei"},{"last_name":"Simcoe","full_name":"Simcoe, Robert A.","first_name":"Robert A."},{"last_name":"Yue","full_name":"Yue, Minghao","first_name":"Minghao"}],"article_number":"129","project":[{"_id":"bd9b2118-d553-11ed-ba76-db24564edfea","name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224"}],"publication":"The Astrophysical Journal","day":"07","year":"2024","has_accepted_license":"1","date_created":"2024-03-25T08:54:47Z","date_published":"2024-03-07T00:00:00Z","doi":"10.3847/1538-4357/ad2345","acknowledgement":"We thank the anonymous referee for constructive comments that helped improve the manuscript. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program Nos. 1243 and 1895. The specific observations analyzed can be accessed via doi:10.17909/4xx0-zj76. Funded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work for R.P.N. was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. Support for this work for G.I. was provided by NASA through grant JWST-GO-01895 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract No. MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant No. 140.\r\nFacility: JWST - James Webb Space Telescope, HST - Hubble Space Telescope satellite\r\nSoftware: Python, matplotlib (Hunter 2007), numpy (Harris et al. 2020), scipy (Virtanen et al. 2020), Astropy (Astropy Collaboration et al. 2013, 2018), Imfit (Erwin 2015).","oa":1,"quality_controlled":"1","publisher":"American Astronomical Society"},{"file_date_updated":"2024-03-25T09:42:10Z","department":[{"_id":"FyKo"}],"ddc":["580"],"date_updated":"2024-03-25T09:44:53Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"15179","issue":"10","volume":10,"file":[{"file_name":"2024_ScienceAdv_Palkina.pdf","date_created":"2024-03-25T09:42:10Z","creator":"dernst","file_size":1499302,"date_updated":"2024-03-25T09:42:10Z","success":1,"checksum":"a19c43b260ea0bbaf895a29712e3153c","file_id":"15185","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","month":"03","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors."}],"title":"A hybrid pathway for self-sustained luminescence","author":[{"last_name":"Palkina","full_name":"Palkina, Kseniia A.","first_name":"Kseniia A."},{"last_name":"Karataeva","full_name":"Karataeva, Tatiana A.","first_name":"Tatiana A."},{"first_name":"Maxim M.","last_name":"Perfilov","full_name":"Perfilov, Maxim M."},{"full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova","first_name":"Liliia I."},{"first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M.","last_name":"Markina"},{"last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Garcia-Perez, Elena","last_name":"Garcia-Perez","first_name":"Elena"},{"last_name":"Vazquez-Vilar","full_name":"Vazquez-Vilar, Marta","first_name":"Marta"},{"last_name":"Rodriguez-Rodriguez","full_name":"Rodriguez-Rodriguez, Marta","first_name":"Marta"},{"last_name":"Vazquez-Vilriales","full_name":"Vazquez-Vilriales, Victor","first_name":"Victor"},{"last_name":"Shakhova","full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S."},{"full_name":"Mitiouchkina, Tatiana","last_name":"Mitiouchkina","first_name":"Tatiana"},{"first_name":"Olga A.","last_name":"Belozerova","full_name":"Belozerova, Olga A."},{"last_name":"Kovalchuk","full_name":"Kovalchuk, Sergey I.","first_name":"Sergey I."},{"last_name":"Alekberova","full_name":"Alekberova, Anna","first_name":"Anna"},{"last_name":"Malyshevskaia","full_name":"Malyshevskaia, Alena K.","first_name":"Alena K."},{"first_name":"Evgenia N.","full_name":"Bugaeva, Evgenia N.","last_name":"Bugaeva"},{"full_name":"Guglya, Elena B.","last_name":"Guglya","first_name":"Elena B."},{"first_name":"Anastasia","full_name":"Balakireva, Anastasia","last_name":"Balakireva"},{"last_name":"Sytov","full_name":"Sytov, Nikita","first_name":"Nikita"},{"full_name":"Bezlikhotnova, Anastasia","last_name":"Bezlikhotnova","first_name":"Anastasia"},{"full_name":"Boldyreva, Daria I.","last_name":"Boldyreva","first_name":"Daria I."},{"first_name":"Vladislav V.","full_name":"Babenko, Vladislav V.","last_name":"Babenko"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"last_name":"Choob","full_name":"Choob, Vladimir V.","first_name":"Vladimir V."},{"full_name":"Orzaez, Diego","last_name":"Orzaez","first_name":"Diego"},{"last_name":"Yampolsky","full_name":"Yampolsky, Ilia V.","first_name":"Ilia V."},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S.","first_name":"Karen S."}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992.","chicago":"Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.","short":"K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).","ieee":"K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,” Science Advances, vol. 10, no. 10. American Association for the Advancement of Science, 2024.","apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992","mla":"Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1992."},"article_number":"adk1992","doi":"10.1126/sciadv.adk1992","date_published":"2024-03-01T00:00:00Z","date_created":"2024-03-25T08:54:33Z","day":"01","publication":"Science Advances","has_accepted_license":"1","year":"2024","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund)."}]