[{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"intvolume":" 34","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14813","checksum":"51220b76d72a614208f84bdbfbaf9b72","creator":"dernst","file_size":5183861,"date_updated":"2024-01-16T10:53:31Z","file_name":"2024_CurrentBiology_Arslan.pdf","date_created":"2024-01-16T10:53:31Z"}],"publication_status":"published","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"ec_funded":1,"volume":34,"issue":"1","_id":"14795","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":["570"],"date_updated":"2024-01-17T08:20:40Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"file_date_updated":"2024-01-16T10:53:31Z","acknowledgement":"We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H.","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Current Biology","day":"08","year":"2024","has_accepted_license":"1","date_created":"2024-01-14T23:00:56Z","date_published":"2024-01-08T00:00:00Z","doi":"10.1016/j.cub.2023.11.067","page":"171-182.e8","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.067.","ista":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8.","mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:10.1016/j.cub.2023.11.067.","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","ieee":"F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” Current Biology, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.","apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., & Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2023.11.067","ama":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 2024;34(1):171-182.e8. doi:10.1016/j.cub.2023.11.067"},"title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","article_processing_charge":"Yes (via OA deal)","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","last_name":"Arslan"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"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"}]},{"date_created":"2024-01-15T10:25:38Z","doi":"10.1364/optica.507451","date_published":"2024-01-20T00:00:00Z","page":"26-31","publication":"Optica","day":"20","year":"2024","has_accepted_license":"1","oa":1,"publisher":"Optica Publishing Group","quality_controlled":"1","acknowledgement":"We thank Rishabh Sahu and Sebastian Wald for technical contributions to the experiment. Funding by Institute of Science and Technology Austria.","title":"Laser-cavity locking utilizing beam ellipticity: accessing the 10−7 instability scale relative to cavity linewidth","article_processing_charge":"Yes","author":[{"first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","last_name":"Diorico","orcid":"0000-0002-4947-8924","full_name":"Diorico, Fritz R"},{"first_name":"Artem","id":"0f02ed6a-b514-11ee-b891-8379c5f19cb7","last_name":"Zhutov","full_name":"Zhutov, Artem"},{"last_name":"Hosten","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"F. R. Diorico, A. Zhutov, and O. Hosten, “Laser-cavity locking utilizing beam ellipticity: accessing the 10−7 instability scale relative to cavity linewidth,” Optica, vol. 11, no. 1. Optica Publishing Group, pp. 26–31, 2024.","short":"F.R. Diorico, A. Zhutov, O. Hosten, Optica 11 (2024) 26–31.","apa":"Diorico, F. R., Zhutov, A., & Hosten, O. (2024). Laser-cavity locking utilizing beam ellipticity: accessing the 10−7 instability scale relative to cavity linewidth. Optica. Optica Publishing Group. https://doi.org/10.1364/optica.507451","ama":"Diorico FR, Zhutov A, Hosten O. Laser-cavity locking utilizing beam ellipticity: accessing the 10−7 instability scale relative to cavity linewidth. Optica. 2024;11(1):26-31. doi:10.1364/optica.507451","mla":"Diorico, Fritz R., et al. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10−7 Instability Scale Relative to Cavity Linewidth.” Optica, vol. 11, no. 1, Optica Publishing Group, 2024, pp. 26–31, doi:10.1364/optica.507451.","ista":"Diorico FR, Zhutov A, Hosten O. 2024. Laser-cavity locking utilizing beam ellipticity: accessing the 10−7 instability scale relative to cavity linewidth. Optica. 11(1), 26–31.","chicago":"Diorico, Fritz R, Artem Zhutov, and Onur Hosten. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10−7 Instability Scale Relative to Cavity Linewidth.” Optica. Optica Publishing Group, 2024. https://doi.org/10.1364/optica.507451."},"issue":"1","volume":11,"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"eb99ca7d0fe73e22f121875175546ed7","file_id":"14824","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_Optica_Diorico.pdf","date_created":"2024-01-17T08:53:16Z","creator":"dernst","file_size":4558986,"date_updated":"2024-01-17T08:53:16Z"}],"publication_status":"published","publication_identifier":{"issn":["2334-2536"]},"intvolume":" 11","month":"01","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Frequency-stable lasers form the back bone of precision measurements in science and technology. Such lasers typically attain their stability through frequency locking to reference cavities. State-of-the-art locking performances to date had been achieved using frequency modulation based methods, complemented with active drift cancellation systems. We demonstrate an all passive, modulation-free laser-cavity locking technique (squash locking) that utilizes changes in spatial beam ellipticity for error signal generation, and a coherent polarization post-selection for noise resilience. By comparing two identically built proof-of-principle systems, we show a frequency locking instability of 5×10−7 relative to the cavity linewidth at 10 s averaging. The results surpass the demonstrated performances of methods engineered over the last five decades, potentially enabling an advancement in the precision control of lasers, while creating avenues for bridging the performance gaps between industrial grade lasers with scientific ones due to the afforded simplicity and scalability."}],"file_date_updated":"2024-01-17T08:53:16Z","department":[{"_id":"OnHo"}],"ddc":["530"],"date_updated":"2024-01-17T08:53:47Z","keyword":["Atomic and Molecular Physics","and Optics","Electronic","Optical and Magnetic Materials"],"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":"14802"},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful discussions about different variants of the problem. This work is supported by the European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025, the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant 470029389 (FlexNets), 2021-2024.","date_created":"2024-01-16T13:40:41Z","date_published":"2024-01-11T00:00:00Z","doi":"10.1016/j.tcs.2023.114353","year":"2024","publication":"Theoretical Computer Science","day":"11","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"article_number":"114353","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda"},{"last_name":"Yeo","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"title":"Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation","citation":{"chicago":"Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” Theoretical Computer Science. Elsevier, 2024. https://doi.org/10.1016/j.tcs.2023.114353.","ista":"Schmid S, Svoboda J, Yeo MX. 2024. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. Theoretical Computer Science. 989, 114353.","mla":"Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” Theoretical Computer Science, vol. 989, 114353, Elsevier, 2024, doi:10.1016/j.tcs.2023.114353.","apa":"Schmid, S., Svoboda, J., & Yeo, M. X. (2024). Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.114353","ama":"Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. Theoretical Computer Science. 2024;989. doi:10.1016/j.tcs.2023.114353","ieee":"S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation,” Theoretical Computer Science, vol. 989. Elsevier, 2024.","short":"S. Schmid, J. Svoboda, M.X. Yeo, Theoretical Computer Science 989 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1016/j.tcs.2023.114353","open_access":"1"}],"intvolume":" 989","month":"01","abstract":[{"text":"We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how many nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v's capacity on \r\n increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes' decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+E) . (1+3) for some arbitrary E>0.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":989,"publication_status":"epub_ahead","publication_identifier":{"issn":["0304-3975"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","keyword":["General Computer Science","Theoretical Computer Science"],"status":"public","_id":"14820","department":[{"_id":"KrCh"},{"_id":"KrPi"}],"date_updated":"2024-01-17T09:23:03Z"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290.","date_created":"2024-01-14T23:00:56Z","doi":"10.1038/s41467-023-44114-0","date_published":"2024-01-02T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Nature Communications","day":"02","project":[{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046"},{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515"},{"_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811","name":"Quantum bits with Kitaev Transmons","grant_number":"101115315"},{"call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices","grant_number":"P32235"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Conventional and unconventional topological superconductors","grant_number":"F8606"}],"article_number":"169","external_id":{"pmid":["38167818"]},"article_processing_charge":"Yes","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini","full_name":"Valentini, Marco"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","full_name":"Sagi, Oliver","last_name":"Sagi"},{"full_name":"Baghumyan, Levon","last_name":"Baghumyan","first_name":"Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7"},{"first_name":"Thijs","id":"a0ece13c-b527-11ee-929d-bad130106eee","full_name":"de Gijsel, Thijs","last_name":"de Gijsel"},{"id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","first_name":"Jason","last_name":"Jung","full_name":"Jung, Jason"},{"first_name":"Stefano","last_name":"Calcaterra","full_name":"Calcaterra, Stefano"},{"full_name":"Ballabio, Andrea","last_name":"Ballabio","first_name":"Andrea"},{"full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L"},{"last_name":"Aggarwal","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra","first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb"},{"full_name":"Janik, Marian","last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian"},{"last_name":"Adletzberger","full_name":"Adletzberger, Thomas","first_name":"Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rubén","last_name":"Seoane Souto","full_name":"Seoane Souto, Rubén"},{"first_name":"Martin","full_name":"Leijnse, Martin","last_name":"Leijnse"},{"full_name":"Danon, Jeroen","last_name":"Danon","first_name":"Jeroen"},{"first_name":"Constantin","full_name":"Schrade, Constantin","last_name":"Schrade"},{"first_name":"Erik","last_name":"Bakkers","full_name":"Bakkers, Erik"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"title":"Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium","citation":{"ista":"Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169.","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-023-44114-0.","ieee":"M. Valentini et al., “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” Nature Communications, vol. 15. Springer Nature, 2024.","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","apa":"Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-44114-0","ama":"Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 2024;15. doi:10.1038/s41467-023-44114-0","mla":"Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” Nature Communications, vol. 15, 169, Springer Nature, 2024, doi:10.1038/s41467-023-44114-0."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 15","month":"01","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on the same silicon technology compatible platform.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":15,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"checksum":"ef79173b45eeaf984ffa61ef2f8a52ab","file_id":"14825","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-01-17T11:03:00Z","file_name":"2024_NatureComm_Valentini.pdf","creator":"dernst","date_updated":"2024-01-17T11:03:00Z","file_size":2336595}],"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","_id":"14793","file_date_updated":"2024-01-17T11:03:00Z","department":[{"_id":"GeKa"}],"date_updated":"2024-01-17T11:07:55Z","ddc":["530"]},{"date_created":"2024-01-14T23:00:57Z","doi":"10.1007/s00440-023-01254-0","date_published":"2024-01-04T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Probability Theory and Related Fields","day":"04","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"NC has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No 948819).\r\nFM is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the SPP 2265 Random Geometric Systems. FM has been funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC 2044 -390685587, Mathematics Münster: Dynamics–Geometry–Structure. FM has been funded by the Max Planck Institute for Mathematics in the Sciences.","external_id":{"arxiv":["2303.00353"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas","last_name":"Clozeau"},{"first_name":"Francesco","full_name":"Mattesini, Francesco","last_name":"Mattesini"}],"title":"Annealed quantitative estimates for the quadratic 2D-discrete random matching problem","citation":{"short":"N. Clozeau, F. Mattesini, Probability Theory and Related Fields (2024).","ieee":"N. Clozeau and F. Mattesini, “Annealed quantitative estimates for the quadratic 2D-discrete random matching problem,” Probability Theory and Related Fields. Springer Nature, 2024.","ama":"Clozeau N, Mattesini F. Annealed quantitative estimates for the quadratic 2D-discrete random matching problem. Probability Theory and Related Fields. 2024. doi:10.1007/s00440-023-01254-0","apa":"Clozeau, N., & Mattesini, F. (2024). Annealed quantitative estimates for the quadratic 2D-discrete random matching problem. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01254-0","mla":"Clozeau, Nicolas, and Francesco Mattesini. “Annealed Quantitative Estimates for the Quadratic 2D-Discrete Random Matching Problem.” Probability Theory and Related Fields, Springer Nature, 2024, doi:10.1007/s00440-023-01254-0.","ista":"Clozeau N, Mattesini F. 2024. Annealed quantitative estimates for the quadratic 2D-discrete random matching problem. Probability Theory and Related Fields.","chicago":"Clozeau, Nicolas, and Francesco Mattesini. “Annealed Quantitative Estimates for the Quadratic 2D-Discrete Random Matching Problem.” Probability Theory and Related Fields. Springer Nature, 2024. https://doi.org/10.1007/s00440-023-01254-0."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"ec_funded":1,"publication_status":"epub_ahead","publication_identifier":{"issn":["0178-8051"],"eissn":["1432-2064"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1007/s00440-023-01254-0","open_access":"1"}],"scopus_import":"1","month":"01","abstract":[{"lang":"eng","text":"We study a random matching problem on closed compact 2 -dimensional Riemannian manifolds (with respect to the squared Riemannian distance), with samples of random points whose common law is absolutely continuous with respect to the volume measure with strictly positive and bounded density. We show that given two sequences of numbers n and m=m(n) of points, asymptotically equivalent as n goes to infinity, the optimal transport plan between the two empirical measures μn and νm is quantitatively well-approximated by (Id,exp(∇hn))#μn where hn solves a linear elliptic PDE obtained by a regularized first-order linearization of the Monge-Ampère equation. This is obtained in the case of samples of correlated random points for which a stretched exponential decay of the α -mixing coefficient holds and for a class of discrete-time Markov chains having a unique absolutely continuous invariant measure with respect to the volume measure."}],"oa_version":"Published Version","department":[{"_id":"JuFi"}],"date_updated":"2024-01-17T11:18:34Z","ddc":["510"],"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":"14797"},{"publication":"STAR Protocols","day":"01","year":"2024","date_created":"2024-01-14T23:00:56Z","doi":"10.1016/j.xpro.2023.102795","date_published":"2024-01-01T00:00:00Z","acknowledgement":"We thank Florian Pauler for discussion and his expert technical support. This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging and Optics Facility (IOF) and Preclinical Facility (PCF). A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences.","oa":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102795.","ista":"Hansen AH, Hippenmeyer S. 2024. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 5(1), 102795.","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 5, no. 1, 102795, Elsevier, 2024, doi:10.1016/j.xpro.2023.102795.","apa":"Hansen, A. H., & Hippenmeyer, S. (2024). Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102795","ama":"Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 2024;5(1). doi:10.1016/j.xpro.2023.102795","short":"A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024).","ieee":"A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers,” STAR Protocols, vol. 5, no. 1. Elsevier, 2024."},"title":"Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers","article_processing_charge":"Yes","external_id":{"pmid":["38165800"]},"author":[{"last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"article_number":"102795","project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["2666-1667"]},"volume":5,"issue":"1","related_material":{"link":[{"url":"http://github.com/hippenmeyerlab","relation":"software"}]},"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"intvolume":" 5","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.xpro.2023.102795"}],"scopus_import":"1","date_updated":"2024-01-17T10:32:31Z","department":[{"_id":"SiHi"}],"_id":"14794","status":"public","type":"journal_article","article_type":"review"},{"abstract":[{"lang":"eng","text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 187","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"publication_status":"published","file":[{"success":1,"file_id":"14874","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2024_Cell_Kuhn.pdf","date_created":"2024-01-22T13:41:41Z","creator":"dernst","file_size":13194060,"date_updated":"2024-01-22T13:41:41Z"}],"language":[{"iso":"eng"}],"volume":187,"issue":"1","ec_funded":1,"_id":"14826","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_updated":"2024-01-22T13:43:40Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2024-01-22T13:41:41Z","acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","quality_controlled":"1","publisher":"Elsevier","oa":1,"has_accepted_license":"1","year":"2024","day":"04","publication":"Cell","page":"130-148.e17","date_published":"2024-01-04T00:00:00Z","doi":"10.1016/j.cell.2023.11.021","date_created":"2024-01-17T12:45:40Z","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}],"citation":{"chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell. Elsevier, 2024. https://doi.org/10.1016/j.cell.2023.11.021.","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:10.1016/j.cell.2023.11.021.","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","ieee":"A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"last_name":"Mutte","full_name":"Mutte, Sumanth","first_name":"Sumanth"},{"first_name":"Shiv Mani","last_name":"Dubey","full_name":"Dubey, Shiv Mani"},{"first_name":"Vanessa Polet","last_name":"Carrillo Carrasco","full_name":"Carrillo Carrasco, Vanessa Polet"},{"last_name":"Boeren","full_name":"Boeren, Sjef","first_name":"Sjef"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"full_name":"Koehorst, Jasper","last_name":"Koehorst","first_name":"Jasper"},{"first_name":"Takayuki","last_name":"Kohchi","full_name":"Kohchi, Takayuki"},{"full_name":"Nishihama, Ryuichi","last_name":"Nishihama","first_name":"Ryuichi"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"last_name":"Sprakel","full_name":"Sprakel, Joris","first_name":"Joris"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38128538"]},"title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response"},{"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.","lang":"eng"}],"month":"01","intvolume":" 103","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.ejcb.2023.151380","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0171-9335"]},"publication_status":"epub_ahead","volume":103,"issue":"1","_id":"14834","status":"public","keyword":["Cell Biology","General Medicine","Histology","Pathology and Forensic Medicine"],"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)"},"ddc":["570"],"date_updated":"2024-01-23T08:37:13Z","department":[{"_id":"MaLo"}],"acknowledgement":"We acknowledge members of the Loose laboratory at ISTA for helpful discussions—in particular M. Kojic for his insightful comments. This work was supported by the Austrian Science Fund (FWF P34607) to M.L.","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"12","publication":"European Journal of Cell Biology","has_accepted_license":"1","year":"2024","doi":"10.1016/j.ejcb.2023.151380","date_published":"2024-01-12T00:00:00Z","date_created":"2024-01-18T08:16:43Z","article_number":"151380","project":[{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology, vol. 103, no. 1, 151380, Elsevier, 2024, doi:10.1016/j.ejcb.2023.151380.","ieee":"P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches,” European Journal of Cell Biology, vol. 103, no. 1. Elsevier, 2024.","short":"P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).","apa":"Radler, P., & Loose, M. (2024). A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2023.151380","ama":"Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 2024;103(1). doi:10.1016/j.ejcb.2023.151380","chicago":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology. Elsevier, 2024. https://doi.org/10.1016/j.ejcb.2023.151380.","ista":"Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 103(1), 151380."},"title":"A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches","author":[{"orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"pmid":["38218128"]}},{"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous referee for the constructive feedback that helped to improve the manuscript. We thank Michael Maseda, Daniel Schaerer, Charlotte Simmonds, and Rashmi Gottumukkala for useful comments and productive discussions. We also thank the organizers and participants of the 24th MUSE Science Busy Week in Leiden. IGK acknowledges an Excellence Master Fellowship granted by the Faculty of Science of the University of Geneva. 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 number 200020_207349 and SNSF Professorship grant number 190079. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant number 140. This paper is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240, 096.A-0090, 097.A-0160, and 098.A-0017. We made extensive use of several open-source software packages and we are thankful to the respective authors for sharing their work: NUMPY (Harris et al. 2020), ASTROPY (Astropy Collaboration 2022), MATPLOTLIB (Hunter 2007), IPYTHON (Perez & Granger 2007), and TOPCAT (Taylor 2005).","page":"9853-9871","date_created":"2024-01-22T08:22:17Z","doi":"10.1093/mnras/stad3853","date_published":"2024-02-01T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","external_id":{"arxiv":["2305.07044"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4","first_name":"Ivan","full_name":"Kramarenko, Ivan","last_name":"Kramarenko"},{"full_name":"Kerutt, J","last_name":"Kerutt","first_name":"J"},{"last_name":"Verhamme","full_name":"Verhamme, A","first_name":"A"},{"first_name":"P A","full_name":"Oesch, P A","last_name":"Oesch"},{"first_name":"L","last_name":"Barrufet","full_name":"Barrufet, L"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"last_name":"Kusakabe","full_name":"Kusakabe, H","first_name":"H"},{"first_name":"I","full_name":"Goovaerts, I","last_name":"Goovaerts"},{"first_name":"T T","full_name":"Thai, T T","last_name":"Thai"}],"title":"Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape","citation":{"chicago":"Kramarenko, Ivan, J Kerutt, A Verhamme, P A Oesch, L Barrufet, Jorryt J Matthee, H Kusakabe, I Goovaerts, and T T Thai. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stad3853.","ista":"Kramarenko I, Kerutt J, Verhamme A, Oesch PA, Barrufet L, Matthee JJ, Kusakabe H, Goovaerts I, Thai TT. 2024. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 527(4), 9853–9871.","mla":"Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:10.1093/mnras/stad3853.","short":"I. Kramarenko, J. Kerutt, A. Verhamme, P.A. Oesch, L. Barrufet, J.J. Matthee, H. Kusakabe, I. Goovaerts, T.T. Thai, Monthly Notices of the Royal Astronomical Society 527 (2024) 9853–9871.","ieee":"I. Kramarenko et al., “Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape,” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4. Oxford University Press, pp. 9853–9871, 2024.","apa":"Kramarenko, I., Kerutt, J., Verhamme, A., Oesch, P. A., Barrufet, L., Matthee, J. J., … Thai, T. T. (2024). Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad3853","ama":"Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 2024;527(4):9853-9871. doi:10.1093/mnras/stad3853"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 527","month":"02","abstract":[{"text":"The physical conditions giving rise to high escape fractions of ionizing radiation (LyC fesc) in star-forming galaxies – most likely protagonists of cosmic reionization – are not yet fully understood. Using the VLT/MUSE observations of ∼1400 Ly α emitters at 2.9 < z < 6.7, we compare stacked rest-frame UV spectra of candidates for LyC leakers and non-leakers selected based on their Ly α profiles. We find that the stacks of potential LyC leakers, i.e. galaxies with narrow, symmetric Ly α profiles with small peak separation, generally show (i) strong nebular O iii]λ1666, [Si iii]λ1883, and [C iii]λ1907 +C iii]λ1909 emission, indicating a high-ionization state of the interstellar medium (ISM); (ii) high equivalent widths of He iiλ1640 (∼1 − 3 Å), suggesting the presence of hard ionizing radiation fields; (iii) Si ii*λ1533 emission, revealing substantial amounts of neutral hydrogen off the line of sight; (iv) high C ivλλ1548,1550 to [C iii]λ1907 +C iii]λ1909 ratios (C iv/C iii] ≳0.75) , signalling the presence of low column density channels in the ISM. In contrast, the stacks with broad, asymmetric Ly α profiles with large peak separation show weak nebular emission lines, low He iiλ1640 equivalent widths (≲1 Å), and low C iv/C iii] (≲0.25), implying low-ionization states and high-neutral hydrogen column densities. Our results suggest that C iv/C iii] might be sensitive to the physical conditions that govern LyC photon escape, providing a promising tool for identification of ionizing sources among star-forming galaxies in the epoch of reionization.","lang":"eng"}],"oa_version":"Published Version","issue":"4","volume":527,"publication_status":"published","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9d02df4035c4951cf63dee0db1e462e9","file_id":"14879","success":1,"creator":"dernst","date_updated":"2024-01-23T12:30:45Z","file_size":4521738,"date_created":"2024-01-23T12:30:45Z","file_name":"2024_MNAstronomSoc_Kramarenko.pdf"}],"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","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","_id":"14852","department":[{"_id":"GradSch"},{"_id":"JoMa"}],"file_date_updated":"2024-01-23T12:30:45Z","date_updated":"2024-01-23T12:33:50Z","ddc":["520"]},{"has_accepted_license":"1","year":"2024","day":"10","publication":"Journal of Experimental Biology","doi":"10.1242/jeb.246217","date_published":"2024-01-10T00:00:00Z","date_created":"2024-01-22T08:14:49Z","acknowledgement":"We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions, and help with sampling and colour analyses. We thank Muralidhar and the central LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch funding was provided by the Department of Science and Technology Fund for Improvement of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute of Science (DBT-IISc) partnership program and a Science and Engineering Research Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian Institute of Science. Deposited in PMC for immediate release.","publisher":"The Company of Biologists","quality_controlled":"1","oa":1,"citation":{"chicago":"Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal of Experimental Biology. The Company of Biologists, 2024. https://doi.org/10.1242/jeb.246217.","ista":"Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 227(1), jeb246217.","mla":"Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal of Experimental Biology, vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:10.1242/jeb.246217.","ama":"Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 2024;227(1). doi:10.1242/jeb.246217","apa":"Pal, A., Joshi, M., & Thaker, M. (2024). Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.246217","short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","ieee":"A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite levels using more signal modalities than females utilise,” Journal of Experimental Biology, vol. 227, no. 1. The Company of Biologists, 2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"full_name":"Joshi, Mihir","last_name":"Joshi","first_name":"Mihir"},{"first_name":"Maria","full_name":"Thaker, Maria","last_name":"Thaker"}],"external_id":{"pmid":["38054353"]},"article_processing_charge":"Yes (via OA deal)","title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","article_number":"jeb246217","publication_identifier":{"eissn":["0022-0949"],"issn":["1477-9145"]},"publication_status":"published","file":[{"checksum":"136325372f6f45abaa62a71e2d23bfb6","file_id":"14877","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-01-23T12:08:24Z","file_name":"2024_JourExperimBiology_Pal.pdf","creator":"dernst","date_updated":"2024-01-23T12:08:24Z","file_size":594128}],"language":[{"iso":"eng"}],"volume":227,"related_material":{"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"issue":"1","abstract":[{"lang":"eng","text":"Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals."}],"pmid":1,"oa_version":"Published Version","month":"01","intvolume":" 227","date_updated":"2024-01-23T12:13:08Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2024-01-23T12:08:24Z","_id":"14850","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","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"]},{"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2024-01-19T00:00:00Z","doi":"10.15479/at:ista:14711","date_created":"2023-12-26T22:49:53Z","page":"183","day":"19","has_accepted_license":"1","year":"2024","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation"}],"title":"Local adaptation, genetic load and extinction in metapopulations","author":[{"last_name":"Olusanya","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711","apa":"Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","mla":"Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711."},"month":"01","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management."}],"acknowledged_ssus":[{"_id":"SSU"}],"related_material":{"record":[{"id":"10658","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10787"},{"relation":"part_of_dissertation","status":"public","id":"14732"}]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file":[{"creator":"oolusany","date_updated":"2024-01-03T18:30:13Z","file_size":16986244,"date_created":"2024-01-03T18:30:13Z","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"de179b1c6758f182ff0c70d8b38c1501","file_id":"14730"},{"date_updated":"2024-01-03T18:31:34Z","file_size":6460403,"creator":"oolusany","date_created":"2024-01-03T18:31:34Z","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0e331585e3cd4823320aab4e69e64ccf","file_id":"14731","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","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)"},"_id":"14711","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"file_date_updated":"2024-01-03T18:31:34Z","ddc":["576"],"supervisor":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka"},{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"date_updated":"2024-01-26T12:00:54Z"},{"citation":{"chicago":"De Nooijer, Phoebe, Soeren Terziadis, Alexandra Weinberger, Zuzana Masárová, Tamara Mchedlidze, Maarten Löffler, and Günter Rote. “Removing Popular Faces in Curve Arrangements.” In 31st International Symposium on Graph Drawing and Network Visualization, 14466:18–33. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49275-4_2.","ista":"De Nooijer P, Terziadis S, Weinberger A, Masárová Z, Mchedlidze T, Löffler M, Rote G. 2024. Removing popular faces in curve arrangements. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14466, 18–33.","mla":"De Nooijer, Phoebe, et al. “Removing Popular Faces in Curve Arrangements.” 31st International Symposium on Graph Drawing and Network Visualization, vol. 14466, Springer Nature, 2024, pp. 18–33, doi:10.1007/978-3-031-49275-4_2.","ieee":"P. De Nooijer et al., “Removing popular faces in curve arrangements,” in 31st International Symposium on Graph Drawing and Network Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14466, pp. 18–33.","short":"P. De Nooijer, S. Terziadis, A. Weinberger, Z. Masárová, T. Mchedlidze, M. Löffler, G. Rote, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 18–33.","ama":"De Nooijer P, Terziadis S, Weinberger A, et al. Removing popular faces in curve arrangements. In: 31st International Symposium on Graph Drawing and Network Visualization. Vol 14466. Springer Nature; 2024:18-33. doi:10.1007/978-3-031-49275-4_2","apa":"De Nooijer, P., Terziadis, S., Weinberger, A., Masárová, Z., Mchedlidze, T., Löffler, M., & Rote, G. (2024). Removing popular faces in curve arrangements. In 31st International Symposium on Graph Drawing and Network Visualization (Vol. 14466, pp. 18–33). Isola delle Femmine, Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49275-4_2"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"De Nooijer","full_name":"De Nooijer, Phoebe","first_name":"Phoebe"},{"full_name":"Terziadis, Soeren","last_name":"Terziadis","first_name":"Soeren"},{"full_name":"Weinberger, Alexandra","last_name":"Weinberger","first_name":"Alexandra"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana","last_name":"Masárová"},{"first_name":"Tamara","full_name":"Mchedlidze, Tamara","last_name":"Mchedlidze"},{"first_name":"Maarten","last_name":"Löffler","full_name":"Löffler, Maarten"},{"full_name":"Rote, Günter","last_name":"Rote","first_name":"Günter"}],"article_processing_charge":"No","external_id":{"arxiv":["2202.12175"]},"title":"Removing popular faces in curve arrangements","year":"2024","day":"06","publication":"31st International Symposium on Graph Drawing and Network Visualization","page":"18-33","doi":"10.1007/978-3-031-49275-4_2","date_published":"2024-01-06T00:00:00Z","date_created":"2024-01-28T23:01:43Z","acknowledgement":"This work was initiated at the 16th European Research Week on Geometric Graphs in Strobl in 2019. A.W. is supported by the Austrian Science Fund (FWF): W1230. S.T. has been funded by the Vienna Science and Technology Fund (WWTF) [10.47379/ICT19035]. A preliminary version of this work has been presented at the 38th European Workshop on Computational Geometry (EuroCG 2022) in Perugia [9]. A full version of this paper, which includes appendices but is otherwise identical, is available as a technical report [10].","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2024-01-29T09:45:06Z","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"_id":"14888","type":"conference","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2023-09-22","location":"Isola delle Femmine, Palermo, Italy","start_date":"2023-09-20"},"status":"public","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031492747"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":14466,"abstract":[{"lang":"eng","text":"A face in a curve arrangement is called popular if it is bounded by the same curve multiple times. Motivated by the automatic generation of curved nonogram puzzles, we investigate possibilities to eliminate the popular faces in an arrangement by inserting a single additional curve. This turns out to be NP-hard; however, it becomes tractable when the number of popular faces is small: We present a probabilistic FPT-approach in the number of popular faces."}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2202.12175"}],"month":"01","intvolume":" 14466"},{"external_id":{"isi":["001145442300001"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Feitosa Tomé, Douglas","last_name":"Feitosa Tomé","first_name":"Douglas","id":"0eed2d40-3d48-11ec-8d38-f789cc2e40b2"},{"first_name":"Ying","last_name":"Zhang","full_name":"Zhang, Ying"},{"first_name":"Tomomi","full_name":"Aida, Tomomi","last_name":"Aida"},{"last_name":"Mosto","full_name":"Mosto, Olivia","first_name":"Olivia"},{"full_name":"Lu, Yifeng","last_name":"Lu","first_name":"Yifeng"},{"last_name":"Chen","full_name":"Chen, Mandy","first_name":"Mandy"},{"full_name":"Sadeh, Sadra","last_name":"Sadeh","first_name":"Sadra"},{"last_name":"Roy","full_name":"Roy, Dheeraj S.","first_name":"Dheeraj S."},{"last_name":"Clopath","full_name":"Clopath, Claudia","first_name":"Claudia"}],"title":"Dynamic and selective engrams emerge with memory consolidation","citation":{"chicago":"Feitosa Tomé, Douglas, Ying Zhang, Tomomi Aida, Olivia Mosto, Yifeng Lu, Mandy Chen, Sadra Sadeh, Dheeraj S. Roy, and Claudia Clopath. “Dynamic and Selective Engrams Emerge with Memory Consolidation.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-023-01551-w.","ista":"Feitosa Tomé D, Zhang Y, Aida T, Mosto O, Lu Y, Chen M, Sadeh S, Roy DS, Clopath C. 2024. Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience.","mla":"Feitosa Tomé, Douglas, et al. “Dynamic and Selective Engrams Emerge with Memory Consolidation.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-023-01551-w.","apa":"Feitosa Tomé, D., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., … Clopath, C. (2024). Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01551-w","ama":"Feitosa Tomé D, Zhang Y, Aida T, et al. Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience. 2024. doi:10.1038/s41593-023-01551-w","ieee":"D. Feitosa Tomé et al., “Dynamic and selective engrams emerge with memory consolidation,” Nature Neuroscience. Springer Nature, 2024.","short":"D. Feitosa Tomé, Y. Zhang, T. Aida, O. Mosto, Y. Lu, M. Chen, S. Sadeh, D.S. Roy, C. Clopath, Nature Neuroscience (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank S. Erisken from Inscopix for helping us establish in vivo one-photon calcium imaging for this work. We thank K. Su at Tsinghua University for assistance with this work. This work was funded by the President’s PhD Scholarship from Imperial College London (D.F.T.), the Wellcome Trust (225412/Z/22/Z) (S.S.), the Biotechnology and Biological Sciences Research Council (BB/N013956/1 and BB/N019008/1) (C.C.), the Wellcome Trust (200790/Z/16/Z) (C.C.), the Simons Foundation (564408) (C.C.) and the Engineering and Physical Sciences Research Council (EP/R035806/1) (CC). The School of Life Sciences and the IDG/McGovern Institute for Brain Research supported Y.Z. The Warren Alpert Distinguished Scholar Award and National Institutes of Health 1K99NS125131-01 supported D.S.R.","date_created":"2024-01-28T23:01:43Z","date_published":"2024-01-19T00:00:00Z","doi":"10.1038/s41593-023-01551-w","year":"2024","isi":1,"publication":"Nature Neuroscience","day":"19","article_type":"original","type":"journal_article","status":"public","_id":"14887","department":[{"_id":"TiVo"}],"date_updated":"2024-01-29T09:22:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-023-01551-w"}],"scopus_import":"1","month":"01","abstract":[{"text":"Episodic memories are encoded by experience-activated neuronal ensembles that remain necessary and sufficient for recall. However, the temporal evolution of memory engrams after initial encoding is unclear. In this study, we employed computational and experimental approaches to examine how the neural composition and selectivity of engrams change with memory consolidation. Our spiking neural network model yielded testable predictions: memories transition from unselective to selective as neurons drop out of and drop into engrams; inhibitory activity during recall is essential for memory selectivity; and inhibitory synaptic plasticity during memory consolidation is critical for engrams to become selective. Using activity-dependent labeling, longitudinal calcium imaging and a combination of optogenetic and chemogenetic manipulations in mouse dentate gyrus, we conducted contextual fear conditioning experiments that supported our model’s predictions. Our results reveal that memory engrams are dynamic and that changes in engram composition mediated by inhibitory plasticity are crucial for the emergence of memory selectivity.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"14892","status":"public","relation":"research_data"}]},"publication_status":"epub_ahead","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"language":[{"iso":"eng"}]},{"date_published":"2024-01-08T00:00:00Z","doi":"10.1016/j.xplc.2023.100669","date_created":"2023-09-01T11:32:02Z","day":"08","publication":"Plant Communications","has_accepted_license":"1","year":"2024","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"This work was supported by the ERC grant (PR1023ERC02) to H. T. and J. F., and by the ministry of science and technology (grant number 110-2636-B-005-001) to K. J. L.","title":"Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution","author":[{"id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","first_name":"Han","orcid":"0000-0001-6152-6637","full_name":"Tang, Han","last_name":"Tang"},{"first_name":"KJ","last_name":"Lu","full_name":"Lu, KJ"},{"first_name":"Y","full_name":"Zhang, Y","last_name":"Zhang"},{"last_name":"Cheng","full_name":"Cheng, YL","first_name":"YL"},{"first_name":"SL","last_name":"Tu","full_name":"Tu, SL"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"article_processing_charge":"Yes","external_id":{"pmid":["37528584"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Tang, Han, KJ Lu, Y Zhang, YL Cheng, SL Tu, and Jiří Friml. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” Plant Communications. Elsevier, 2024. https://doi.org/10.1016/j.xplc.2023.100669.","ista":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. 2024. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 5(1), 100669.","mla":"Tang, Han, et al. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” Plant Communications, vol. 5, no. 1, 100669, Elsevier, 2024, doi:10.1016/j.xplc.2023.100669.","ama":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 2024;5(1). doi:10.1016/j.xplc.2023.100669","apa":"Tang, H., Lu, K., Zhang, Y., Cheng, Y., Tu, S., & Friml, J. (2024). Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2023.100669","short":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, J. Friml, Plant Communications 5 (2024).","ieee":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, and J. Friml, “Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution,” Plant Communications, vol. 5, no. 1. Elsevier, 2024."},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"100669","issue":"1","volume":5,"ec_funded":1,"file":[{"creator":"dernst","file_size":2825565,"date_updated":"2024-01-30T12:59:57Z","file_name":"2023_PlantCommunications_Tang.pdf","date_created":"2024-01-30T12:59:57Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"edbc44c6d4a394d2bf70f92fdbb08f0a","file_id":"14911"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2590-3462"]},"publication_status":"published","month":"01","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms.","lang":"eng"}],"department":[{"_id":"JiFr"}],"file_date_updated":"2024-01-30T12:59:57Z","ddc":["580"],"date_updated":"2024-01-30T13:00:47Z","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)"},"_id":"14251"},{"ddc":["530"],"date_updated":"2024-01-31T12:01:16Z","file_date_updated":"2024-01-31T11:59:30Z","department":[{"_id":"ZhAl"}],"_id":"14886","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":"2024-01-31T11:59:30Z","file_name":"2024_PhysicalReviewResearch_Lorenc.pdf","date_updated":"2024-01-31T11:59:30Z","file_size":2863627,"creator":"dernst","checksum":"42d58f93ae74e7f2c4de058ef75ff8b2","file_id":"14918","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["2643-1564"]},"volume":6,"issue":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"It is a basic principle that an effect cannot come before the cause. Dispersive relations that follow from this fundamental fact have proven to be an indispensable tool in physics and engineering. They are most powerful in the domain of linear response where they are known as Kramers-Kronig relations. However, when it comes to nonlinear phenomena the implications of causality are much less explored, apart from several notable exceptions. Here in this paper we demonstrate how to apply the dispersive formalism to analyze the ultrafast nonlinear response in the context of the paradigmatic nonlinear Kerr effect. We find that the requirement of causality introduces a noticeable effect even under assumption that Kerr effect is mediated by quasi-instantaneous off-resonant electronic hyperpolarizability. We confirm this by experimentally measuring the time-resolved Kerr dynamics in GaAs by means of a hybrid pump-probe Mach-Zehnder interferometer and demonstrate the presence of an intrinsic lagging between amplitude and phase responses as predicted by dispersive analysis. Our results describe a general property of the time-resolved nonlinear processes thereby highlighting the importance of accounting for dispersive effects in the nonlinear optical processes involving ultrashort pulses."}],"intvolume":" 6","month":"01","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Lorenc, D., & Alpichshev, Z. (2024). Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013042","ama":"Lorenc D, Alpichshev Z. Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013042","ieee":"D. Lorenc and Z. Alpichshev, “Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","short":"D. Lorenc, Z. Alpichshev, Physical Review Research 6 (2024).","mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Dispersive Effects in Ultrafast Nonlinear Phenomena: The Case of Optical Kerr Effect.” Physical Review Research, vol. 6, no. 1, 013042, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013042.","ista":"Lorenc D, Alpichshev Z. 2024. Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. 6(1), 013042.","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Dispersive Effects in Ultrafast Nonlinear Phenomena: The Case of Optical Kerr Effect.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013042."},"title":"Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect","article_processing_charge":"Yes","author":[{"first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc","full_name":"Lorenc, Dusan"},{"last_name":"Alpichshev","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"article_number":"013042","publication":"Physical Review Research","day":"11","year":"2024","has_accepted_license":"1","date_created":"2024-01-28T23:01:42Z","date_published":"2024-01-11T00:00:00Z","doi":"10.1103/PhysRevResearch.6.013042","acknowledgement":"The work was supported by the Institute of Science and Technology Austria (ISTA). We thank Prof. John M. Dudley, Dr. Ugur Sezer, and Dr. Artem Volosniev for valuable discussions.","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"date_created":"2024-01-30T11:58:02Z","doi":"10.5334/ijc.1275","date_published":"2024-01-11T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"International Journal of the Commons","day":"11","oa":1,"quality_controlled":"1","publisher":"Ubiquity Press","acknowledgement":"The authors would like to thank the special issue co-editors, Marco Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped improve the manuscript. The paper also benefited from suggestions by other author participants in this special issue. We would also like to thank the 2022 Santa Fe Institute Complex Systems Summer School for providing space to initiate this study.","article_processing_charge":"Yes","author":[{"first_name":"Keiko","full_name":"Nomura, Keiko","last_name":"Nomura"},{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","first_name":"Simon","full_name":"Rella, Simon","last_name":"Rella"},{"first_name":"Haily","last_name":"Merritt","full_name":"Merritt, Haily"},{"first_name":"Mathieu","last_name":"Baltussen","full_name":"Baltussen, Mathieu"},{"full_name":"Bird, Darcy","last_name":"Bird","first_name":"Darcy"},{"first_name":"Annika","full_name":"Tjuka, Annika","last_name":"Tjuka"},{"first_name":"Dan","full_name":"Falk, Dan","last_name":"Falk"}],"title":"Tipping points of space debris in low earth orbit","citation":{"chicago":"Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons. Ubiquity Press, 2024. https://doi.org/10.5334/ijc.1275.","ista":"Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024. Tipping points of space debris in low earth orbit. International Journal of the Commons. 18(1).","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons, vol. 18, no. 1, Ubiquity Press, 2024, doi:10.5334/ijc.1275.","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., & Falk, D. (2024). Tipping points of space debris in low earth orbit. International Journal of the Commons. Ubiquity Press. https://doi.org/10.5334/ijc.1275","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. International Journal of the Commons. 2024;18(1). doi:10.5334/ijc.1275","ieee":"K. Nomura et al., “Tipping points of space debris in low earth orbit,” International Journal of the Commons, vol. 18, no. 1. Ubiquity Press, 2024.","short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":18,"issue":"1","publication_status":"published","publication_identifier":{"issn":["1875-0281"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"b80ebc889033c365d8f8c05a0c655382","file_id":"14939","success":1,"creator":"dernst","date_updated":"2024-02-05T10:06:35Z","file_size":1305786,"date_created":"2024-02-05T10:06:35Z","file_name":"2023_IntJourCommons_Nomura.pdf"}],"scopus_import":"1","intvolume":" 18","month":"01","abstract":[{"lang":"eng","text":"Global services like navigation, communication, and Earth observation have increased dramatically in the 21st century due to advances in outer space industries. But as orbits become increasingly crowded with both satellites and inevitable space debris pollution, continued operations become endangered by the heightened risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical threshold of orbiting debris triggers a runaway positive feedback loop of debris collisions, creating debris congestion that can render orbits unusable. As this potential tipping point becomes more widely recognized, there have been renewed calls for debris mitigation and removal. Here, we combine complex systems and social-ecological systems approaches to study how these efforts may affect space debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically, we model how debris levels are affected by future launch rates, cleanup activities, and collisions between extant debris. We contextualize and interpret our dynamic model within a discussion of existing space debris governance and other social, economic, and geopolitical factors that may influence effective collective management of the orbital commons. In line with previous studies, our model finds that debris congestion may be reached in less than 200 years, though a holistic management strategy combining removal and mitigation actions can avoid such outcomes while continuing space activities. Moreover, although active debris removal may be particularly effective, the current lack of market and governance support may impede its implementation. Research into these critical dynamics and the multi-faceted variables that influence debris outcomes can support policymakers in curating impactful governance strategies and realistic transition pathways to sustaining debris-free orbits. Overall, our study is useful for communicating about space debris sustainability in policy and education settings by providing an exploration of policy portfolio options supported by a simple and clear social-ecological modeling approach."}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"file_date_updated":"2024-02-05T10:06:35Z","date_updated":"2024-02-05T10:10:27Z","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","keyword":["Sociology and Political Science"],"status":"public","_id":"14901"},{"oa_version":"Preprint","abstract":[{"text":"We perform a stochastic homogenization analysis for composite materials exhibiting a random microstructure. Under the assumptions of stationarity and ergodicity, we characterize the Gamma-limit of a micromagnetic energy functional defined on magnetizations taking value in the unit sphere and including both symmetric and antisymmetric exchange contributions. This Gamma-limit corresponds to a micromagnetic energy functional with homogeneous coefficients. We provide explicit formulas for the effective magnetic properties of the composite material in terms of homogenization correctors. Additionally, the variational analysis of the two exchange energy terms is performed in the more general setting of functionals defined on manifold-valued maps with Sobolev regularity, in the case in which the target manifold is a bounded, orientable smooth surface with tubular neighborhood of uniform thickness. Eventually, we present an explicit characterization of minimizers of the effective exchange in the case of magnetic multilayers, providing quantitative evidence of Dzyaloshinskii’s predictions on the emergence of helical structures in composite ferromagnetic materials with stochastic microstructure.","lang":"eng"}],"intvolume":" 34","month":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.05151","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"volume":34,"issue":"2","_id":"14884","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-02-05T08:54:44Z","department":[{"_id":"JuFi"}],"acknowledgement":"All authors acknowledge support of the Austrian Science Fund (FWF) through the SFB project F65. The research of E. Davoli and L. D’Elia has additionally been supported by the FWF through grants V662, Y1292, and P35359, as well as from OeAD through the WTZ grant CZ09/2023.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Journal of Nonlinear Science","day":"23","year":"2024","date_created":"2024-01-28T23:01:42Z","doi":"10.1007/s00332-023-10005-3","date_published":"2024-01-23T00:00:00Z","article_number":"30","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Davoli E, D’Elia L, Ingmanns J. Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions. Journal of Nonlinear Science. 2024;34(2). doi:10.1007/s00332-023-10005-3","apa":"Davoli, E., D’Elia, L., & Ingmanns, J. (2024). Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-10005-3","ieee":"E. Davoli, L. D’Elia, and J. Ingmanns, “Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions,” Journal of Nonlinear Science, vol. 34, no. 2. Springer Nature, 2024.","short":"E. Davoli, L. D’Elia, J. Ingmanns, Journal of Nonlinear Science 34 (2024).","mla":"Davoli, Elisa, et al. “Stochastic Homogenization of Micromagnetic Energies and Emergence of Magnetic Skyrmions.” Journal of Nonlinear Science, vol. 34, no. 2, 30, Springer Nature, 2024, doi:10.1007/s00332-023-10005-3.","ista":"Davoli E, D’Elia L, Ingmanns J. 2024. Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions. Journal of Nonlinear Science. 34(2), 30.","chicago":"Davoli, Elisa, Lorenza D’Elia, and Jonas Ingmanns. “Stochastic Homogenization of Micromagnetic Energies and Emergence of Magnetic Skyrmions.” Journal of Nonlinear Science. Springer Nature, 2024. https://doi.org/10.1007/s00332-023-10005-3."},"title":"Stochastic homogenization of micromagnetic energies and emergence of magnetic skyrmions","external_id":{"arxiv":["2306.05151"]},"article_processing_charge":"No","author":[{"first_name":"Elisa","last_name":"Davoli","full_name":"Davoli, Elisa"},{"last_name":"D’Elia","full_name":"D’Elia, Lorenza","first_name":"Lorenza"},{"full_name":"Ingmanns, Jonas","last_name":"Ingmanns","first_name":"Jonas","id":"71523d30-15b2-11ec-abd3-f80aa909d6b0"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pimenta-Marques, Ana, Tania Perestrelo, Patricia Dos Reis Rodrigues, Paulo Duarte, Ana Ferreira-Silva, Mariana Lince-Faria, and Mónica Bettencourt-Dias. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” EMBO Reports. Embo Press, 2024. https://doi.org/10.1038/s44319-023-00020-6.","ista":"Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, Duarte P, Ferreira-Silva A, Lince-Faria M, Bettencourt-Dias M. 2024. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO reports. 25(1), 102–127.","mla":"Pimenta-Marques, Ana, et al. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” EMBO Reports, vol. 25, no. 1, Embo Press, 2024, pp. 102–27, doi:10.1038/s44319-023-00020-6.","short":"A. Pimenta-Marques, T. Perestrelo, P. Dos Reis Rodrigues, P. Duarte, A. Ferreira-Silva, M. Lince-Faria, M. Bettencourt-Dias, EMBO Reports 25 (2024) 102–127.","ieee":"A. Pimenta-Marques et al., “Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM,” EMBO reports, vol. 25, no. 1. Embo Press, pp. 102–127, 2024.","ama":"Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, et al. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO reports. 2024;25(1):102-127. doi:10.1038/s44319-023-00020-6","apa":"Pimenta-Marques, A., Perestrelo, T., Dos Reis Rodrigues, P., Duarte, P., Ferreira-Silva, A., Lince-Faria, M., & Bettencourt-Dias, M. (2024). Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO Reports. Embo Press. https://doi.org/10.1038/s44319-023-00020-6"},"title":"Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Pimenta-Marques","full_name":"Pimenta-Marques, Ana","first_name":"Ana"},{"full_name":"Perestrelo, Tania","last_name":"Perestrelo","first_name":"Tania"},{"last_name":"Dos Reis Rodrigues","orcid":"0000-0003-1681-508X","full_name":"Dos Reis Rodrigues, Patricia","first_name":"Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F"},{"last_name":"Duarte","full_name":"Duarte, Paulo","first_name":"Paulo"},{"full_name":"Ferreira-Silva, Ana","last_name":"Ferreira-Silva","first_name":"Ana"},{"full_name":"Lince-Faria, Mariana","last_name":"Lince-Faria","first_name":"Mariana"},{"full_name":"Bettencourt-Dias, Mónica","last_name":"Bettencourt-Dias","first_name":"Mónica"}],"publication":"EMBO reports","day":"10","year":"2024","has_accepted_license":"1","date_created":"2024-02-04T23:00:53Z","date_published":"2024-01-10T00:00:00Z","doi":"10.1038/s44319-023-00020-6","page":"102-127","acknowledgement":"We thank all members of the Cell Cycle and Regulation Lab for the discussions and for the critical reading of the manuscript. We thank Tomer Avidor-Reiss (University of Toledo, Toledo, OH), Daniel St. Johnston (The Gurdon Institute, Cambridge, UK), David Glover (University of Cambridge, Cambridge, UK), Jingyan Fu (Agricultural University, Beijing, China) Jordan Raff (University of Oxford, Oxford, UK) and Timothy Megraw (Florida State University, Tallahassee, FL) for sharing tools. We acknowledge the technical support of Instituto Gulbenkian de Ciência (IGC)‘s Advanced Imaging Facility, in particular Gabriel Martins, Nuno Pimpão Martins and José Marques. We also thank Tiago Paixão from the IGC’s Quantitative & Digital Science Unit and Marco Louro from the CCR lab for the support provided on statistical analysis. IGC’s Advanced Imaging Facility (AIF-UIC) is supported by the national Portuguese funding ref# PPBI-POCI-01-0145-FEDER -022122. We thank the IGC’s Fly Facility, supported by CONGENTO (LISBOA-01-0145-FEDER-022170). This work was supported by an ERC grant (ERC-2015-CoG-683258) awarded to MBD and a grant from the Portuguese Research Council (FCT) awarded to APM (PTDC/BIA-BID/32225/2017).","oa":1,"quality_controlled":"1","publisher":"Embo Press","ddc":["570"],"date_updated":"2024-02-05T12:37:07Z","department":[{"_id":"MiSi"}],"file_date_updated":"2024-02-05T12:35:03Z","_id":"14933","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_updated":"2024-02-05T12:35:03Z","file_size":9645056,"creator":"dernst","date_created":"2024-02-05T12:35:03Z","file_name":"2023_EmboReports_PimentaMarques.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14941","checksum":"53c3ef43d9bd6d7bff3ffcf57d763cac","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1469-3178"]},"issue":"1","volume":25,"oa_version":"Published Version","abstract":[{"text":"Centrioles are part of centrosomes and cilia, which are microtubule organising centres (MTOC) with diverse functions. Despite their stability, centrioles can disappear during differentiation, such as in oocytes, but little is known about the regulation of their structural integrity. Our previous research revealed that the pericentriolar material (PCM) that surrounds centrioles and its recruiter, Polo kinase, are downregulated in oogenesis and sufficient for maintaining both centrosome structural integrity and MTOC activity. We now show that the expression of specific components of the centriole cartwheel and wall, including ANA1/CEP295, is essential for maintaining centrosome integrity. We find that Polo kinase requires ANA1 to promote centriole stability in cultured cells and eggs. In addition, ANA1 expression prevents the loss of centrioles observed upon PCM-downregulation. However, the centrioles maintained by overexpressing and tethering ANA1 are inactive, unlike the MTOCs observed upon tethering Polo kinase. These findings demonstrate that several centriole components are needed to maintain centrosome structure. Our study also highlights that centrioles are more dynamic than previously believed, with their structural stability relying on the continuous expression of multiple components.","lang":"eng"}],"intvolume":" 25","month":"01","scopus_import":"1"},{"title":"Antler allometry, the Irish elk and Gould revisited","department":[{"_id":"MaRo"}],"author":[{"full_name":"Tsuboi, Masahito","last_name":"Tsuboi","first_name":"Masahito"},{"first_name":"Bjørn Tore","last_name":"Kopperud","full_name":"Kopperud, Bjørn Tore"},{"first_name":"Michael","full_name":"Matschiner, Michael","last_name":"Matschiner"},{"first_name":"Mark","last_name":"Grabowski","full_name":"Grabowski, Mark"},{"last_name":"Syrowatka","full_name":"Syrowatka, Chrsitine","id":"205ffb76-7fe7-11eb-aa17-958bd11b99ad","first_name":"Chrsitine"},{"last_name":"Pélabon","full_name":"Pélabon, Christophe","first_name":"Christophe"},{"full_name":"Hansen, Thomas F.","last_name":"Hansen","first_name":"Thomas F."}],"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-05T12:43:58Z","citation":{"short":"M. Tsuboi, B.T. Kopperud, M. Matschiner, M. Grabowski, C. Syrowatka, C. Pélabon, T.F. Hansen, Evolutionary Biology (2024).","ieee":"M. Tsuboi et al., “Antler allometry, the Irish elk and Gould revisited,” Evolutionary Biology. Springer Nature, 2024.","apa":"Tsuboi, M., Kopperud, B. T., Matschiner, M., Grabowski, M., Syrowatka, C., Pélabon, C., & Hansen, T. F. (2024). Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. Springer Nature. https://doi.org/10.1007/s11692-023-09624-1","ama":"Tsuboi M, Kopperud BT, Matschiner M, et al. Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. 2024. doi:10.1007/s11692-023-09624-1","mla":"Tsuboi, Masahito, et al. “Antler Allometry, the Irish Elk and Gould Revisited.” Evolutionary Biology, Springer Nature, 2024, doi:10.1007/s11692-023-09624-1.","ista":"Tsuboi M, Kopperud BT, Matschiner M, Grabowski M, Syrowatka C, Pélabon C, Hansen TF. 2024. Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology.","chicago":"Tsuboi, Masahito, Bjørn Tore Kopperud, Michael Matschiner, Mark Grabowski, Chrsitine Syrowatka, Christophe Pélabon, and Thomas F. Hansen. “Antler Allometry, the Irish Elk and Gould Revisited.” Evolutionary Biology. Springer Nature, 2024. https://doi.org/10.1007/s11692-023-09624-1."},"status":"public","article_type":"original","type":"journal_article","_id":"14932","date_published":"2024-01-29T00:00:00Z","doi":"10.1007/s11692-023-09624-1","date_created":"2024-02-04T23:00:53Z","day":"29","language":[{"iso":"eng"}],"publication":"Evolutionary Biology","publication_identifier":{"eissn":["1934-2845"],"issn":["0071-3260"]},"publication_status":"epub_ahead","year":"2024","month":"01","quality_controlled":"1","publisher":"Springer Nature","scopus_import":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s11692-023-09624-1","open_access":"1"}],"oa_version":"Published Version","acknowledgement":"Open access funding provided by University of Oslo (incl Oslo University Hospital).\r\nWe thank Adrian Lister, Louis Tomsett, Roberto Portela Miguez and Roula Pappa (NHMUK), Brian O'Toole and Eileen Westwig (AMNH), Daniela Kalthoff (NHRM), Alexander Bibl and Zachos Frank (NHMW), Darrin Lunde and John Ososky (NMNH), Matthew Parkes and Nigel Monaghan (NMI), Elizabetta Cioppi and Luca Bellucci (IGF), and Yoshihiro Tanaka and Hiroyuki Taruno (OMNH), who helped us in obtaining the museum data, and a special thanks to Jørgen Sikkeland (NTNU NHM) for assistance in obtaining the ontogenetic data for the red deer. We thank Olja Toljagic and Kjetil L. Voje for discussions, Ayumu Tsuboi for assistance with data collection, and Jean-Michel Gaillard and the anonymous reviewers for comments on the manuscript. We thank the Centre of Advanced Study (CAS) at the Norwegian Academy of Sciences and Letters for hosting us during the academic year of 2019/2020 when much of the analysis and writing were done. MT was funded by JSPS Research Fellowship for Young Scientists (201603238).","abstract":[{"lang":"eng","text":"The huge antlers of the extinct Irish elk have invited evolutionary speculation since Darwin. In the 1970s, Stephen Jay Gould presented the first extensive data on antler size in the Irish elk and combined these with comparative data from other deer to test the hypothesis that the gigantic antlers were the outcome of a positive allometry that constrained large-bodied deer to have proportionally even larger antlers. He concluded that the Irish elk had antlers as predicted for its size and interpreted this within his emerging framework of developmental constraints as an explanatory factor in evolution. Here we reanalyze antler allometry based on new morphometric data for 57 taxa of the family Cervidae. We also present a new phylogeny for the Cervidae, which we use for comparative analyses. In contrast to Gould, we find that the antlers of Irish elk were larger than predicted from the allometry within the true deer, Cervini, as analyzed by Gould, but follow the allometry across Cervidae as a whole. After dissecting the discrepancy, we reject the allometric-constraint hypothesis because, contrary to Gould, we find no similarity between static and evolutionary allometries, and because we document extensive non-allometric evolution of antler size across the Cervidae."}]},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s11118-023-10118-0"}],"publisher":"Springer Nature","scopus_import":"1","quality_controlled":"1","month":"01","abstract":[{"lang":"eng","text":"We study random perturbations of a Riemannian manifold (M, g) by means of so-called\r\nFractional Gaussian Fields, which are defined intrinsically by the given manifold. The fields\r\nh• : ω \u0002→ hω will act on the manifold via the conformal transformation g \u0002→ gω := e2hω g.\r\nOur focus will be on the regular case with Hurst parameter H > 0, the critical case H = 0\r\nbeing the celebrated Liouville geometry in two dimensions. We want to understand how basic\r\ngeometric and functional-analytic quantities like diameter, volume, heat kernel, Brownian\r\nmotion, spectral bound, or spectral gap change under the influence of the noise. And if so, is\r\nit possible to quantify these dependencies in terms of key parameters of the noise? Another\r\ngoal is to define and analyze in detail the Fractional Gaussian Fields on a general Riemannian\r\nmanifold, a fascinating object of independent interest."}],"acknowledgement":"The authors would like to thank Matthias Erbar and Ronan Herry for valuable discussions on this project. They are also grateful to Nathanaël Berestycki, and Fabrice Baudoin for respectively pointing out the references [7], and [6, 24], and to Julien Fageot and Thomas Letendre for pointing out a mistake in a previous version of the proof of Proposition 3.10. The authors feel very much indebted to an anonymous reviewer for his/her careful reading and the many valuable suggestions that have significantly contributed to the improvement of the paper. L.D.S. gratefully acknowledges financial support by the Deutsche Forschungsgemeinschaft through CRC 1060 as well as through SPP 2265, and by the Austrian Science Fund (FWF) grant F65 at Institute of Science and Technology Austria. This research was funded in whole or in part by the Austrian Science Fund (FWF) ESPRIT 208. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. E.K. and K.-T.S. gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through the Hausdorff Center for Mathematics and through CRC 1060 as well as through SPP 2265.\r\nOpen Access funding enabled and organized by Projekt DEAL.","oa_version":"Published Version","date_created":"2024-02-04T23:00:54Z","doi":"10.1007/s11118-023-10118-0","date_published":"2024-01-26T00:00:00Z","year":"2024","publication_status":"epub_ahead","publication_identifier":{"eissn":["1572-929X"],"issn":["0926-2601"]},"publication":"Potential Analysis","language":[{"iso":"eng"}],"day":"26","type":"journal_article","article_type":"original","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"status":"public","_id":"14934","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"full_name":"Sturm, Karl Theodor","last_name":"Sturm","first_name":"Karl Theodor"}],"department":[{"_id":"JaMa"}],"title":"A discovery tour in random Riemannian geometry","date_updated":"2024-02-05T13:04:23Z","citation":{"mla":"Dello Schiavo, Lorenzo, et al. “A Discovery Tour in Random Riemannian Geometry.” Potential Analysis, Springer Nature, 2024, doi:10.1007/s11118-023-10118-0.","ieee":"L. Dello Schiavo, E. Kopfer, and K. T. Sturm, “A discovery tour in random Riemannian geometry,” Potential Analysis. Springer Nature, 2024.","short":"L. Dello Schiavo, E. Kopfer, K.T. Sturm, Potential Analysis (2024).","apa":"Dello Schiavo, L., Kopfer, E., & Sturm, K. T. (2024). A discovery tour in random Riemannian geometry. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-023-10118-0","ama":"Dello Schiavo L, Kopfer E, Sturm KT. A discovery tour in random Riemannian geometry. Potential Analysis. 2024. doi:10.1007/s11118-023-10118-0","chicago":"Dello Schiavo, Lorenzo, Eva Kopfer, and Karl Theodor Sturm. “A Discovery Tour in Random Riemannian Geometry.” Potential Analysis. Springer Nature, 2024. https://doi.org/10.1007/s11118-023-10118-0.","ista":"Dello Schiavo L, Kopfer E, Sturm KT. 2024. A discovery tour in random Riemannian geometry. Potential Analysis."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"issue":"2","volume":30,"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"intvolume":" 30","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.15240"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Let $\\ell$ be a prime number. We classify the subgroups $G$ of $\\operatorname{Sp}_4(\\mathbb{F}_\\ell)$ and $\\operatorname{GSp}_4(\\mathbb{F}_\\ell)$ that act irreducibly on $\\mathbb{F}_\\ell^4$, but such that every element of $G$ fixes an $\\mathbb{F}_\\ell$-vector subspace of dimension 1. We use this classification to prove that the local-global principle for isogenies of degree $\\ell$ between abelian surfaces over number fields holds in many cases -- in particular, whenever the abelian surface has non-trivial endomorphisms and $\\ell$ is large enough with respect to the field of definition. Finally, we prove that there exist arbitrarily large primes $\\ell$ for which some abelian surface\r\n$A/\\mathbb{Q}$ fails the local-global principle for isogenies of degree $\\ell$.","lang":"eng"}],"department":[{"_id":"TiBr"}],"date_updated":"2024-02-05T12:25:00Z","status":"public","article_type":"original","type":"journal_article","_id":"12312","date_created":"2023-01-16T11:45:53Z","date_published":"2024-01-26T00:00:00Z","doi":"10.1007/s00029-023-00908-0","publication":"Selecta Mathematica","day":"26","year":"2024","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"It is a pleasure to thank Samuele Anni for his interest in this project and for several discussions on the topic of this paper, which led in particular to Remark 6.30 and to a better understanding of the difficulties with [6]. We also thank John Cullinan for correspondence about [6] and Barinder Banwait for his many insightful comments on the first version of this paper. Finally, we thank the referee for their thorough reading of the manuscript.\r\nOpen access funding provided by Università di Pisa within the CRUI-CARE Agreement. The authors have been partially supported by MIUR (Italy) through PRIN 2017 “Geometric, algebraic and analytic methods in arithmetic\" and PRIN 2022 “Semiabelian varieties, Galois representations and related Diophantine problems\", and by the University of Pisa through PRA 2018-19 and 2022 “Spazi di moduli, rappresentazioni e strutture combinatorie\". The first author is a member of the INdAM group GNSAGA.","title":"On the local-global principle for isogenies of abelian surfaces","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2206.15240"]},"author":[{"first_name":"Davide","last_name":"Lombardo","full_name":"Lombardo, Davide"},{"last_name":"Verzobio","full_name":"Verzobio, Matteo","orcid":"0000-0002-0854-0306","first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for Isogenies of Abelian Surfaces.” Selecta Mathematica, vol. 30, no. 2, 18, Springer Nature, 2024, doi:10.1007/s00029-023-00908-0.","apa":"Lombardo, D., & Verzobio, M. (2024). On the local-global principle for isogenies of abelian surfaces. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-023-00908-0","ama":"Lombardo D, Verzobio M. On the local-global principle for isogenies of abelian surfaces. Selecta Mathematica. 2024;30(2). doi:10.1007/s00029-023-00908-0","ieee":"D. Lombardo and M. Verzobio, “On the local-global principle for isogenies of abelian surfaces,” Selecta Mathematica, vol. 30, no. 2. Springer Nature, 2024.","short":"D. Lombardo, M. Verzobio, Selecta Mathematica 30 (2024).","chicago":"Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for Isogenies of Abelian Surfaces.” Selecta Mathematica. Springer Nature, 2024. https://doi.org/10.1007/s00029-023-00908-0.","ista":"Lombardo D, Verzobio M. 2024. On the local-global principle for isogenies of abelian surfaces. Selecta Mathematica. 30(2), 18."},"article_number":"18"},{"publication_status":"published","publication_identifier":{"eissn":["2169-8996"],"issn":["2169-897X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"14943","checksum":"cad5b93caadb40c14e5faedc34f7bba7","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-02-06T08:38:27Z","file_name":"2024_JGRAtmospheres_Shaw.pdf","creator":"dernst","date_updated":"2024-02-06T08:38:27Z","file_size":7481087}],"volume":129,"issue":"2","related_material":{"record":[{"id":"14919","status":"public","relation":"research_data"}]},"abstract":[{"lang":"eng","text":"The near-surface boundary layer can mediate the response of mountain glaciers to external climate, cooling the overlying air and promoting a density-driven glacier wind. The fundamental processes are conceptually well understood, though the magnitudes of cooling and presence of glacier winds are poorly quantified in space and time, increasing the forcing uncertainty for melt models. We utilize a new data set of on-glacier meteorological measurements on three neighboring glaciers in the Swiss Alps to explore their distinct response to regional climate under the extreme 2022 summer. We find that synoptic wind origins and local terrain modifications, not only glacier size, play an important role in the ability of a glacier to cool the near-surface air. Warm air intrusions from valley or synoptically-driven winds onto the glacier can occur between ∼19% and 64% of the time and contribute between 3% and 81% of the total sensible heat flux to the surface during warm afternoon hours, depending on the fetch of the glacier flowline and its susceptibility to boundary layer erosion. In the context of extreme summer warmth, indicative of future conditions, the boundary layer cooling (up to 6.5°C cooler than its surroundings) and resultant katabatic wind flow are highly heterogeneous between the study glaciers, highlighting the complex and likely non-linear response of glaciers to an uncertain future."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 129","month":"01","date_updated":"2024-02-06T08:44:02Z","ddc":["550"],"department":[{"_id":"FrPe"}],"file_date_updated":"2024-02-06T08:38:27Z","_id":"14885","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","year":"2024","has_accepted_license":"1","publication":"Journal of Geophysical Research: Atmospheres","day":"28","date_created":"2024-01-28T23:01:42Z","date_published":"2024-01-28T00:00:00Z","doi":"10.1029/2023JD040214","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101026058. The authors acknowledge the invaluable field assistance of Marta Corrà, Achille Jouberton, Marin Kneib, Stefan Fugger, Celine Ducret and Alexander Groos. The authors would also like to thank Luca Carturan for advice regarding AWS setup and maintenance and Simone Fatichi for provision and support in the use of the Tethys-Chloris model. Open access funding provided by ETH-Bereich Forschungsanstalten.","oa":1,"quality_controlled":"1","publisher":"Wiley","citation":{"chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca Pellicciotti. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres. Wiley, 2024. https://doi.org/10.1029/2023JD040214.","ista":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. 2024. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 129(2), e2023JD040214.","mla":"Shaw, Thomas, et al. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” Journal of Geophysical Research: Atmospheres, vol. 129, no. 2, e2023JD040214, Wiley, 2024, doi:10.1029/2023JD040214.","ieee":"T. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pellicciotti, “Local controls on near-surface glacier cooling under warm atmospheric conditions,” Journal of Geophysical Research: Atmospheres, vol. 129, no. 2. Wiley, 2024.","short":"T. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 129 (2024).","ama":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 2024;129(2). doi:10.1029/2023JD040214","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E. S., & Pellicciotti, F. (2024). Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. Wiley. https://doi.org/10.1029/2023JD040214"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Shaw","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas"},{"id":"317987aa-9421-11ee-ac5a-b941b041abba","first_name":"Pascal","full_name":"Buri, Pascal","last_name":"Buri"},{"last_name":"Mccarthy","full_name":"Mccarthy, Michael","first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f"},{"last_name":"Miles","full_name":"Miles, Evan S.","first_name":"Evan S."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087","last_name":"Pellicciotti"}],"title":"Local controls on near-surface glacier cooling under warm atmospheric conditions","article_number":"e2023JD040214"},{"department":[{"_id":"FrPe"}],"ddc":["550"],"date_updated":"2024-02-06T08:35:39Z","status":"public","keyword":["Public Health","Environmental and Occupational Health","General Environmental Science","Renewable Energy","Sustainability and the Environment"],"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":"14938","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1748-9326"]},"publication_status":"accepted","month":"02","main_file_link":[{"url":"https://doi.org/10.1088/1748-9326/ad25a0","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"High elevation headwater catchments are complex hydrological systems that seasonally buffer water and release it in the form of snow and ice melt, modulating downstream runoff regimes and water availability. In High Mountain Asia (HMA), where a wide range of climates from semi-arid to monsoonal exist, the importance of the cryospheric contributions to the water budget varies with the amount and seasonal distribution of precipitation. Losses due to evapotranspiration and sublimation are to date largely unquantified components of the water budget in such catchments, although they can be comparable in magnitude to glacier melt contributions to streamflow. 
Here, we simulate the hydrology of three high elevation headwater catchments in distinct climates in HMA over 10 years using an ecohydrological model geared towards high-mountain areas including snow and glaciers, forced with reanalysis data. 
Our results show that evapotranspiration and sublimation together are most important at the semi-arid site, Kyzylsu, on the northernmost slopes of the Pamir mountain range. Here, the evaporative loss amounts to 28% of the water throughput, which we define as the total water added to, or removed from the water balance within a year. In comparison, evaporative losses are 19% at the Central Himalayan site Langtang and 13% at the wettest site, 24K, on the Southeastern Tibetan Plateau. At the three sites, respectively, sublimation removes 15%, 13% and 6% of snowfall, while evapotranspiration removes the equivalent of 76%, 28% and 19% of rainfall. In absolute terms, and across a comparable elevation range, the highest ET flux is 413 mm yr-1 at 24K, while the highest sublimation flux is 91 mm yr-1 at Kyzylsu. During warm and dry years, glacier melt was found to only partially compensate for the annual supply deficit.","lang":"eng"}],"title":"Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia","author":[{"last_name":"Fugger","full_name":"Fugger, Stefan","id":"86698d64-c4c6-11ee-af02-cdf1e6a7d31f","first_name":"Stefan"},{"last_name":"Shaw","full_name":"Shaw, Thomas","orcid":"0000-0001-7640-6152","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e"},{"last_name":"Jouberton","full_name":"Jouberton, Achille","first_name":"Achille"},{"first_name":"Evan","last_name":"Miles","full_name":"Miles, Evan"},{"full_name":"Buri, Pascal","last_name":"Buri","id":"317987aa-9421-11ee-ac5a-b941b041abba","first_name":"Pascal"},{"full_name":"McCarthy, Michael","last_name":"McCarthy","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","first_name":"Michael"},{"first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","full_name":"Fyffe, Catriona Louise","last_name":"Fyffe"},{"first_name":"Simone","full_name":"Fatichi, Simone","last_name":"Fatichi"},{"first_name":"Marin","last_name":"Kneib","full_name":"Kneib, Marin"},{"full_name":"Molnar, Peter","last_name":"Molnar","first_name":"Peter"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fugger S, Shaw T, Jouberton A, Miles E, Buri P, McCarthy M, Fyffe CL, Fatichi S, Kneib M, Molnar P, Pellicciotti F. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters.","chicago":"Fugger, Stefan, Thomas Shaw, Achille Jouberton, Evan Miles, Pascal Buri, Michael McCarthy, Catriona Louise Fyffe, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters. IOP Publishing, n.d. https://doi.org/10.1088/1748-9326/ad25a0.","ama":"Fugger S, Shaw T, Jouberton A, et al. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. doi:10.1088/1748-9326/ad25a0","apa":"Fugger, S., Shaw, T., Jouberton, A., Miles, E., Buri, P., McCarthy, M., … Pellicciotti, F. (n.d.). Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/ad25a0","ieee":"S. Fugger et al., “Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia,” Environmental Research Letters. IOP Publishing.","short":"S. Fugger, T. Shaw, A. Jouberton, E. Miles, P. Buri, M. McCarthy, C.L. Fyffe, S. Fatichi, M. Kneib, P. Molnar, F. Pellicciotti, Environmental Research Letters (n.d.).","mla":"Fugger, Stefan, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters, IOP Publishing, doi:10.1088/1748-9326/ad25a0."},"doi":"10.1088/1748-9326/ad25a0","date_published":"2024-02-02T00:00:00Z","date_created":"2024-02-05T09:01:11Z","day":"02","publication":"Environmental Research Letters","has_accepted_license":"1","year":"2024","quality_controlled":"1","publisher":"IOP Publishing","oa":1},{"conference":{"location":"Hong Kong, China","end_date":"2024-01-03","start_date":"2024-01-03","name":"CPAL: Conference on Parsimony and Learning"},"type":"conference","status":"public","_id":"14213","external_id":{"arxiv":["2304.01430"]},"article_processing_charge":"No","author":[{"last_name":"Lao","full_name":"Lao, Dong","first_name":"Dong"},{"full_name":"Hu, Zhengyang","last_name":"Hu","first_name":"Zhengyang"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Yang, Yanchao","last_name":"Yang","first_name":"Yanchao"},{"first_name":"Stefano","full_name":"Soatto, Stefano","last_name":"Soatto"}],"file_date_updated":"2024-02-12T08:40:36Z","title":"Divided attention: Unsupervised multi-object discovery with contextually separated slots","department":[{"_id":"FrLo"}],"citation":{"mla":"Lao, Dong, et al. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” 1st Conference on Parsimony and Learning, 2024.","ama":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. Divided attention: Unsupervised multi-object discovery with contextually separated slots. In: 1st Conference on Parsimony and Learning. ; 2024.","apa":"Lao, D., Hu, Z., Locatello, F., Yang, Y., & Soatto, S. (2024). Divided attention: Unsupervised multi-object discovery with contextually separated slots. In 1st Conference on Parsimony and Learning. Hong Kong, China.","ieee":"D. Lao, Z. Hu, F. Locatello, Y. Yang, and S. Soatto, “Divided attention: Unsupervised multi-object discovery with contextually separated slots,” in 1st Conference on Parsimony and Learning, Hong Kong, China, 2024.","short":"D. Lao, Z. Hu, F. Locatello, Y. Yang, S. Soatto, in:, 1st Conference on Parsimony and Learning, 2024.","chicago":"Lao, Dong, Zhengyang Hu, Francesco Locatello, Yanchao Yang, and Stefano Soatto. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” In 1st Conference on Parsimony and Learning, 2024.","ista":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. 2024. Divided attention: Unsupervised multi-object discovery with contextually separated slots. 1st Conference on Parsimony and Learning. CPAL: Conference on Parsimony and Learning."},"date_updated":"2024-02-12T08:56:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"oa":1,"quality_controlled":"1","month":"01","abstract":[{"lang":"eng","text":"We introduce a method to segment the visual field into independently moving regions, trained with no ground truth or supervision. It consists of an adversarial conditional encoder-decoder architecture based on Slot Attention, modified to use the image as context to decode optical flow without attempting to reconstruct the image itself. In the resulting multi-modal representation, one modality (flow) feeds the encoder to produce separate latent codes (slots), whereas the other modality (image) conditions the decoder to generate the first (flow) from the slots. This design frees the representation from having to encode complex nuisance variability in the image due to, for instance, illumination and reflectance properties of the scene. Since customary autoencoding based on minimizing the reconstruction error does not preclude the entire flow from being encoded into a single slot, we modify the loss to an adversarial criterion based on Contextual Information Separation. The resulting min-max optimization fosters the separation of objects and their assignment to different attention slots, leading to Divided Attention, or DivA. DivA outperforms recent unsupervised multi-object motion segmentation methods while tripling run-time speed up to 104FPS and reducing the performance gap from supervised methods to 12% or less. DivA can handle different numbers of objects and different image sizes at training and test time, is invariant to permutation of object labels, and does not require explicit regularization."}],"oa_version":"Published Version","date_created":"2023-08-22T14:19:59Z","date_published":"2024-01-03T00:00:00Z","year":"2024","publication_status":"published","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"1st Conference on Parsimony and Learning","file":[{"success":1,"file_id":"14978","checksum":"8fad894c34f1b3d5a14fb8ffb12f7277","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2024_CPAL_Lao.pdf","date_created":"2024-02-12T08:40:36Z","creator":"dernst","file_size":8038511,"date_updated":"2024-02-12T08:40:36Z"}],"day":"03"},{"doi":"10.1103/physrevresearch.6.013141","date_published":"2024-02-05T00:00:00Z","date_created":"2024-02-12T11:42:18Z","has_accepted_license":"1","year":"2024","day":"05","publication":"Physical Review Research","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We thank Pere Rosselló for his contributions to the initial modeling of the presented sensing technique. This work was supported by Institute of Science and Technology Austria, and\r\nthe European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).","author":[{"full_name":"Agafonova, Sofya","orcid":"0000-0003-0582-2946","last_name":"Agafonova","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80"},{"last_name":"Mishra","full_name":"Mishra, Umang","first_name":"Umang","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51"},{"full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924","last_name":"Diorico","first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hosten","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2306.12804"]},"title":"Zigzag optical cavity for sensing and controlling torsional motion","citation":{"mla":"Agafonova, Sofya, et al. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” Physical Review Research, vol. 6, no. 1, 013141, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013141.","ieee":"S. Agafonova, U. Mishra, F. R. Diorico, and O. Hosten, “Zigzag optical cavity for sensing and controlling torsional motion,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","short":"S. Agafonova, U. Mishra, F.R. Diorico, O. Hosten, Physical Review Research 6 (2024).","ama":"Agafonova S, Mishra U, Diorico FR, Hosten O. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013141","apa":"Agafonova, S., Mishra, U., Diorico, F. R., & Hosten, O. (2024). Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013141","chicago":"Agafonova, Sofya, Umang Mishra, Fritz R Diorico, and Onur Hosten. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013141.","ista":"Agafonova S, Mishra U, Diorico FR, Hosten O. 2024. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 6(1), 013141."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","grant_number":"101087907","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6"}],"article_number":"013141","issue":"1","volume":6,"publication_identifier":{"eissn":["2643-1564"]},"publication_status":"published","file":[{"file_name":"2024_PhysicalRevResearch_Agafonova.pdf","date_created":"2024-02-12T11:46:50Z","file_size":1437167,"date_updated":"2024-02-12T11:46:50Z","creator":"dernst","success":1,"file_id":"14981","checksum":"3a39ebffb24c1cc1dd0b547a726dc52d","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"month":"02","intvolume":" 6","abstract":[{"text":"Precision sensing and manipulation of milligram-scale mechanical oscillators has attracted growing interest in the fields of table-top explorations of gravity and tests of quantum mechanics at macroscopic scales. Torsional oscillators present an opportunity in this regard due to their remarked isolation from environmental noise. For torsional motion, an effective employment of optical cavities to enhance optomechanical interactions—as already established for linear oscillators—so far faced certain challenges. Here, we propose a concept for sensing and manipulating torsional motion, where exclusively the torsional rotations of a pendulum are mapped onto the path length of a single two-mirror optical cavity. The concept inherently alleviates many limitations of previous approaches. A proof-of-principle experiment is conducted with a rigidly controlled pendulum to explore the sensing aspects of the concept and to identify practical limitations in a potential state-of-the art setup. Based on this study, we anticipate development of precision torque sensors utilizing torsional pendulums that can support sensitivities below 10−19Nm/√Hz, while the motion of the pendulums are dominated by quantum radiation pressure noise at sub-microwatts of incoming laser power. These developments will provide horizons for experiments at the interface of quantum mechanics and gravity.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"OnHo"}],"file_date_updated":"2024-02-12T11:46:50Z","date_updated":"2024-02-12T11:49:06Z","ddc":["530"],"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","_id":"14980"},{"page":"28-33","date_created":"2024-01-22T08:19:36Z","doi":"10.1002/piuz.202301690","date_published":"2024-01-01T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Physik in unserer Zeit","day":"01","oa":1,"publisher":"Wiley","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","last_name":"Karle","first_name":"Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"title":"Die faszinierende Topologie rotierender Quanten","citation":{"ieee":"V. Karle and M. Lemeshko, “Die faszinierende Topologie rotierender Quanten,” Physik in unserer Zeit, vol. 55, no. 1. Wiley, pp. 28–33, 2024.","short":"V. Karle, M. Lemeshko, Physik in unserer Zeit 55 (2024) 28–33.","apa":"Karle, V., & Lemeshko, M. (2024). Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. Wiley. https://doi.org/10.1002/piuz.202301690","ama":"Karle V, Lemeshko M. Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. 2024;55(1):28-33. doi:10.1002/piuz.202301690","mla":"Karle, Volker, and Mikhail Lemeshko. “Die faszinierende Topologie rotierender Quanten.” Physik in unserer Zeit, vol. 55, no. 1, Wiley, 2024, pp. 28–33, doi:10.1002/piuz.202301690.","ista":"Karle V, Lemeshko M. 2024. Die faszinierende Topologie rotierender Quanten. Physik in unserer Zeit. 55(1), 28–33.","chicago":"Karle, Volker, and Mikhail Lemeshko. “Die faszinierende Topologie rotierender Quanten.” Physik in unserer Zeit. Wiley, 2024. https://doi.org/10.1002/piuz.202301690."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"1","volume":55,"publication_status":"published","publication_identifier":{"issn":["0031-9252"],"eissn":["1521-3943"]},"language":[{"iso":"ger"}],"file":[{"checksum":"3051dadcf9bc57da97e36b647c596ab1","file_id":"14878","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-01-23T12:18:07Z","file_name":"2024_PhysikZeit_Karle.pdf","date_updated":"2024-01-23T12:18:07Z","file_size":1155244,"creator":"dernst"}],"intvolume":" 55","month":"01","abstract":[{"text":"Die Quantenrotation ist ein spannendes Phänomen, das in vielen verschiedenen Systemen auftritt, von Molekülen und Atomen bis hin zu subatomaren Teilchen wie Neutronen und Protonen. Durch den Einsatz von starken Laserpulsen ist es möglich, die mathematisch anspruchsvolle Topologie der Rotation von Molekülen aufzudecken und topologisch geschützte Zustände zu erzeugen, die unerwartetes Verhalten zeigen. Diese Entdeckungen könnten Auswirkungen auf die Molekülphysik und physikalische Chemie haben und die Entwicklung neuer Technologien ermöglichen. Die Verbindung von Quantenrotation und Topologie stellt ein aufregendes, interdisziplinäres Forschungsfeld dar und bietet neue Wege zur Kontrolle und Nutzung von quantenmechanischen Phänomenen.","lang":"ger"}],"oa_version":"Published Version","file_date_updated":"2024-01-23T12:18:07Z","department":[{"_id":"MiLe"}],"date_updated":"2024-02-15T14:29:04Z","ddc":["530"],"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 Earth and Planetary Sciences","General Environmental Science"],"status":"public","_id":"14851"},{"abstract":[{"text":"We prove a version of the tamely ramified geometric Langlands correspondence in positive characteristic for GLn(k). Let k be an algebraically closed field of characteristic p>n. Let X be a smooth projective curve over k with marked points, and fix a parabolic subgroup of GLn(k) at each marked point. We denote by Bunn,P the moduli stack of (quasi-)parabolic vector bundles on X, and by Locn,P the moduli stack of parabolic flat connections such that the residue is nilpotent with respect to the parabolic reduction at each marked point. We construct an equivalence between the bounded derived category Db(Qcoh(Loc0n,P)) of quasi-coherent sheaves on an open substack Loc0n,P⊂Locn,P, and the bounded derived category Db(D0Bunn,P-mod) of D0Bunn,P-modules, where D0Bunn,P is a localization of DBunn,P the sheaf of crystalline differential operators on Bunn,P. Thus we extend the work of Bezrukavnikov-Braverman to the tamely ramified case. We also prove a correspondence between flat connections on X with regular singularities and meromorphic Higgs bundles on the Frobenius twist X(1) of X with first order poles .","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/imrn/rnae005"}],"month":"02","publication_status":"epub_ahead","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"language":[{"iso":"eng"}],"ec_funded":1,"_id":"14986","type":"journal_article","article_type":"original","keyword":["General Mathematics"],"status":"public","date_updated":"2024-02-19T10:22:44Z","department":[{"_id":"TaHa"}],"acknowledgement":"This work was supported by the NSF [DMS-1502125to S.S.]; and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement [101034413 to S.S.].\r\nI would like to thank my advisor Tom Nevins for many helpful discussions on this subject and for his comments on this paper. I would like to thank Christopher Dodd, Michael Groechenig, and Tamas Hausel for helpful conversations. I would like to thank Tsao-Hsien Chen for useful comments on an earlier version of this paper.","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","year":"2024","publication":"International Mathematics Research Notices","day":"05","date_created":"2024-02-14T12:16:17Z","doi":"10.1093/imrn/rnae005","date_published":"2024-02-05T00:00:00Z","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"citation":{"chicago":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” International Mathematics Research Notices. Oxford University Press, 2024. https://doi.org/10.1093/imrn/rnae005.","ista":"Shen S. 2024. Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices.","mla":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” International Mathematics Research Notices, Oxford University Press, 2024, doi:10.1093/imrn/rnae005.","short":"S. Shen, International Mathematics Research Notices (2024).","ieee":"S. Shen, “Tamely ramified geometric Langlands correspondence in positive characteristic,” International Mathematics Research Notices. Oxford University Press, 2024.","apa":"Shen, S. (2024). Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnae005","ama":"Shen S. Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices. 2024. doi:10.1093/imrn/rnae005"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1810.12491"]},"author":[{"id":"544cccd3-9005-11ec-87bc-94aef1c5b814","first_name":"Shiyu","full_name":"Shen, Shiyu","last_name":"Shen"}],"title":"Tamely ramified geometric Langlands correspondence in positive characteristic"},{"day":"16","language":[{"iso":"eng"}],"publication":"bioRxiv","year":"2024","publication_status":"submitted","doi":"10.1101/2024.02.15.580289","date_published":"2024-02-16T00:00:00Z","date_created":"2024-02-20T09:20:32Z","oa_version":"Preprint","acknowledgement":"We would like to extend our thanks to members of the Sweeney, Tosches, Shein-Idelson,\r\nYamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion and support.\r\nWe additionally thank the Beckman Institute Clover Center and Viviana Gradinaru (Caltech),\r\nKimberly Ritola (UNC NeuroTools), Flavia Gama Gomez Leite (ISTA Viral Core), and Hüseyin\r\nCihan Önal (Shigemoto Group, ISTA) for their consultation and assistance regarding AAVs, as\r\nwell as Andras Simon and Alberto Joven for feedback and discussions on AAVs in Pleurodeles.\r\nTo do these experiments, we have also benefited from the tremendous support of our animal care and imaging facilities at our respective institutions, as well as the amphibian stock centers\r\n(National Xenopus Resource Center, European Xenopus Resource Center, Xenopus Express)\r\nand our funding sources: U.S. National Science Foundation (NSF) Grant Number IOS 2110086\r\n(D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); United States-Israel Binational Science Foundation\r\n(BSF) Grant Number 2020702 (M.S.-I.); NSF Award Number 1645105 (G.J.G., M.E.H.); FTI\r\nStrategy Lower Austria Dissertation Grant Number FTI21-D-046 (D.V.); Horizon Europe ERC\r\nStarting Grant Number 101041551 (L.B.S.); NIH grant number R35GM146973 (M.A.T.); Rita Allen\r\nFoundation award number GA_032522_FE (M.A.T.); European Molecular Biology Organization\r\nLong-Term Fellowship ALTF 874-2021 (A.D.); National Science Foundation Graduate Research\r\nFellowship DGE 2036197 (E.C.J.B.); NIH grant number P40OD010997 (M.E.H).","abstract":[{"lang":"eng","text":"The development, evolution, and function of the vertebrate central nervous system (CNS) can be best studied using diverse model organisms. Amphibians, with their unique phylogenetic position at the transition between aquatic and terrestrial lifestyles, are valuable for understanding the origin and evolution of the tetrapod brain and spinal cord. Their metamorphic developmental transitions and unique regenerative abilities also facilitate the discovery of mechanisms for neural circuit remodeling and replacement. The genetic toolkit for amphibians, however, remains limited, with only a few species having sequenced genomes and a small number of transgenic lines available. In mammals, recombinant adeno-associated viral vectors (AAVs) have become a powerful alternative to genome modification for visualizing and perturbing the nervous system. AAVs are DNA viruses that enable neuronal transduction in both developing and adult animals with low toxicity and spatial, temporal, and cell-type specificity. However, AAVs have never been shown to transduce amphibian cells efficiently. To bridge this gap, we established a simple, scalable, and robust strategy to screen AAV serotypes in three distantly-related amphibian species: the frogs Xenopus laevis and Pelophylax bedriagae, and the salamander Pleurodeles waltl, in both developing larval tadpoles and post-metamorphic animals. For each species, we successfully identified at least two AAV serotypes capable of infecting the CNS; however, no pan-amphibian serotype was identified, indicating rapid evolution of AAV tropism. In addition, we developed an AAV-based strategy that targets isochronic cohorts of developing neurons – a critical tool for parsing neural circuit assembly. Finally, to enable visualization and manipulation of neural circuits, we identified AAV variants for retrograde tracing of neuronal projections in adult animals. Our findings expand the toolkit for amphibians to include AAVs, establish a generalizable workflow for AAV screening in non-canonical research organisms, generate testable hypotheses for the evolution of AAV tropism, and lay the foundation for modern cross-species comparisons of vertebrate CNS development, function, and evolution. "}],"month":"02","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.02.15.580289"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-20T09:34:25Z","citation":{"chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.15.580289.","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv, 10.1101/2024.02.15.580289.","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” BioRxiv, doi:10.1101/2024.02.15.580289.","ieee":"E. C. B. Jaeger et al., “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” bioRxiv. .","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, BioRxiv (n.d.).","apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (n.d.). Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv. https://doi.org/10.1101/2024.02.15.580289","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv. doi:10.1101/2024.02.15.580289"},"department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","author":[{"full_name":"Jaeger, Eliza C.B.","last_name":"Jaeger","first_name":"Eliza C.B."},{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","first_name":"David","last_name":"Vijatovic","full_name":"Vijatovic, David"},{"last_name":"Deryckere","full_name":"Deryckere, Astrid","first_name":"Astrid"},{"last_name":"Zorin","full_name":"Zorin, Nikol","first_name":"Nikol"},{"first_name":"Akemi L.","full_name":"Nguyen, Akemi L.","last_name":"Nguyen"},{"last_name":"Ivanian","full_name":"Ivanian, Georgiy","first_name":"Georgiy","id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05"},{"first_name":"Jamie","full_name":"Woych, Jamie","last_name":"Woych"},{"full_name":"Arnold, Rebecca C","last_name":"Arnold","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f","first_name":"Rebecca C"},{"first_name":"Alonso","last_name":"Ortega Gurrola","full_name":"Ortega Gurrola, Alonso"},{"last_name":"Shvartsman","full_name":"Shvartsman, Arik","first_name":"Arik"},{"first_name":"Francesca","id":"a9492887-8972-11ed-ae7b-bfae10998254","last_name":"Barbieri","full_name":"Barbieri, Francesca"},{"first_name":"Florina-Alexandra","id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5","full_name":"Toma, Florina-Alexandra","last_name":"Toma"},{"full_name":"Gorbsky, Gary J.","last_name":"Gorbsky","first_name":"Gary J."},{"first_name":"Marko E.","last_name":"Horb","full_name":"Horb, Marko E."},{"first_name":"Hollis T.","full_name":"Cline, Hollis T.","last_name":"Cline"},{"full_name":"Shay, Timothy F.","last_name":"Shay","first_name":"Timothy F."},{"full_name":"Kelley, Darcy B.","last_name":"Kelley","first_name":"Darcy B."},{"last_name":"Yamaguchi","full_name":"Yamaguchi, Ayako","first_name":"Ayako"},{"full_name":"Shein-Idelson, Mark","last_name":"Shein-Idelson","first_name":"Mark"},{"full_name":"Tosches, Maria Antonietta","last_name":"Tosches","first_name":"Maria Antonietta"},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601"}],"article_processing_charge":"No","_id":"15016","status":"public","project":[{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046","name":"Entwicklung und Funktion der V1 Interneuronen vom Schwimmen zum Laufen während der Metamorphose von Xenopus"},{"name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"}],"type":"preprint"},{"acknowledgement":"János Pach’s Research partially supported by European Research Council (ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH), grant K-131529. Work by Morteza Saghafian is partially supported by the European Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2024","publication":"31st International Symposium on Graph Drawing and Network Visualization","day":"01","page":"339-346","date_created":"2024-02-18T23:01:03Z","date_published":"2024-01-01T00:00:00Z","doi":"10.1007/978-3-031-49272-3_23","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"short":"J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346.","ieee":"J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs into star-forests,” in 31st International Symposium on Graph Drawing and Network Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp. 339–346.","apa":"Pach, J., Saghafian, M., & Schnider, P. (2024). Decomposition of geometric graphs into star-forests. In 31st International Symposium on Graph Drawing and Network Visualization (Vol. 14465, pp. 339–346). Isola delle Femmine, Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49272-3_23","ama":"Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests. In: 31st International Symposium on Graph Drawing and Network Visualization. Vol 14465. Springer Nature; 2024:339-346. doi:10.1007/978-3-031-49272-3_23","mla":"Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.” 31st International Symposium on Graph Drawing and Network Visualization, vol. 14465, Springer Nature, 2024, pp. 339–46, doi:10.1007/978-3-031-49272-3_23.","ista":"Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs into star-forests. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346.","chicago":"Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric Graphs into Star-Forests.” In 31st International Symposium on Graph Drawing and Network Visualization, 14465:339–46. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49272-3_23."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2306.13201"]},"author":[{"full_name":"Pach, János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","full_name":"Saghafian, Morteza","last_name":"Saghafian"},{"full_name":"Schnider, Patrick","last_name":"Schnider","first_name":"Patrick"}],"title":"Decomposition of geometric graphs into star-forests","abstract":[{"lang":"eng","text":"We solve a problem of Dujmović and Wood (2007) by showing that a complete convex geometric graph on n vertices cannot be decomposed into fewer than n-1 star-forests, each consisting of noncrossing edges. This bound is clearly tight. We also discuss similar questions for abstract graphs."}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.13201","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 14465","month":"01","publication_status":"published","publication_identifier":{"issn":["03029743"],"isbn":["9783031492716"],"eissn":["16113349"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":14465,"_id":"15012","conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2023-09-20","end_date":"2023-09-22","location":"Isola delle Femmine, Palermo, Italy"},"type":"conference","status":"public","date_updated":"2024-02-20T09:13:07Z","department":[{"_id":"HeEd"}]},{"department":[{"_id":"KrCh"}],"file_date_updated":"2024-02-26T09:04:58Z","ddc":["000"],"date_updated":"2024-02-26T09:16:12Z","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":{"location":"Tokyo, Japan","end_date":"2023-12-08","start_date":"2023-12-06","name":"OPODIS: Conference on Principles of Distributed Systems"},"_id":"15006","volume":286,"ec_funded":1,"file":[{"file_name":"2024_LIPICs_Hirvonen.pdf","date_created":"2024-02-26T09:04:58Z","creator":"dernst","file_size":867363,"date_updated":"2024-02-26T09:04:58Z","success":1,"file_id":"15028","checksum":"4fc7eea6e4ba140b904781fc7df868ec","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"],"isbn":["9783959773089"]},"publication_status":"published","month":"01","intvolume":" 286","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Graphical games are a useful framework for modeling the interactions of (selfish) agents who are connected via an underlying topology and whose behaviors influence each other. They have wide applications ranging from computer science to economics and biology. Yet, even though an agent’s payoff only depends on the actions of their direct neighbors in graphical games, computing the Nash equilibria and making statements about the convergence time of \"natural\" local dynamics in particular can be highly challenging. In this work, we present a novel approach for classifying complexity of Nash equilibria in graphical games by establishing a connection to local graph algorithms, a subfield of distributed computing. In particular, we make the observation that the equilibria of graphical games are equivalent to locally verifiable labelings (LVL) in graphs; vertex labelings which are verifiable with constant-round local algorithms. This connection allows us to derive novel lower bounds on the convergence time to equilibrium of best-response dynamics in graphical games. Since we establish that distributed convergence can sometimes be provably slow, we also introduce and give bounds on an intuitive notion of \"time-constrained\" inefficiency of best responses. We exemplify how our results can be used in the implementation of mechanisms that ensure convergence of best responses to a Nash equilibrium. Our results thus also give insight into the convergence of strategy-proof algorithms for graphical games, which is still not well understood.","lang":"eng"}],"title":"On the convergence time in graphical games: A locality-sensitive approach","author":[{"first_name":"Juho","last_name":"Hirvonen","full_name":"Hirvonen, Juho"},{"orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","last_name":"Schmid","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"}],"external_id":{"arxiv":["2102.13457"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hirvonen, Juho, et al. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” 27th International Conference on Principles of Distributed Systems, vol. 286, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.11.","ieee":"J. Hirvonen, L. Schmid, K. Chatterjee, and S. Schmid, “On the convergence time in graphical games: A locality-sensitive approach,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","short":"J. Hirvonen, L. Schmid, K. Chatterjee, S. Schmid, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","apa":"Hirvonen, J., Schmid, L., Chatterjee, K., & Schmid, S. (2024). On the convergence time in graphical games: A locality-sensitive approach. 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.2023.11","ama":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. On the convergence time in graphical games: A locality-sensitive approach. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.11","chicago":"Hirvonen, Juho, Laura Schmid, Krishnendu Chatterjee, and Stefan Schmid. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” 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.2023.11.","ista":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. 2024. On the convergence time in graphical games: A locality-sensitive approach. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 11."},"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"article_number":"11","doi":"10.4230/LIPIcs.OPODIS.2023.11","date_published":"2024-01-18T00:00:00Z","date_created":"2024-02-18T23:01:01Z","day":"18","publication":"27th International Conference on Principles of Distributed Systems","has_accepted_license":"1","year":"2024","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"This work was partially funded by the Academy of Finland, grant 314888, the European Research Council CoG 863818 (ForM-SMArt), and the Austrian Science Fund (FWF) project I 4800-N (ADVISE). LS was supported by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324."},{"department":[{"_id":"AnSa"}],"file_date_updated":"2024-02-26T08:20:00Z","date_updated":"2024-02-26T08:45:56Z","ddc":["570"],"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"},"type":"journal_article","article_type":"original","status":"public","_id":"15001","ec_funded":1,"related_material":{"record":[{"status":"public","id":"15027","relation":"research_data"}]},"volume":121,"issue":"7","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"file_id":"15026","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-02-26T08:20:00Z","file_name":"2024_PNAS_Curk.pdf","creator":"dernst","date_updated":"2024-02-26T08:20:00Z","file_size":7699487}],"scopus_import":"1","intvolume":" 121","month":"02","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","article_processing_charge":"Yes","external_id":{"pmid":["38335256"]},"author":[{"first_name":"Samo","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","last_name":"Curk","full_name":"Curk, Samo","orcid":"0000-0001-6160-9766"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"last_name":"Meisl","full_name":"Meisl, Georg","first_name":"Georg"},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","citation":{"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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"article_number":"e2220075121","date_created":"2024-02-18T23:01:00Z","date_published":"2024-02-13T00:00:00Z","doi":"10.1073/pnas.2220075121","year":"2024","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"13","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","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.)."},{"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.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"30","publication":"Physical Review Letters","year":"2024","doi":"10.1103/PhysRevLett.132.050401","date_published":"2024-01-30T00:00:00Z","date_created":"2024-02-18T23:01:00Z","article_number":"050401","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","short":"E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters 132 (2024).","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.","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."},"title":"Fractal states of the Schwinger model","author":[{"first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","full_name":"Petrova, Elena","last_name":"Petrova"},{"first_name":"Egor S.","last_name":"Tiunov","full_name":"Tiunov, Egor S."},{"last_name":"Bañuls","full_name":"Bañuls, Mari Carmen","first_name":"Mari Carmen"},{"last_name":"Fedorov","full_name":"Fedorov, Aleksey K.","first_name":"Aleksey K."}],"external_id":{"arxiv":["2201.10220"]},"article_processing_charge":"No","oa_version":"Preprint","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."}],"month":"01","intvolume":" 132","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.10220","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","volume":132,"issue":"5","_id":"15002","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-02-26T08:03:31Z","department":[{"_id":"MaSe"}]},{"year":"2024","publication":"Probability Theory and Related Fields","day":"02","date_created":"2023-02-02T10:45:15Z","date_published":"2024-02-02T00:00:00Z","doi":"10.1007/s00440-023-01249-x","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).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"ista":"Agresti A, Veraar M. 2024. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields.","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.","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","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","ieee":"A. Agresti and M. Veraar, “The critical variational setting for stochastic evolution equations,” Probability Theory and Related Fields. Springer Nature, 2024.","short":"A. Agresti, M. Veraar, Probability Theory and Related Fields (2024).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2206.00230"]},"article_processing_charge":"No","author":[{"full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti","first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"title":"The critical variational setting for stochastic evolution equations","project":[{"grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"language":[{"iso":"eng"}],"ec_funded":1,"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","main_file_link":[{"url":"https://doi.org/10.1007/s00440-023-01249-x","open_access":"1"}],"scopus_import":"1","month":"02","date_updated":"2024-02-26T09:39:07Z","department":[{"_id":"JuFi"}],"_id":"12485","article_type":"original","type":"journal_article","status":"public"},{"month":"01","intvolume":" 287","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":287,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"15030","checksum":"b89716aae6a5599f187897e39de1e53a","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","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":{"name":"ITCS: Innovations in Theoretical Computer Science Conference","start_date":"2024-01-30","end_date":"2024-02-02","location":"Berkeley, CA, United States"},"_id":"15008","file_date_updated":"2024-02-26T10:10:48Z","department":[{"_id":"MoHe"}],"ddc":["000"],"date_updated":"2024-02-26T10:12:19Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"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.","date_published":"2024-01-24T00:00:00Z","doi":"10.4230/LIPIcs.ITCS.2024.55","date_created":"2024-02-18T23:01:02Z","day":"24","publication":"15th Innovations in Theoretical Computer Science Conference","has_accepted_license":"1","year":"2024","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","grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"article_number":"55","title":"Electrical flows for polylogarithmic competitive oblivious routing","author":[{"last_name":"Goranci","full_name":"Goranci, Gramoz","first_name":"Gramoz"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"first_name":"Sushant","full_name":"Sachdeva, Sushant","last_name":"Sachdeva"},{"first_name":"A. R.","last_name":"Sricharan","full_name":"Sricharan, A. R."}],"article_processing_charge":"No","external_id":{"arxiv":["2303.02491"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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."}},{"article_number":"12","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2307.02954"]},"article_processing_charge":"No","author":[{"last_name":"Alpos","full_name":"Alpos, Orestis","first_name":"Orestis"},{"first_name":"Ignacio","full_name":"Amores-Sesar, Ignacio","last_name":"Amores-Sesar"},{"full_name":"Cachin, Christian","last_name":"Cachin","first_name":"Christian"},{"first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","last_name":"Yeo"}],"title":"Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks","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","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2024","has_accepted_license":"1","publication":"27th International Conference on Principles of Distributed Systems","day":"18","date_created":"2024-02-18T23:01:02Z","date_published":"2024-01-18T00:00:00Z","doi":"10.4230/LIPIcs.OPODIS.2023.12","_id":"15007","conference":{"start_date":"2023-12-06","end_date":"2023-12-08","location":"Tokyo, Japan","name":"OPODIS: Conference on Principles of Distributed Systems"},"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","status":"public","date_updated":"2024-02-26T10:18:18Z","ddc":["000"],"department":[{"_id":"KrPi"}],"file_date_updated":"2024-02-26T10:16:57Z","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"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 286","month":"01","publication_status":"published","publication_identifier":{"isbn":["9783959773089"],"issn":["1868-8969"]},"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,"file_id":"15031","checksum":"2993e810a45e8c8056106834b07aea92","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":286},{"project":[{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"external_id":{"arxiv":["2310.18034"]},"article_processing_charge":"No","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","first_name":"David","last_name":"Saulpic","full_name":"Saulpic, David"},{"id":"8b563fd0-b441-11ee-9101-a3891c61efa6","first_name":"Leonhard","full_name":"Sidl, Leonhard","last_name":"Sidl"}],"title":"Experimental evaluation of fully dynamic k-means via coresets","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.","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.","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.","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Society for Industrial & Applied Mathematics","quality_controlled":"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.","page":"220-233","date_created":"2024-01-09T16:22:47Z","doi":"10.1137/1.9781611977929.17","date_published":"2024-01-04T00:00:00Z","year":"2024","publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","day":"04","conference":{"name":"ALENEX: Workshop on Algorithm Engineering and Experiments","start_date":"2024-01-07","location":"Alexandria, VA, United States","end_date":"2024-01-08"},"type":"conference","status":"public","_id":"14769","department":[{"_id":"MoHe"}],"date_updated":"2024-02-26T09:51:31Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.18034","open_access":"1"}],"scopus_import":"1","month":"01","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"}],"oa_version":"Preprint","ec_funded":1,"publication_status":"published","publication_identifier":{"eisbn":["9781611977929"]},"language":[{"iso":"eng"}]},{"date_created":"2024-02-18T23:01:02Z","doi":"10.1093/gbe/evae006","date_published":"2024-01-20T00:00:00Z","publication":"Genome Biology and Evolution","day":"20","year":"2024","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","external_id":{"pmid":["38245839"]},"article_processing_charge":"Yes","author":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","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","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","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."},"article_number":"evae006","related_material":{"record":[{"status":"public","id":"14705","relation":"research_data"}]},"volume":16,"issue":"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"]},"intvolume":" 16","month":"01","scopus_import":"1","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"}],"department":[{"_id":"BeVi"}],"file_date_updated":"2024-02-26T09:54:59Z","ddc":["570"],"date_updated":"2024-02-26T09:59:30Z","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":"15009"},{"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":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"023101","article_processing_charge":"No","external_id":{"arxiv":["2307.07256"]},"author":[{"full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","last_name":"Karle","first_name":"Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"title":"Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics","citation":{"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.","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.","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.","short":"V. Karle, M. Lemeshko, Physical Review A 109 (2024).","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","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","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."},"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"},{"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":"research_data","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"status":"public","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"_id":"14705","article_processing_charge":"No","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file_date_updated":"2023-12-22T14:14:06Z","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","date_updated":"2024-02-26T09:59:29Z","citation":{"short":"M.N. Elkrewi, (2024).","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.","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"01","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","contributor":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","contributor_type":"researcher","last_name":"Bett"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Beatriz"},{"first_name":"Marwan N","contributor_type":"researcher","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"date_created":"2023-12-22T13:40:48Z","date_published":"2024-01-02T00:00:00Z","doi":"10.15479/AT:ISTA:14705","related_material":{"record":[{"status":"public","id":"15009","relation":"used_in_publication"}]},"year":"2024","has_accepted_license":"1","day":"02","file":[{"file_size":847,"date_updated":"2023-12-22T13:54:21Z","creator":"melkrewi","file_name":"readme.txt.txt","date_created":"2023-12-22T13:54:21Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"file_id":"14707","checksum":"bdaf1392867786634ec5466d528c36ca"},{"date_created":"2023-12-22T14:14:06Z","file_name":"data_artemia_franciscana_genome.zip","creator":"melkrewi","date_updated":"2023-12-22T14:14:06Z","file_size":343632753,"file_id":"14708","checksum":"973e1cbdab923a71709782177980829f","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed"}]},{"status":"public","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"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":"15018","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"ddc":["530"],"date_updated":"2024-02-26T10:36:35Z","month":"02","intvolume":" 174","main_file_link":[{"url":"https://doi.org/10.1016/j.mssp.2024.108231","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":174,"issue":"5","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1369-8001"]},"publication_status":"epub_ahead","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515"}],"article_number":"108231","title":"Compressively strained epitaxial Ge layers for quantum computing applications","author":[{"full_name":"Shimura, Yosuke","last_name":"Shimura","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"},{"orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"},{"first_name":"Paola","full_name":"Favia, Paola","last_name":"Favia"},{"full_name":"Han, Han","last_name":"Han","first_name":"Han"},{"last_name":"Wan","full_name":"Wan, Danny","first_name":"Danny"},{"last_name":"de Greve","full_name":"de Greve, Kristiaan","first_name":"Kristiaan"},{"first_name":"Roger","full_name":"Loo, Roger","last_name":"Loo"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."},"quality_controlled":"1","publisher":"Elsevier","oa":1,"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.","doi":"10.1016/j.mssp.2024.108231","date_published":"2024-02-20T00:00:00Z","date_created":"2024-02-22T14:10:40Z","day":"20","publication":"Materials Science in Semiconductor Processing","has_accepted_license":"1","year":"2024"},{"volume":234,"publication_status":"published","publication_identifier":{"eissn":["2640-3498"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://proceedings.mlr.press/v234/kurtic24a","open_access":"1"}],"alternative_title":["PMLR"],"scopus_import":"1","intvolume":" 234","month":"01","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","department":[{"_id":"DaAl"}],"date_updated":"2024-02-26T10:30:52Z","conference":{"name":"CPAL: Conference on Parsimony and Learning","end_date":"2024-01-06","location":"Hongkong, China","start_date":"2024-01-03"},"type":"conference","status":"public","_id":"15011","page":"542-553","date_created":"2024-02-18T23:01:03Z","date_published":"2024-01-08T00:00:00Z","year":"2024","publication":"Proceedings of Machine Learning Research","day":"08","oa":1,"publisher":"ML Research Press","quality_controlled":"1","article_processing_charge":"No","external_id":{"arxiv":["2312.13547"]},"author":[{"last_name":"Kurtic","full_name":"Kurtic, Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","citation":{"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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_number":"064503","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"citation":{"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).","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2311.11784"],"pmid":["38349632"]},"author":[{"first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","last_name":"Robin","full_name":"Robin, Paul","orcid":"0000-0002-5728-9189"}],"title":"Correlation-induced viscous dissipation in concentrated electrolytes","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","year":"2024","has_accepted_license":"1","publication":"Journal of Chemical Physics","day":"14","date_created":"2024-02-25T23:00:55Z","date_published":"2024-02-14T00:00:00Z","doi":"10.1063/5.0188215","_id":"15024","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","date_updated":"2024-02-27T08:16:06Z","ddc":["540"],"file_date_updated":"2024-02-27T08:12:52Z","department":[{"_id":"EdHa"}],"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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 160","month":"02","publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2024_JourChemicalPhysics_Robin.pdf","date_created":"2024-02-27T08:12:52Z","creator":"dernst","file_size":5452738,"date_updated":"2024-02-27T08:12:52Z","success":1,"file_id":"15034","checksum":"0a5e0ae70849bce674466fc054390ec0","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"issue":"6","volume":160},{"day":"01","publication":"Annals of Applied Probability","year":"2024","date_published":"2024-02-01T00:00:00Z","doi":"10.1214/23-AAP2000","date_created":"2024-02-25T23:00:56Z","page":"1623-1662","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.","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","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","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","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."},"title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Benjamin","id":"b0cc634c-d549-11ee-96c8-87338c7ad808","last_name":"McKenna","full_name":"McKenna, Benjamin","orcid":"0000-0003-2625-495X"}],"article_processing_charge":"No","external_id":{"arxiv":["2208.12206"]},"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1050-5164"]},"publication_status":"published","issue":"1B","volume":34,"ec_funded":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."}],"month":"02","intvolume":" 34","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.12206"}],"date_updated":"2024-02-27T08:29:05Z","department":[{"_id":"LaEr"}],"_id":"15025","status":"public","article_type":"original","type":"journal_article"},{"has_accepted_license":"1","year":"2024","day":"21","publication":"eLife","date_published":"2024-02-21T00:00:00Z","doi":"10.7554/elife.68993","date_created":"2024-02-27T07:10:11Z","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","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"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","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.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (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","author":[{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski"},{"full_name":"Matijevic, Ivana","last_name":"Matijevic","first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"Yes","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"volume":13,"ec_funded":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68993","open_access":"1"}],"month":"02","intvolume":" 13","date_updated":"2024-02-28T12:29:43Z","ddc":["580"],"department":[{"_id":"JiFr"}],"_id":"15033","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":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"]},{"department":[{"_id":"SyCr"}],"date_updated":"2024-03-04T07:14:41Z","type":"journal_article","article_type":"original","status":"public","_id":"14479","issue":"4","volume":34,"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.26.564092"}],"month":"02","intvolume":" 34","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","author":[{"full_name":"Csata, Eniko","last_name":"Csata","first_name":"Eniko"},{"first_name":"Alfonso","full_name":"Perez-Escudero, Alfonso","last_name":"Perez-Escudero"},{"first_name":"Emmanuel","last_name":"Laury","full_name":"Laury, Emmanuel"},{"id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna","last_name":"Leitner","full_name":"Leitner, Hanna"},{"first_name":"Gerard","full_name":"Latil, Gerard","last_name":"Latil"},{"first_name":"Juerge","last_name":"Heinze","full_name":"Heinze, Juerge"},{"last_name":"Simpson","full_name":"Simpson, Stephen","first_name":"Stephen"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"}],"article_processing_charge":"No","external_id":{"pmid":["38307022"]},"title":"Fungal infection alters collective nutritional intake of ant colonies","citation":{"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.","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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"902-909.e6","date_published":"2024-02-26T00:00:00Z","doi":"10.1016/j.cub.2024.01.017","date_created":"2023-10-31T13:30:20Z","year":"2024","day":"26","publication":"Current Biology","publisher":"Elsevier","quality_controlled":"1","oa":1,"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."},{"day":"17","publication":"Few-Body Systems","has_accepted_license":"1","year":"2024","doi":"10.1007/s00601-024-01880-x","date_published":"2024-02-17T00:00:00Z","date_created":"2024-03-01T11:39:33Z","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).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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."},"title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","author":[{"last_name":"Varshney","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"external_id":{"arxiv":["2401.08454"]},"article_processing_charge":"Yes (via OA deal)","article_number":"12","file":[{"file_name":"2024_FewBodySys_Varshney.pdf","date_created":"2024-03-04T07:07:10Z","creator":"dernst","file_size":436712,"date_updated":"2024-03-04T07:07:10Z","success":1,"checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","file_id":"15049","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1432-5411"]},"publication_status":"published","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"}],"month":"02","intvolume":" 65","scopus_import":"1","ddc":["530"],"date_updated":"2024-03-04T07:08:16Z","department":[{"_id":"MiLe"}],"file_date_updated":"2024-03-04T07:07:10Z","_id":"15045","status":"public","keyword":["Atomic and Molecular Physics","and Optics"],"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)"}},{"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","has_accepted_license":"1","year":"2024","day":"13","publication":"Physical Review Research","article_number":"013158","author":[{"first_name":"Shuwei","last_name":"Jin","full_name":"Jin, Shuwei"},{"last_name":"Dai","full_name":"Dai, Kunlun","first_name":"Kunlun"},{"first_name":"Joris","last_name":"Verstraten","full_name":"Verstraten, Joris"},{"full_name":"Dixmerias, Maxime","last_name":"Dixmerias","first_name":"Maxime"},{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder"},{"first_name":"Christophe","full_name":"Salomon, Christophe","last_name":"Salomon"},{"last_name":"Peaudecerf","full_name":"Peaudecerf, Bruno","first_name":"Bruno"},{"first_name":"Tim","last_name":"de Jongh","full_name":"de Jongh, Tim"},{"first_name":"Tarik","last_name":"Yefsah","full_name":"Yefsah, Tarik"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2304.08433"]},"title":"Multipurpose platform for analog quantum simulation","citation":{"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).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"02","intvolume":" 6","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","issue":"1","volume":6,"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"checksum":"ba2ae3e3a011f8897d3803c9366a67e2","file_id":"15054","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-03-04T07:53:08Z","file_name":"2024_PhysicalReviewResearch_Jin.pdf","date_updated":"2024-03-04T07:53:08Z","file_size":4025988,"creator":"dernst"}],"language":[{"iso":"eng"}],"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","keyword":["General Physics and Astronomy"],"_id":"15053","department":[{"_id":"MiLe"}],"file_date_updated":"2024-03-04T07:53:08Z","date_updated":"2024-03-04T07:55:29Z","ddc":["530"]},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","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."}],"month":"02","intvolume":" 151","scopus_import":"1","file":[{"success":1,"file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2024_Development_Schauer.pdf","date_created":"2024-03-04T07:24:43Z","creator":"dernst","file_size":14839986,"date_updated":"2024-03-04T07:24:43Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication_status":"published","issue":"4","volume":151,"related_material":{"record":[{"relation":"research_data","status":"public","id":"14926"}]},"ec_funded":1,"_id":"15048","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)"},"ddc":["570"],"date_updated":"2024-03-04T07:28:25Z","file_date_updated":"2024-03-04T07:24:43Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"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. ","quality_controlled":"1","publisher":"The Company of Biologists","oa":1,"day":"01","publication":"Development","has_accepted_license":"1","year":"2024","doi":"10.1242/dev.202316","date_published":"2024-02-01T00:00:00Z","date_created":"2024-03-03T23:00:50Z","page":"1-18","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"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."},"title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","author":[{"orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","last_name":"Schauer","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_processing_charge":"Yes (via OA deal)"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"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.","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024.","short":"R. Hauschild, (2024).","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"},"title":"Matlab script for analysis of clone dispersal","department":[{"_id":"Bio"}],"file_date_updated":"2024-02-02T14:40:31Z","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","type":"software","tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"file":[{"content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","success":1,"checksum":"df7f358ae19a176cf710c0a802ce31b1","file_id":"14927","file_size":736,"date_updated":"2024-02-02T14:40:31Z","creator":"rhauschild","file_name":"README.md","date_created":"2024-02-02T14:40:31Z"},{"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","checksum":"10194cc11619eccd8f4b24472e465b7f","file_id":"14928","success":1,"date_updated":"2024-02-02T14:40:31Z","file_size":3543,"creator":"rhauschild","date_created":"2024-02-02T14:40:31Z","file_name":"Supplementary_file_1.zip"}],"day":"02","has_accepted_license":"1","year":"2024","related_material":{"record":[{"relation":"used_in_publication","id":"15048","status":"public"}]},"date_published":"2024-02-02T00:00:00Z","doi":"10.15479/AT:ISTA:14926","date_created":"2024-02-02T14:42:26Z","license":"https://opensource.org/licenses/MIT","month":"02","publisher":"ISTA","oa":1},{"citation":{"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.","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.","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","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).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"pmid":["38394192"]},"author":[{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","first_name":"Jiawei","full_name":"Bao, Jiawei","last_name":"Bao"},{"first_name":"Bjorn","last_name":"Stevens","full_name":"Stevens, Bjorn"},{"last_name":"Kluft","full_name":"Kluft, Lukas","first_name":"Lukas"},{"last_name":"Muller","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"title":"Intensification of daily tropical precipitation extremes from more organized convection","article_number":"eadj6801","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"year":"2024","has_accepted_license":"1","publication":"Science Advances","day":"23","date_created":"2024-03-03T23:00:50Z","doi":"10.1126/sciadv.adj6801","date_published":"2024-02-23T00:00:00Z","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,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","date_updated":"2024-03-05T09:26:47Z","ddc":["550"],"department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-04T07:34:00Z","_id":"15047","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":["2375-2548"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"15051","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","success":1,"date_updated":"2024-03-04T07:34:00Z","file_size":800926,"creator":"dernst","date_created":"2024-03-04T07:34:00Z","file_name":"2024_ScienceAdv_Bao.pdf"}],"ec_funded":1,"volume":10,"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","description":"News on ISTA Website"}]},"issue":"8","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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"02"},{"file_date_updated":"2024-02-06T13:56:15Z","department":[{"_id":"SiHi"},{"_id":"RySh"}],"ddc":["570"],"date_updated":"2024-03-05T09:43:02Z","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)"},"_id":"12875","issue":"2","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/"}]},"volume":112,"file":[{"success":1,"file_id":"14944","checksum":"32b3788f7085cf44a84108d8faaff3ce","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2024_Neuron_Cheung.pdf","date_created":"2024-02-06T13:56:15Z","file_size":5942467,"date_updated":"2024-02-06T13:56:15Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","month":"01","intvolume":" 112","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."}],"title":"Multipotent progenitors instruct ontogeny of the superior colliculus","author":[{"last_name":"Cheung","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"last_name":"Krausgruber","full_name":"Krausgruber, Thomas","first_name":"Thomas"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher"},{"full_name":"Schrammel, Martin","last_name":"Schrammel","first_name":"Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d"},{"full_name":"Özgen, Natalie Y","last_name":"Özgen","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","first_name":"Natalie Y"},{"id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","first_name":"Alexis","last_name":"Ivec","full_name":"Ivec, Alexis"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["38096816"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","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.","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."},"project":[{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1016/j.neuron.2023.11.009","date_published":"2024-01-17T00:00:00Z","date_created":"2023-04-27T09:41:48Z","page":"230-246.e11","day":"17","publication":"Neuron","has_accepted_license":"1","year":"2024","quality_controlled":"1","publisher":"Elsevier","oa":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. "},{"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,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41594-023-01201-6"}],"month":"02","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release"}]},"_id":"14979","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","keyword":["Molecular Biology","Structural Biology"],"date_updated":"2024-03-05T09:27:47Z","ddc":["570"],"department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2024","day":"05","publication":"Nature Structural & Molecular Biology","date_published":"2024-02-05T00:00:00Z","doi":"10.1038/s41594-023-01201-6","date_created":"2024-02-12T09:59:45Z","project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445"}],"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.","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","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","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)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","last_name":"Datler"},{"first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse","last_name":"Hansen"},{"first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","last_name":"Thader"},{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"full_name":"Bauer, Lukas W","last_name":"Bauer","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"external_id":{"pmid":["38316877"]},"article_processing_charge":"Yes (in subscription journal)","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores"},{"day":"09","publication":"Nature Physics","has_accepted_license":"1","year":"2024","date_published":"2024-01-09T00:00:00Z","doi":"10.1038/s41567-023-02302-1","date_created":"2024-01-21T23:00:57Z","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).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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."},"title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","author":[{"last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shinde, Rushikesh","last_name":"Shinde","first_name":"Rushikesh"},{"last_name":"Bolger-Munro","full_name":"Bolger-Munro, Madison","orcid":"0000-0002-8176-4824","first_name":"Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E"},{"first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"last_name":"Szep","full_name":"Szep, Gregory","first_name":"Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Steccari, Irene","last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene"},{"id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","first_name":"David","full_name":"Labrousse Arias, David","last_name":"Labrousse Arias"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones","first_name":"Andrew"},{"first_name":"Raphaël","full_name":"Voituriez, Raphaël","last_name":"Voituriez"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (in subscription journal)","project":[{"call_identifier":"FWF","_id":"2646861A-B435-11E9-9278-68D0E5697425","name":"Control of embryonic cleavage pattern","grant_number":"I03601"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication_status":"epub_ahead","related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/","relation":"press_release"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","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."}],"month":"01","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41567-023-02302-1","open_access":"1"}],"date_updated":"2024-03-05T09:33:38Z","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"_id":"14846","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)"}},{"oa":1,"publisher":"Institute of Science and Technology Austria","year":"2024","has_accepted_license":"1","day":"23","page":"158","date_created":"2024-02-23T14:02:04Z","doi":"10.15479/at:ista:15020","date_published":"2024-02-23T00:00:00Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"citation":{"ama":"Hledik M. Genetic information and biological optimization. 2024. doi: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","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"}],"title":"Genetic information and biological optimization","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"02","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"b2d3da47c98d481577a4baf68944fe41","file_id":"15021","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_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_name":"hledik thesis source.zip","date_created":"2024-02-23T13:50:54Z","file_size":14014790,"date_updated":"2024-02-23T14:20:16Z","creator":"mhledik","file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a","content_type":"application/zip","relation":"source_file","access_level":"closed"}],"ec_funded":1,"related_material":{"record":[{"id":"7553","status":"public","relation":"part_of_dissertation"},{"id":"12081","status":"public","relation":"part_of_dissertation"},{"id":"7606","status":"public","relation":"part_of_dissertation"}]},"_id":"15020","type":"dissertation","keyword":["Theoretical biology","Optimality","Evolution","Information"],"status":"public","date_updated":"2024-03-06T14:22:52Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"ddc":["576","519"],"file_date_updated":"2024-02-23T14:20:16Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}]},{"article_processing_charge":"No","author":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"title":"Eva Benkova","citation":{"chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039.","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","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","short":"E. Benková, Eva Benkova, Elsevier, 2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Elsevier","page":"R3-R5","date_created":"2024-01-21T23:00:56Z","doi":"10.1016/j.cub.2023.11.039","date_published":"2024-01-08T00:00:00Z","year":"2024","publication":"Current Biology","day":"08","type":"other_academic_publication","status":"public","_id":"14842","department":[{"_id":"EvBe"}],"date_updated":"2024-03-12T12:19:12Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2023.11.039","open_access":"1"}],"intvolume":" 34","month":"01","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":34,"issue":"1","publication_status":"published","publication_identifier":{"eissn":["1879-0445"]},"language":[{"iso":"eng"}]},{"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.","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"day":"20","publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","year":"2024","date_published":"2024-02-20T00:00:00Z","doi":"10.1073/pnas.2301449121","date_created":"2024-03-05T09:23:55Z","article_number":"e2301449121","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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)."},"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","author":[{"first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal","id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane"},{"first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","last_name":"Le Monnier"},{"last_name":"Roy","full_name":"Roy, Utsa","first_name":"Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"full_name":"Sadakata, Tetsushi","last_name":"Sadakata","first_name":"Tetsushi"},{"first_name":"Makoto","full_name":"Sanbo, Makoto","last_name":"Sanbo"},{"full_name":"Hirabayashi, Masumi","last_name":"Hirabayashi","first_name":"Masumi"},{"last_name":"Rhee","full_name":"Rhee, JeongSeop","first_name":"JeongSeop"},{"last_name":"Brose","full_name":"Brose, Nils","first_name":"Nils"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["38346189"]},"article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"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"}],"month":"02","intvolume":" 121","file":[{"file_name":"2024_PNAS_Koppensteiner.pdf","date_created":"2024-03-12T13:42:42Z","creator":"dernst","file_size":13648221,"date_updated":"2024-03-12T13:42:42Z","success":1,"file_id":"15110","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","volume":121,"issue":"8","related_material":{"record":[{"id":"13173","status":"public","relation":"research_data"}],"link":[{"url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","relation":"press_release","description":"News on ISTA Website"}]},"ec_funded":1,"_id":"15084","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":"2024-03-12T13:44:18Z","file_date_updated":"2024-03-12T13:42:42Z","department":[{"_id":"RySh"},{"_id":"PeJo"}]},{"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","department":[{"_id":"KrCh"}],"file_date_updated":"2024-03-12T13:12:22Z","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."}],"oa_version":"Published Version","pmid":1,"issue":"10","volume":121,"related_material":{"record":[{"status":"public","id":"15108","relation":"research_data"}],"link":[{"url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","relation":"press_release","description":"News on ISTA Website"}]},"ec_funded":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"date_created":"2024-03-12T13:12:22Z","file_name":"2024_PNAS_Huebner.pdf","creator":"dernst","date_updated":"2024-03-12T13:12:22Z","file_size":2203220,"checksum":"068520e3efd4d008bb9177e8aedb7d22","file_id":"15109","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"e2315558121","author":[{"first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","last_name":"Hübner","full_name":"Hübner, Valentin"},{"first_name":"Manuel","last_name":"Staab","full_name":"Staab, Manuel"},{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","first_name":"Maria"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38408249"]},"title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","citation":{"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).","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","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.","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."},"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.).","date_published":"2024-03-05T00:00:00Z","doi":"10.1073/pnas.2315558121","date_created":"2024-03-05T09:18:49Z","has_accepted_license":"1","year":"2024","day":"05","publication":"Proceedings of the National Academy of Sciences"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2024-03-12T13:29:26Z","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.","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","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","short":"V. Hübner, M. Kleshnina, (2024).","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","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."},"title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","department":[{"_id":"KrCh"}],"article_processing_charge":"No","author":[{"full_name":"Hübner, Valentin","last_name":"Hübner","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin"},{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","first_name":"Maria"}],"_id":"15108","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":"research_data_reference","day":"09","year":"2024","has_accepted_license":"1","date_created":"2024-03-12T13:02:58Z","doi":"10.5281/ZENODO.10639167","date_published":"2024-02-09T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"15083","status":"public"}]},"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."}],"month":"02","main_file_link":[{"open_access":"1","url":"https://10.5281/zenodo.10639167"}],"oa":1,"publisher":"Zenodo"},{"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":"15097","department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-13T08:59:21Z","ddc":["550"],"date_updated":"2024-03-13T09:01:20Z","intvolume":" 17","month":"02","scopus_import":"1","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"}],"issue":"4","volume":17,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-03-13T08:59:21Z","file_size":13364601,"date_created":"2024-03-13T08:59:21Z","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15111","checksum":"270d2340402729b0532f7072ea914cae","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Hauke","full_name":"Schmidt, Hauke","last_name":"Schmidt"},{"first_name":"Sebastian","last_name":"Rast","full_name":"Rast, Sebastian"},{"first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","last_name":"Bao","full_name":"Bao, Jiawei"},{"last_name":"Cassim","full_name":"Cassim, Amrit","first_name":"Amrit"},{"full_name":"Fang, Shih Wei","last_name":"Fang","first_name":"Shih Wei"},{"last_name":"Jimenez-De La Cuesta","full_name":"Jimenez-De La Cuesta, Diego","first_name":"Diego"},{"first_name":"Paul","last_name":"Keil","full_name":"Keil, Paul"},{"full_name":"Kluft, Lukas","last_name":"Kluft","first_name":"Lukas"},{"last_name":"Kroll","full_name":"Kroll, Clarissa","first_name":"Clarissa"},{"first_name":"Theresa","last_name":"Lang","full_name":"Lang, Theresa"},{"first_name":"Ulrike","full_name":"Niemeier, Ulrike","last_name":"Niemeier"},{"full_name":"Schneidereit, Andrea","last_name":"Schneidereit","first_name":"Andrea"},{"first_name":"Andrew I.L.","last_name":"Williams","full_name":"Williams, Andrew I.L."},{"first_name":"Bjorn","full_name":"Stevens, Bjorn","last_name":"Stevens"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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.","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."},"oa":1,"quality_controlled":"1","publisher":"European Geosciences Union","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.","date_created":"2024-03-10T23:00:53Z","date_published":"2024-02-22T00:00:00Z","doi":"10.5194/gmd-17-1563-2024","page":"1563-1584","publication":"Geoscientific Model Development","day":"22","year":"2024","has_accepted_license":"1"},{"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_number":"2203.02015","title":"Common valuations of division polynomials","author":[{"last_name":"Naskręcki","full_name":"Naskręcki, Bartosz","first_name":"Bartosz"},{"first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","last_name":"Verzobio","full_name":"Verzobio, Matteo","orcid":"0000-0002-0854-0306"}],"external_id":{"arxiv":["2203.02015"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.","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.","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","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","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)."},"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"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.","doi":"10.1017/prm.2024.7","date_published":"2024-02-26T00:00:00Z","date_created":"2023-01-16T11:45:22Z","day":"26","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","has_accepted_license":"1","year":"2024","status":"public","keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"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":"12311","department":[{"_id":"TiBr"}],"ddc":["510"],"date_updated":"2024-03-13T11:55:21Z","month":"02","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/prm.2024.7"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"publication_status":"epub_ahead"},{"month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tig.2024.01.002"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]},"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":"review","type":"journal_article","_id":"15099","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2024-03-13T12:08:57Z","oa":1,"quality_controlled":"1","publisher":"Cell Press","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_created":"2024-03-10T23:00:54Z","doi":"10.1016/j.tig.2024.01.002","date_published":"2024-02-22T00:00:00Z","publication":"Trends in Genetics","day":"22","year":"2024","has_accepted_license":"1","title":"Diverse pathways to speciation revealed by marine snails","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38395682"]},"author":[{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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"}},{"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."}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1007/s00208-024-02812-0","open_access":"1"}],"scopus_import":"1","month":"02","publication_status":"epub_ahead","publication_identifier":{"issn":["0025-5831"],"eissn":["1432-1807"]},"language":[{"iso":"eng"}],"ec_funded":1,"_id":"15098","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-13T12:20:23Z","department":[{"_id":"JuFi"}],"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).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2024","publication":"Mathematische Annalen","day":"27","date_created":"2024-03-10T23:00:54Z","date_published":"2024-02-27T00:00:00Z","doi":"10.1007/s00208-024-02812-0","project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"citation":{"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.","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen.","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.","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2306.11081"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio"},{"last_name":"Luongo","full_name":"Luongo, Eliseo","first_name":"Eliseo"}],"title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions"},{"_id":"15122","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)"},"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."}],"month":"03","intvolume":" 6","scopus_import":"1","file":[{"date_created":"2024-03-19T07:16:38Z","file_name":"2024_PhysicalReviewResearch_Sack.pdf","date_updated":"2024-03-19T07:16:38Z","file_size":2777593,"creator":"dernst","file_id":"15123","checksum":"274c9f1b15b3547a10a03f39e4ccc582","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","volume":6,"issue":"1","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.","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","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.","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","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","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","author":[{"last_name":"Sack","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"},{"first_name":"Daniel J.","full_name":"Egger, Daniel J.","last_name":"Egger"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2307.14427"]},"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.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"01","publication":"Physical Review Research","has_accepted_license":"1","year":"2024","doi":"10.1103/PhysRevResearch.6.013223","date_published":"2024-03-01T00:00:00Z","date_created":"2024-03-17T23:00:59Z"},{"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.","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"day":"01","publication":"Annales de l'institut Henri Poincare Probability and Statistics","year":"2024","doi":"10.1214/22-AIHP1333","date_published":"2024-02-01T00:00:00Z","date_created":"2024-03-17T23:00:58Z","page":"413-430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430.","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.","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.","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.","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."},"title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions","author":[{"orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio"},{"first_name":"Mark","full_name":"Veraar, Mark","last_name":"Veraar"}],"article_processing_charge":"No","external_id":{"arxiv":["2106.01274"]},"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"}],"month":"02","intvolume":" 60","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","volume":60,"issue":"1","_id":"15119","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-19T08:14:17Z","department":[{"_id":"JuFi"}]},{"title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","author":[{"first_name":"Michael","last_name":"Habig","full_name":"Habig, Michael"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"first_name":"Judith","last_name":"Müller","full_name":"Müller, Judith"},{"last_name":"Stukenbrock","full_name":"Stukenbrock, Eva H.","first_name":"Eva H."},{"full_name":"Leitner, Hanna","last_name":"Leitner","first_name":"Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38442176"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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."},"project":[{"call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"article_number":"e2316284121","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","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.","file_date_updated":"2024-03-19T09:02:57Z","department":[{"_id":"SyCr"}],"ddc":["570"],"date_updated":"2024-03-19T09:07:20Z","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"},"_id":"14478","issue":"11","volume":121,"ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15124","checksum":"f5e871db617b682edc71fcd08670dc81","creator":"dernst","file_size":5750361,"date_updated":"2024-03-19T09:02:57Z","file_name":"2024_PNAS_Habig.pdf","date_created":"2024-03-19T09:02:57Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","month":"03","intvolume":" 121","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}]},{"publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"publication_status":"epub_ahead","file":[{"date_created":"2021-09-27T10:54:51Z","file_name":"Generalized-0-Ext.pdf","date_updated":"2021-09-27T10:54:51Z","file_size":603672,"creator":"mdvorak","file_id":"10046","checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","abstract":[{"lang":"eng","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"}],"oa_version":"Preprint","file_date_updated":"2021-09-27T10:54:51Z","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"date_updated":"2024-03-19T08:20:31Z","ddc":["004"],"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":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"_id":"10045","date_published":"2024-03-07T00:00:00Z","doi":"10.1007/s10107-024-02064-5","date_created":"2021-09-27T10:48:23Z","has_accepted_license":"1","year":"2024","day":"07","publication":"Mathematical Programming","publisher":"Springer Nature","quality_controlled":"1","oa":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).","author":[{"full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X","last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2109.10203"]},"article_processing_charge":"Yes (via OA deal)","title":"Generalized minimum 0-extension problem and discrete convexity","citation":{"ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203.","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.","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).","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2109.10203"},{"project":[{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"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":"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.","ista":"Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming.","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.","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.","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"},"title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","author":[{"last_name":"Zheng","full_name":"Zheng, Da Wei","first_name":"Da Wei"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.09217"]},"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.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"06","publication":"Mathematical Programming","year":"2024","doi":"10.1007/s10107-024-02066-3","date_published":"2024-03-06T00:00:00Z","date_created":"2024-03-17T23:00:58Z","_id":"15121","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-03-19T08:32:32Z","department":[{"_id":"MoHe"}],"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","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.09217"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1436-4646"],"issn":["0025-5610"]},"publication_status":"epub_ahead","related_material":{"record":[{"status":"public","id":"13236","relation":"earlier_version"}]},"ec_funded":1},{"_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","date_updated":"2024-03-19T11:41:32Z","ddc":["550"],"department":[{"_id":"AnSa"}],"file_date_updated":"2024-03-19T10:22:42Z","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 121","month":"03","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"file":[{"file_id":"15125","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-03-19T10:22:42Z","file_name":"2024_PNAS_Giubertoni.pdf","date_updated":"2024-03-19T10:22:42Z","file_size":12952586,"creator":"dernst"}],"volume":121,"related_material":{"record":[{"status":"public","id":"15126","relation":"research_data"}]},"issue":"11","article_number":"e2313162121","citation":{"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","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).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38451946"]},"author":[{"last_name":"Giubertoni","full_name":"Giubertoni, Giulia","first_name":"Giulia"},{"first_name":"Liru","full_name":"Feng, Liru","last_name":"Feng"},{"first_name":"Kevin","full_name":"Klein, Kevin","last_name":"Klein"},{"full_name":"Giannetti, Guido","last_name":"Giannetti","first_name":"Guido"},{"last_name":"Rutten","full_name":"Rutten, Luco","first_name":"Luco"},{"first_name":"Yeji","full_name":"Choi, Yeji","last_name":"Choi"},{"first_name":"Anouk","full_name":"Van Der Net, Anouk","last_name":"Van Der Net"},{"first_name":"Gerard","last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard"},{"last_name":"Caporaletti","full_name":"Caporaletti, Federico","first_name":"Federico"},{"full_name":"Micha, Dimitra","last_name":"Micha","first_name":"Dimitra"},{"full_name":"Hunger, Johannes","last_name":"Hunger","first_name":"Johannes"},{"last_name":"Deblais","full_name":"Deblais, Antoine","first_name":"Antoine"},{"last_name":"Bonn","full_name":"Bonn, Daniel","first_name":"Daniel"},{"last_name":"Sommerdijk","full_name":"Sommerdijk, Nico","first_name":"Nico"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Ilie, Ioana M.","last_name":"Ilie","first_name":"Ioana M."},{"last_name":"Koenderink","full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H."},{"last_name":"Woutersen","full_name":"Woutersen, Sander","first_name":"Sander"}],"title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","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","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","date_published":"2024-03-12T00:00:00Z","doi":"10.1073/pnas.2313162121"},{"date_created":"2024-03-19T10:47:16Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15116"}]},"doi":"10.21942/UVA.24829896","date_published":"2024-02-14T00:00:00Z","year":"2024","has_accepted_license":"1","day":"14","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.21942/UVA.24829896"}],"publisher":"Figshare","month":"02","abstract":[{"lang":"eng","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\"."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"G.","full_name":"Giubertoni, G.","last_name":"Giubertoni"},{"first_name":"S.","last_name":"Woutersen","full_name":"Woutersen, S."}],"title":"Dataset Collagen Self Assembly in H2O and D2O","citation":{"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.","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"},"date_updated":"2024-03-19T11:41:33Z","ddc":["550"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","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":"research_data_reference","status":"public","_id":"15126"},{"abstract":[{"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","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","date_updated":"2024-03-14T08:55:07Z","file_size":4106872,"creator":"scultrer","file_id":"15112","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"15113","checksum":"bcbd213490f5a7e68855a092bbce93f1","date_updated":"2024-03-14T14:14:35Z","file_size":4746234,"creator":"scultrer","date_created":"2024-03-14T08:56:24Z","file_name":"Thesis (1).zip"}],"ec_funded":1,"related_material":{"record":[{"id":"11660","status":"public","relation":"part_of_dissertation"},{"id":"11658","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"13182","relation":"part_of_dissertation"},{"status":"public","id":"15090","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"15091","status":"public"},{"status":"public","id":"15093","relation":"part_of_dissertation"}]},"_id":"15094","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","status":"public","date_updated":"2024-03-20T09:36:57Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"ddc":["514","500","516"],"file_date_updated":"2024-03-14T14:14:35Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"oa":1,"publisher":"Institute of Science and Technology Austria","year":"2024","has_accepted_license":"1","day":"08","page":"108","date_created":"2024-03-08T15:28:10Z","date_published":"2024-03-08T00:00:00Z","doi":"10.15479/at:ista:15094","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","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"}],"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.","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","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano"}],"title":"Persistence and Morse theory for discrete geometric structures"},{"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"citation":{"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","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","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":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Lara","last_name":"Ost","full_name":"Ost, Lara"}],"external_id":{"arxiv":["2311.01115"]},"article_processing_charge":"No","title":"Dynamically maintaining the persistent homology of time series","editor":[{"last_name":"Woodruff","full_name":"Woodruff, David P.","first_name":"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","_id":"15093","type":"conference","conference":{"start_date":"2024-01-07","end_date":"2024-01-10","location":"Alexandria, VA, USA","name":"SODA: Symposium on Discrete Algorigthms"},"status":"public","date_updated":"2024-03-20T09:36:56Z","department":[{"_id":"HeEd"},{"_id":"MoHe"}],"abstract":[{"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.","lang":"eng"}],"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},{"month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"oa":1,"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."}],"date_created":"2024-03-08T10:13:59Z","date_published":"2024-02-07T00:00:00Z","related_material":{"record":[{"id":"15094","status":"public","relation":"dissertation_contains"}]},"publication":"arXiv","language":[{"iso":"eng"}],"day":"07","year":"2024","publication_status":"submitted","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","title":"Chromatic alpha complexes","department":[{"_id":"HeEd"}],"external_id":{"arxiv":["2212.03128"]},"article_processing_charge":"No","author":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano"},{"last_name":"Draganov","full_name":"Draganov, Ondrej","first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128."},"date_updated":"2024-03-20T09:36:56Z"},{"project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"author":[{"first_name":"Everton J.","full_name":"Agnes, Everton J.","last_name":"Agnes"},{"last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"article_processing_charge":"Yes (via OA deal)","title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks","citation":{"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.","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.","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.","short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience (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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.","doi":"10.1038/s41593-024-01597-4","date_published":"2024-03-20T00:00:00Z","date_created":"2024-03-24T23:01:00Z","year":"2024","day":"20","publication":"Nature Neuroscience","type":"journal_article","article_type":"original","status":"public","_id":"15171","department":[{"_id":"TiVo"}],"date_updated":"2024-03-25T07:04:05Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-024-01597-4"}],"month":"03","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}]},{"file_date_updated":"2024-03-25T08:02:43Z","department":[{"_id":"JoMa"}],"ddc":["550"],"date_updated":"2024-03-25T08:04:13Z","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":"15170","volume":964,"language":[{"iso":"eng"}],"file":[{"date_updated":"2024-03-25T08:02:43Z","file_size":2700137,"creator":"dernst","date_created":"2024-03-25T08:02:43Z","file_name":"2024_AstrophysicalJourn_Greene.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"389a880e176799d5c062ea7cb82d08c9","file_id":"15176","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"intvolume":" 964","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"title":"UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5","article_processing_charge":"Yes","external_id":{"arxiv":["2309.05714"]},"author":[{"last_name":"Greene","full_name":"Greene, Jenny E.","first_name":"Jenny E."},{"first_name":"Ivo","last_name":"Labbe","full_name":"Labbe, Ivo"},{"last_name":"Goulding","full_name":"Goulding, Andy D.","first_name":"Andy D."},{"first_name":"Lukas J.","full_name":"Furtak, Lukas J.","last_name":"Furtak"},{"first_name":"Iryna","full_name":"Chemerynska, Iryna","last_name":"Chemerynska"},{"first_name":"Vasily","full_name":"Kokorev, Vasily","last_name":"Kokorev"},{"first_name":"Pratika","last_name":"Dayal","full_name":"Dayal, Pratika"},{"last_name":"Volonteri","full_name":"Volonteri, Marta","first_name":"Marta"},{"first_name":"Christina C.","full_name":"Williams, Christina C.","last_name":"Williams"},{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"full_name":"Setton, David J.","last_name":"Setton","first_name":"David J."},{"full_name":"Burgasser, Adam J.","last_name":"Burgasser","first_name":"Adam J."},{"last_name":"Bezanson","full_name":"Bezanson, Rachel","first_name":"Rachel"},{"full_name":"Atek, Hakim","last_name":"Atek","first_name":"Hakim"},{"first_name":"Gabriel","full_name":"Brammer, Gabriel","last_name":"Brammer"},{"last_name":"Cutler","full_name":"Cutler, Sam E.","first_name":"Sam E."},{"full_name":"Feldmann, Robert","last_name":"Feldmann","first_name":"Robert"},{"last_name":"Fujimoto","full_name":"Fujimoto, Seiji","first_name":"Seiji"},{"first_name":"Karl","full_name":"Glazebrook, Karl","last_name":"Glazebrook"},{"first_name":"Anna","last_name":"De Graaff","full_name":"De Graaff, Anna"},{"first_name":"Gourav","full_name":"Khullar, Gourav","last_name":"Khullar"},{"last_name":"Leja","full_name":"Leja, Joel","first_name":"Joel"},{"first_name":"Danilo","last_name":"Marchesini","full_name":"Marchesini, Danilo"},{"last_name":"Maseda","full_name":"Maseda, Michael V.","first_name":"Michael V."},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X"},{"full_name":"Miller, Tim B.","last_name":"Miller","first_name":"Tim B."},{"first_name":"Rohan P.","full_name":"Naidu, Rohan P.","last_name":"Naidu"},{"full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara","first_name":"Themiya"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"first_name":"Richard","full_name":"Pan, Richard","last_name":"Pan"},{"full_name":"Papovich, Casey","last_name":"Papovich","first_name":"Casey"},{"last_name":"Price","full_name":"Price, Sedona H.","first_name":"Sedona H."},{"first_name":"Pieter","last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter"},{"first_name":"John R.","last_name":"Weaver","full_name":"Weaver, John R."},{"first_name":"Katherine E.","last_name":"Whitaker","full_name":"Whitaker, Katherine E."},{"first_name":"Adi","full_name":"Zitrin, Adi","last_name":"Zitrin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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","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).","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."},"article_number":"39","date_created":"2024-03-24T23:00:59Z","doi":"10.3847/1538-4357/ad1e5f","date_published":"2024-03-01T00:00:00Z","publication":"Astrophysical Journal","day":"01","year":"2024","has_accepted_license":"1","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","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."},{"article_number":"34","project":[{"name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312","_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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."},"title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","author":[{"first_name":"Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","last_name":"Filakovský","full_name":"Filakovský, Marek"},{"full_name":"Nakajima, Tamio Vesa","last_name":"Nakajima","first_name":"Tamio Vesa"},{"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","first_name":"Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"article_processing_charge":"No","external_id":{"arxiv":["2312.12981"]},"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).","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"day":"01","publication":"41st International Symposium on Theoretical Aspects of Computer Science","has_accepted_license":"1","year":"2024","doi":"10.4230/LIPIcs.STACS.2024.34","date_published":"2024-03-01T00:00:00Z","date_created":"2024-03-24T23:00:59Z","_id":"15168","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":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","location":"Clermont-Ferrand, France","end_date":"2024-03-14","start_date":"2024-03-12"},"ddc":["510"],"date_updated":"2024-03-25T07:45:54Z","department":[{"_id":"UlWa"}],"file_date_updated":"2024-03-25T07:44:30Z","oa_version":"Published Version","abstract":[{"lang":"eng","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)."}],"month":"03","intvolume":" 289","alternative_title":["LIPIcs"],"scopus_import":"1","file":[{"date_updated":"2024-03-25T07:44:30Z","file_size":927290,"creator":"dernst","date_created":"2024-03-25T07:44:30Z","file_name":"2024_LIPICs_Filakovsky.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"15175","checksum":"0524d4189fd1ed08989546511343edf3","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959773119"]},"publication_status":"published","volume":289,"ec_funded":1},{"volume":126,"publication_identifier":{"issn":["1350-4533"],"eissn":["1873-4030"]},"publication_status":"published","file":[{"date_created":"2024-03-25T08:29:52Z","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","date_updated":"2024-03-25T08:29:52Z","file_size":10039402,"creator":"dernst","checksum":"974acbf2731e7382dcf5920ac762e551","file_id":"15177","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 126","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","file_date_updated":"2024-03-25T08:29:52Z","department":[{"_id":"PreCl"}],"date_updated":"2024-03-25T08:31:01Z","ddc":["610"],"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","_id":"15164","doi":"10.1016/j.medengphy.2024.104143","date_published":"2024-04-01T00:00:00Z","date_created":"2024-03-24T23:00:58Z","has_accepted_license":"1","year":"2024","day":"01","publication":"Medical Engineering and Physics","publisher":"Elsevier","quality_controlled":"1","oa":1,"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.","author":[{"full_name":"Silva-Henao, Juan D.","last_name":"Silva-Henao","first_name":"Juan D."},{"id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie","last_name":"Schober","full_name":"Schober, Sophie"},{"full_name":"Pahr, Dieter H.","last_name":"Pahr","first_name":"Dieter H."},{"full_name":"Reisinger, Andreas G.","last_name":"Reisinger","first_name":"Andreas G."}],"article_processing_charge":"Yes (in subscription journal)","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","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","article_number":"104143"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"},"title":"Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy","author":[{"first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder"},{"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"]},"article_number":"033315","day":"19","publication":"Physical Review A","year":"2024","date_published":"2024-03-19T00:00:00Z","doi":"10.1103/PhysRevA.109.033315","date_created":"2024-03-24T23:00:59Z","acknowledgement":"We thank Félix Werner and Kris Van Houcke for interesting discussions.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"date_updated":"2024-03-25T07:36:55Z","department":[{"_id":"MiLe"}],"_id":"15167","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","volume":109,"issue":"3","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"03","intvolume":" 109","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2311.14536"}]},{"intvolume":" 347","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.11615"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"volume":347,"issue":"6","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0012-365X"]},"status":"public","type":"journal_article","article_type":"original","_id":"15163","department":[{"_id":"MaKw"}],"date_updated":"2024-03-25T08:09:43Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them.","date_created":"2024-03-24T23:00:58Z","date_published":"2024-03-19T00:00:00Z","doi":"10.1016/j.disc.2024.113962","publication":"Discrete Mathematics","day":"19","year":"2024","article_number":"113962","title":"Decompositions into two linear forests of bounded lengths","external_id":{"arxiv":["2301.11615"]},"article_processing_charge":"No","author":[{"first_name":"Rutger","last_name":"Campbell","full_name":"Campbell, Rutger"},{"first_name":"Florian","last_name":"Hörsch","full_name":"Hörsch, Florian"},{"last_name":"Moore","full_name":"Moore, Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","first_name":"Benjamin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” Discrete Mathematics, vol. 347, no. 6. Elsevier, 2024.","short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024).","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","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","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.","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."}},{"project":[{"_id":"bd9b2118-d553-11ed-ba76-db24564edfea","grant_number":"101076224","name":"Young galaxies as tracers and agents of cosmic reionization"}],"article_number":"129","article_processing_charge":"Yes","author":[{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"first_name":"Rohan P.","full_name":"Naidu, Rohan P.","last_name":"Naidu"},{"first_name":"Gabriel","last_name":"Brammer","full_name":"Brammer, Gabriel"},{"full_name":"Chisholm, John","last_name":"Chisholm","first_name":"John"},{"last_name":"Eilers","full_name":"Eilers, Anna-Christina","first_name":"Anna-Christina"},{"full_name":"Goulding, Andy","last_name":"Goulding","first_name":"Andy"},{"full_name":"Greene, Jenny","last_name":"Greene","first_name":"Jenny"},{"first_name":"Daichi","last_name":"Kashino","full_name":"Kashino, Daichi"},{"last_name":"Labbe","full_name":"Labbe, Ivo","first_name":"Ivo"},{"first_name":"Simon J.","full_name":"Lilly, Simon J.","last_name":"Lilly"},{"full_name":"Mackenzie, Ruari","last_name":"Mackenzie","first_name":"Ruari"},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"first_name":"Andrea","last_name":"Weibel","full_name":"Weibel, Andrea"},{"full_name":"Wuyts, Stijn","last_name":"Wuyts","first_name":"Stijn"},{"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"},{"first_name":"Pieter","full_name":"van Dokkum, Pieter","last_name":"van Dokkum"},{"full_name":"Illingworth, Garth","last_name":"Illingworth","first_name":"Garth"},{"last_name":"Kramarenko","full_name":"Kramarenko, Ivan","first_name":"Ivan"},{"first_name":"Michael V.","full_name":"Maseda, Michael V.","last_name":"Maseda"},{"full_name":"Mason, Charlotte","last_name":"Mason","first_name":"Charlotte"},{"full_name":"Meyer, Romain A.","last_name":"Meyer","first_name":"Romain A."},{"last_name":"Nelson","full_name":"Nelson, Erica J.","first_name":"Erica J."},{"first_name":"Naveen A.","full_name":"Reddy, Naveen A.","last_name":"Reddy"},{"last_name":"Shivaei","full_name":"Shivaei, Irene","first_name":"Irene"},{"full_name":"Simcoe, Robert A.","last_name":"Simcoe","first_name":"Robert A."},{"last_name":"Yue","full_name":"Yue, Minghao","first_name":"Minghao"}],"title":"Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys","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.","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).","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"American Astronomical Society","quality_controlled":"1","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).","date_created":"2024-03-25T08:54:47Z","doi":"10.3847/1538-4357/ad2345","date_published":"2024-03-07T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"The Astrophysical Journal","day":"07","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":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","_id":"15180","department":[{"_id":"JoMa"}],"file_date_updated":"2024-03-25T09:31:58Z","date_updated":"2024-03-25T09:37:27Z","ddc":["550"],"scopus_import":"1","intvolume":" 963","month":"03","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":963,"issue":"2","publication_status":"published","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"15184","checksum":"dc7af4694f9f94a551417ab49fa43edf","file_size":6047536,"date_updated":"2024-03-25T09:31:58Z","creator":"dernst","file_name":"2024_AstrophysicalJourn_Matthee.pdf","date_created":"2024-03-25T09:31:58Z"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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).","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.","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."},"title":"A hybrid pathway for self-sustained luminescence","article_processing_charge":"Yes","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."},{"last_name":"Perfilov","full_name":"Perfilov, Maxim M.","first_name":"Maxim M."},{"last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I."},{"first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M.","last_name":"Markina"},{"last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elena","last_name":"Garcia-Perez","full_name":"Garcia-Perez, Elena"},{"full_name":"Vazquez-Vilar, Marta","last_name":"Vazquez-Vilar","first_name":"Marta"},{"first_name":"Marta","last_name":"Rodriguez-Rodriguez","full_name":"Rodriguez-Rodriguez, Marta"},{"first_name":"Victor","last_name":"Vazquez-Vilriales","full_name":"Vazquez-Vilriales, Victor"},{"first_name":"Ekaterina S.","last_name":"Shakhova","full_name":"Shakhova, Ekaterina S."},{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana"},{"last_name":"Belozerova","full_name":"Belozerova, Olga A.","first_name":"Olga A."},{"first_name":"Sergey I.","full_name":"Kovalchuk, Sergey I.","last_name":"Kovalchuk"},{"first_name":"Anna","last_name":"Alekberova","full_name":"Alekberova, Anna"},{"first_name":"Alena K.","last_name":"Malyshevskaia","full_name":"Malyshevskaia, Alena K."},{"first_name":"Evgenia N.","full_name":"Bugaeva, Evgenia N.","last_name":"Bugaeva"},{"first_name":"Elena B.","full_name":"Guglya, Elena B.","last_name":"Guglya"},{"first_name":"Anastasia","full_name":"Balakireva, Anastasia","last_name":"Balakireva"},{"first_name":"Nikita","last_name":"Sytov","full_name":"Sytov, Nikita"},{"first_name":"Anastasia","last_name":"Bezlikhotnova","full_name":"Bezlikhotnova, Anastasia"},{"first_name":"Daria I.","last_name":"Boldyreva","full_name":"Boldyreva, Daria I."},{"first_name":"Vladislav V.","last_name":"Babenko","full_name":"Babenko, Vladislav V."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Vladimir V.","last_name":"Choob","full_name":"Choob, Vladimir V."},{"last_name":"Orzaez","full_name":"Orzaez, Diego","first_name":"Diego"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"first_name":"Karen S.","full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan"}],"article_number":"adk1992","publication":"Science Advances","day":"01","year":"2024","has_accepted_license":"1","date_created":"2024-03-25T08:54:33Z","date_published":"2024-03-01T00:00:00Z","doi":"10.1126/sciadv.adk1992","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).","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","ddc":["580"],"date_updated":"2024-03-25T09:44:53Z","department":[{"_id":"FyKo"}],"file_date_updated":"2024-03-25T09:42:10Z","_id":"15179","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","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a19c43b260ea0bbaf895a29712e3153c","file_id":"15185","success":1,"date_updated":"2024-03-25T09:42:10Z","file_size":1499302,"creator":"dernst","date_created":"2024-03-25T09:42:10Z","file_name":"2024_ScienceAdv_Palkina.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"issue":"10","volume":10,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 10","month":"03","scopus_import":"1"},{"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","keyword":["General Earth and Planetary Sciences","Geophysics"],"status":"public","_id":"15186","department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-25T11:28:25Z","date_updated":"2024-03-25T11:32:06Z","ddc":["550"],"intvolume":" 51","month":"03","abstract":[{"text":"The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":51,"issue":"6","publication_status":"published","publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"eacb011091a503b9e7b748fef639ba4c","file_id":"15187","success":1,"date_updated":"2024-03-25T11:28:25Z","file_size":1280108,"creator":"dernst","date_created":"2024-03-25T11:28:25Z","file_name":"2024_GeophysResLetters_Hwong.pdf"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"article_number":" e2023GL106523","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Hwong","orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22"},{"last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"}],"title":"The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation","citation":{"mla":"Hwong, Yi-Ling, and Caroline J. Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters, vol. 51, no. 6, e2023GL106523, American Geophysical Union, 2024, doi:10.1029/2023gl106523.","ieee":"Y.-L. Hwong and C. J. Muller, “The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation,” Geophysical Research Letters, vol. 51, no. 6. American Geophysical Union, 2024.","short":"Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).","apa":"Hwong, Y.-L., & Muller, C. J. (2024). The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl106523","ama":"Hwong Y-L, Muller CJ. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 2024;51(6). doi:10.1029/2023gl106523","chicago":"Hwong, Yi-Ling, and Caroline J Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters. American Geophysical Union, 2024. https://doi.org/10.1029/2023gl106523.","ista":"Hwong Y-L, Muller CJ. 2024. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 51(6), e2023GL106523."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"American Geophysical Union","acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). The authors warmly thank Steven Sherwood, Jiawei Bao, Bidyut Goswami, and Martin Janssens for stimulating and helpful discussions. They also thank Christopher Holloway and an anonymous reviewer for providing helpful feedback that greatly improved this manuscript.\r\n","date_created":"2024-03-25T10:27:30Z","doi":"10.1029/2023gl106523","date_published":"2024-03-19T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Geophysical Research Letters","day":"19"},{"department":[{"_id":"MiLe"}],"file_date_updated":"2024-03-25T09:24:55Z","ddc":["530"],"date_updated":"2024-03-25T09:27:37Z","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":"15181","ec_funded":1,"issue":"1","volume":6,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"15183","checksum":"4e0e58d1f58386fb016284c84db2a300","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2024_PhysicalReviewResearch_Becker.pdf","date_created":"2024-03-25T09:24:55Z","file_size":2207067,"date_updated":"2024-03-25T09:24:55Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"intvolume":" 6","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We demonstrate the failure of the adiabatic Born-Oppenheimer approximation to describe the ground state of a quantum impurity within an ultracold Fermi gas despite substantial mass differences between the bath and impurity species. Increasing repulsion leads to the appearance of nonadiabatic couplings between the fast bath and slow impurity degrees of freedom, which reduce the parity symmetry of the latter according to the pseudo Jahn-Teller effect. The presence of this mechanism is associated to a conical intersection involving the impurity position and the inverse of the interaction strength, which acts as a synthetic dimension. We elucidate the presence of these effects via a detailed ground-state analysis involving the comparison of ab initio fully correlated simulations with effective models. Our study suggests ultracold atomic ensembles as potent emulators of complex molecular phenomena.","lang":"eng"}],"title":"Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions","external_id":{"arxiv":["2310.17995"]},"article_processing_charge":"Yes","author":[{"first_name":"A.","full_name":"Becker, A.","last_name":"Becker"},{"first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis","full_name":"Koutentakis, Georgios"},{"full_name":"Schmelcher, P.","last_name":"Schmelcher","first_name":"P."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Becker, A., Georgios Koutentakis, and P. Schmelcher. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013257.","ista":"Becker A, Koutentakis G, Schmelcher P. 2024. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 6(1), 013257.","mla":"Becker, A., et al. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research, vol. 6, no. 1, 013257, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013257.","ieee":"A. Becker, G. Koutentakis, and P. Schmelcher, “Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","short":"A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 6 (2024).","apa":"Becker, A., Koutentakis, G., & Schmelcher, P. (2024). Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013257","ama":"Becker A, Koutentakis G, Schmelcher P. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013257"},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"article_number":"013257","date_created":"2024-03-25T08:57:07Z","date_published":"2024-03-01T00:00:00Z","doi":"10.1103/physrevresearch.6.013257","publication":"Physical Review Research","day":"01","year":"2024","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994.\r\nG.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413."},{"date_published":"2024-03-13T00:00:00Z","doi":"10.1002/aenm.202400408","date_created":"2024-03-25T08:57:40Z","day":"13","publication":"Advanced Energy Materials","year":"2024","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","author":[{"first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns"},{"full_name":"Milillo, Francesco","last_name":"Milillo","first_name":"Francesco","id":"38b830db-ea88-11ee-bf9b-929beaf79054"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","last_name":"Calcabrini"},{"first_name":"Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine","last_name":"Fiedler"},{"last_name":"Horta","full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona"},{"full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"last_name":"Strumolo","full_name":"Strumolo, Marissa J.","first_name":"Marissa J."},{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"last_name":"Tkadletz","full_name":"Tkadletz, Michael","first_name":"Michael"},{"last_name":"Brutchey","full_name":"Brutchey, Richard L.","first_name":"Richard L."},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials., 2400408.","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials (2024).","ieee":"T. Kleinhanns et al., “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” Advanced Energy Materials. Wiley, 2024.","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 2024. doi:10.1002/aenm.202400408","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. Wiley. https://doi.org/10.1002/aenm.202400408"},"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"article_number":"2400408","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1614-6832"],"eissn":["1614-6840"]},"publication_status":"epub_ahead","month":"03","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1002/aenm.202400408","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"date_updated":"2024-03-25T09:21:05Z","status":"public","type":"journal_article","article_type":"original","_id":"15182"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"GOSWAMI BB. 2024. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 51(5), e2023GL106569.","chicago":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters. Wiley, 2024. https://doi.org/10.1029/2023GL106569.","short":"B.B. GOSWAMI, Geophysical Research Letters 51 (2024).","ieee":"B. B. GOSWAMI, “A pre-monsoon signal of false alarms of Indian monsoon droughts,” Geophysical Research Letters, vol. 51, no. 5. Wiley, 2024.","apa":"GOSWAMI, B. B. (2024). A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. Wiley. https://doi.org/10.1029/2023GL106569","ama":"GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 2024;51(5). doi:10.1029/2023GL106569","mla":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters, vol. 51, no. 5, e2023GL106569, Wiley, 2024, doi:10.1029/2023GL106569."},"title":"A pre-monsoon signal of false alarms of Indian monsoon droughts","article_processing_charge":"Yes","author":[{"first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"Goswami","orcid":"0000-0001-8602-3083","full_name":"Goswami, Bidyut B"}],"article_number":"e2023GL106569","project":[{"grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"publication":"Geophysical Research Letters","day":"16","year":"2024","has_accepted_license":"1","date_created":"2024-03-24T23:00:58Z","doi":"10.1029/2023GL106569","date_published":"2024-03-16T00:00:00Z","acknowledgement":"The author gratefully acknowledges ISTA for supporting this research through funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Project CLUSTER, grant agreement No. 805041).","oa":1,"publisher":"Wiley","quality_controlled":"1","ddc":["550"],"date_updated":"2024-03-25T10:00:57Z","department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-25T08:36:00Z","_id":"15165","status":"public","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"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"243bd966aca968ec7d9e474af8639f8d","file_id":"15178","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2024_GeophysResLetters_Goswami.pdf","date_created":"2024-03-25T08:36:00Z","file_size":2887134,"date_updated":"2024-03-25T08:36:00Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"ec_funded":1,"issue":"5","volume":51,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Current knowledge suggests a drought Indian monsoon (perhaps a severe one) when the El Nino Southern Oscillation and Pacific Decadal Oscillation each exhibit positive phases (a joint positive phase). For the monsoons, which are exceptions in this regard, we found northeast India often gets excess pre-monsoon rainfall. Further investigation reveals that this excess pre-monsoon rainfall is produced by the interaction of the large-scale circulation associated with the joint phase with the mountains in northeast India. We posit that a warmer troposphere, a consequence of excess rainfall over northeast India, drives a stronger monsoon circulation and enhances monsoon rainfall over central India. Hence, we argue that pre-monsoon rainfall over northeast India can be used for seasonal monsoon rainfall prediction over central India. Most importantly, its predictive value is at its peak when the Pacific Ocean exhibits a joint positive phase and the threat of extreme drought monsoon looms over India."}],"intvolume":" 51","month":"03","scopus_import":"1"},{"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"day":"20","publication":"Journal of Cell Biology","has_accepted_license":"1","year":"2024","doi":"10.1083/jcb.202309125","date_published":"2024-03-20T00:00:00Z","date_created":"2024-03-21T06:45:51Z","article_number":"e202309125","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy"},{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"},{"name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","grant_number":"21317","_id":"2615199A-B435-11E9-9278-68D0E5697425"},{"grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125.","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125."},"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","author":[{"last_name":"Zens","full_name":"Zens, Bettina","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"last_name":"Hansen","full_name":"Hansen, Jesse","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"last_name":"Datler","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Zheden","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alanko","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["38506714"]},"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"month":"03","intvolume":" 223","scopus_import":"1","file":[{"file_name":"2024_JCB_Zens.pdf","date_created":"2024-03-25T12:52:04Z","creator":"dernst","file_size":11907016,"date_updated":"2024-03-25T12:52:04Z","success":1,"checksum":"90d1984a93660735e506c2a304bc3f73","file_id":"15188","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"publication_status":"published","issue":"6","volume":223,"ec_funded":1,"_id":"15146","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)"},"ddc":["570"],"date_updated":"2024-03-25T13:03:57Z","file_date_updated":"2024-03-25T12:52:04Z","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}]},{"date_updated":"2024-03-28T10:54:02Z","department":[{"_id":"RoSe"}],"_id":"14931","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1096--0783"],"issn":["0022-1236"]},"publication_status":"epub_ahead","issue":"7","volume":286,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]."}],"month":"01","intvolume":" 286","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.jfa.2024.110320","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis, vol. 286, no. 7. Elsevier, 2024.","apa":"Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 2024;286(7). doi:10.1016/j.jfa.2024.110320"},"title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","author":[{"last_name":"Lauritsen","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2301.04894"]},"article_number":"110320","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"day":"24","publication":"Journal of Functional Analysis","year":"2024","doi":"10.1016/j.jfa.2024.110320","date_published":"2024-01-24T00:00:00Z","date_created":"2024-02-04T23:00:53Z","acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","publisher":"Elsevier","quality_controlled":"1","oa":1},{"article_processing_charge":"No","external_id":{"pmid":["36653709"]},"author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Colinda L.G.J.","full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele"}],"editor":[{"first_name":"Coert","full_name":"Margadant, Coert","last_name":"Margadant"}],"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","citation":{"ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer Nature","page":"183-205","date_created":"2023-01-29T23:00:58Z","doi":"10.1007/978-1-0716-2887-4_12","date_published":"2023-01-19T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Cell Migration in Three Dimensions","day":"19","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":"book_chapter","status":"public","series_title":"MIMB","_id":"12428","department":[{"_id":"EdHa"}],"file_date_updated":"2023-02-03T10:56:39Z","date_updated":"2023-02-03T10:58:56Z","ddc":["570"],"alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","intvolume":" 2608","month":"01","abstract":[{"lang":"eng","text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis."}],"pmid":1,"oa_version":"Published Version","volume":2608,"publication_status":"published","publication_identifier":{"eissn":["1940-6029"],"isbn":["9781071628867"],"eisbn":["9781071628874"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-02-03T10:56:39Z","file_size":826598,"date_created":"2023-02-03T10:56:39Z","file_name":"2023_MIMB_Hannezo.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","file_id":"12500","success":1}]},{"department":[{"_id":"MiLe"}],"file_date_updated":"2023-02-13T10:38:10Z","date_updated":"2023-02-20T07:02:00Z","ddc":["530"],"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","_id":"12534","volume":5,"issue":"1","ec_funded":1,"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"6068b62874c0099628a108bb9c5c6bd2","file_id":"12546","file_size":865150,"date_updated":"2023-02-13T10:38:10Z","creator":"dernst","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","date_created":"2023-02-13T10:38:10Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 5","abstract":[{"lang":"eng","text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics."}],"oa_version":"Published Version","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"article_processing_charge":"No","title":"Dissipative dynamics of an impurity with spin-orbit coupling","citation":{"ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"article_number":"013029","date_published":"2023-01-20T00:00:00Z","doi":"10.1103/physrevresearch.5.013029","date_created":"2023-02-10T09:02:26Z","has_accepted_license":"1","year":"2023","day":"20","publication":"Physical Review Research","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON)."},{"author":[{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"last_name":"Yeung","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","first_name":"Jake"},{"first_name":"Helena","full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza"},{"full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson","first_name":"Buys Anton"},{"first_name":"Vivek","last_name":"Bhardwaj","full_name":"Bhardwaj, Vivek"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"last_name":"van der Linden","full_name":"van der Linden, Reinier","first_name":"Reinier"},{"first_name":"Alexander","last_name":"van Oudenaarden","full_name":"van Oudenaarden, Alexander"}],"article_processing_charge":"No","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","citation":{"ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","page":"333-345","doi":"10.1038/s41588-022-01260-3","date_published":"2023-02-01T00:00:00Z","date_created":"2023-01-12T12:09:09Z","has_accepted_license":"1","year":"2023","day":"01","publication":"Nature Genetics","article_type":"review","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":["Genetics"],"_id":"12158","file_date_updated":"2023-02-27T07:46:45Z","department":[{"_id":"ScienComp"}],"date_updated":"2023-02-27T07:48:24Z","ddc":["570","000"],"scopus_import":"1","month":"02","intvolume":" 55","abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"oa_version":"Published Version","volume":55,"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"publication_status":"published","file":[{"file_name":"2023_NatureGenetics_Zeller.pdf","date_created":"2023-02-27T07:46:45Z","creator":"dernst","file_size":21484855,"date_updated":"2023-02-27T07:46:45Z","success":1,"file_id":"12688","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}]},{"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_updated":"2023-02-27T09:01:16Z","status":"public","type":"conference","conference":{"end_date":"2023-01-25","location":"Florence, Italy","start_date":"2023-01-22","name":"SODA: Symposium on Discrete Algorithms"},"_id":"12676","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781611977554"]},"publication_status":"published","month":"02","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth.","lang":"eng"}],"title":"Faster algorithm for turn-based stochastic games with bounded treewidth","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"},{"full_name":"Svoboda, Jakub","last_name":"Svoboda","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173.","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173."},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"doi":"10.1137/1.9781611977554.ch173","date_published":"2023-02-01T00:00:00Z","date_created":"2023-02-24T12:20:47Z","page":"4590-4605","day":"01","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","year":"2023","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant."},{"department":[{"_id":"DaAl"}],"title":"Fast and scalable channels in Kotlin Coroutines","author":[{"last_name":"Koval","full_name":"Koval, Nikita","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"article_processing_charge":"No","external_id":{"arxiv":["2211.04986"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 107–18. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118.","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481."},"date_updated":"2023-03-20T07:29:28Z","status":"public","type":"conference","conference":{"start_date":"2023-02-25","end_date":"2023-03-01","location":"Montreal, QC, Canada","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"_id":"12735","doi":"10.1145/3572848.3577481","date_published":"2023-02-25T00:00:00Z","date_created":"2023-03-19T23:00:58Z","page":"107-118","day":"25","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798400700156"]},"publication_status":"published","year":"2023","month":"02","quality_controlled":"1","scopus_import":"1","publisher":"Association for Computing Machinery","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04986"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations."}]},{"status":"public","conference":{"location":"Montreal, QB, Canada","end_date":"2023-03-01","start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"type":"conference_poster","_id":"12736","title":"Unexpected scaling in path copying trees","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"article_processing_charge":"No","author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"full_name":"Brown, Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A"},{"first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander","last_name":"Fedorov"},{"full_name":"Kokorin, Ilya","last_name":"Kokorin","first_name":"Ilya"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512."},"date_updated":"2023-03-20T07:57:27Z","month":"02","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"quality_controlled":"1","publisher":"Association for Computing Machinery","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al."}],"date_created":"2023-03-19T23:00:58Z","doi":"10.1145/3572848.3577512","date_published":"2023-02-25T00:00:00Z","page":"438-440","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"25","publication_status":"published","year":"2023","publication_identifier":{"isbn":["9798400700156"]}},{"article_number":"36","citation":{"apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","short":"M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” 40th International Symposium on Theoretical Aspects of Computer Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.STACS.2023.36.","ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Stefan","last_name":"Neumann","full_name":"Neumann, Stefan"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.01744"]},"title":"Dynamic maintenance of monotone dynamic programs and applications","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement 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.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"40th International Symposium on Theoretical Aspects of Computer Science","date_published":"2023-03-01T00:00:00Z","doi":"10.4230/LIPIcs.STACS.2023.36","date_created":"2023-03-26T22:01:07Z","_id":"12760","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":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","start_date":"2023-03-07","end_date":"2023-03-09","location":"Hamburg, Germany"},"status":"public","date_updated":"2023-03-27T06:46:27Z","ddc":["000"],"file_date_updated":"2023-03-27T06:37:22Z","department":[{"_id":"MoHe"}],"abstract":[{"text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"month":"03","intvolume":" 254","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772662"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"22141ab8bc55188e2dfff665e5daecbd","file_id":"12769","success":1,"creator":"dernst","date_updated":"2023-03-27T06:37:22Z","file_size":872706,"date_created":"2023-03-27T06:37:22Z","file_name":"2023_LIPICS_HenzingerM.pdf"}],"language":[{"iso":"eng"}],"volume":254},{"project":[{"grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716."},"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","article_processing_charge":"No","author":[{"last_name":"Burnett","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"10","year":"2023","has_accepted_license":"1","date_created":"2023-03-08T15:19:45Z","date_published":"2023-03-10T00:00:00Z","doi":"10.15479/at:ista:12716","page":"178","_id":"12716","status":"public","type":"dissertation","ddc":["599","573"],"date_updated":"2023-04-05T10:59:04Z","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch"}],"file_date_updated":"2023-03-08T15:08:46Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"oa_version":"Published Version","abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"month":"03","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_id":"12717","file_size":23029260,"date_updated":"2023-03-08T15:08:46Z","creator":"lburnett","file_name":"Burnett_Thesis_2023.docx","date_created":"2023-03-08T15:08:46Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"12718","checksum":"cebc77705288bf4382db9b3541483cd0","success":1,"creator":"lburnett","date_updated":"2023-03-08T15:08:46Z","file_size":11959869,"date_created":"2023-03-08T15:08:46Z","file_name":"Burnett_Thesis_2023_pdfA.pdf"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540.","ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In Tools and Algorithms for the Construction and Analysis of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540."},"title":"Bubaak: Runtime monitoring of program verifiers","article_processing_charge":"No","author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"publication":"Tools and Algorithms for the Construction and Analysis of Systems","day":"20","year":"2023","has_accepted_license":"1","date_created":"2023-04-20T08:22:53Z","date_published":"2023-04-20T00:00:00Z","doi":"10.1007/978-3-031-30820-8_32","page":"535-540","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","ddc":["000"],"date_updated":"2023-04-25T07:02:43Z","department":[{"_id":"ToHe"}],"file_date_updated":"2023-04-25T06:58:36Z","_id":"12854","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)"},"conference":{"start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"type":"conference","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"12864","checksum":"120d2c2a38384058ad0630fdf8288312","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_LNCS_Chalupa.pdf","date_created":"2023-04-25T06:58:36Z","file_size":16096413,"date_updated":"2023-04-25T06:58:36Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eisbn":["9783031308208"],"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"]},"ec_funded":1,"volume":13994,"oa_version":"Published Version","abstract":[{"text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.","lang":"eng"}],"intvolume":" 13994","month":"04","alternative_title":["LNCS"]},{"project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"status":"public","type":"preprint","article_number":"2303.14555","_id":"12846","title":"Area formula for spherical polygons via prequantization","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"author":[{"first_name":"Albert","full_name":"Chern, Albert","last_name":"Chern"},{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","full_name":"Ishida, Sadashige"}],"external_id":{"arxiv":["2303.14555"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-04-25T06:51:21Z","citation":{"short":"A. Chern, S. Ishida, ArXiv (n.d.).","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555."},"month":"03","main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"oa":1,"oa_version":"Preprint","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","abstract":[{"lang":"eng","text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons."}],"date_published":"2023-03-25T00:00:00Z","doi":"10.48550/arXiv.2303.14555","date_created":"2023-04-18T19:16:06Z","day":"25","publication":"arXiv","language":[{"iso":"eng"}],"publication_status":"submitted","year":"2023"},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12865","checksum":"17a7c8e08be609cf2408d37ea55e322c","file_size":580828,"date_updated":"2023-04-25T07:16:36Z","creator":"dernst","file_name":"2023_LNCS_ChalupaM.pdf","date_created":"2023-04-25T07:16:36Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783031308260"],"issn":["0302-9743"],"isbn":["9783031308253"],"eissn":["1611-3349"]},"publication_status":"published","volume":13991,"related_material":{"record":[{"relation":"earlier_version","id":"12407","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"month":"04","intvolume":" 13991","alternative_title":["LNCS"],"ddc":["000"],"date_updated":"2023-04-25T07:19:07Z","department":[{"_id":"ToHe"}],"file_date_updated":"2023-04-25T07:16:36Z","_id":"12856","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":{"name":"FASE: Fundamental Approaches to Software Engineering","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"day":"20","publication":"Fundamental Approaches to Software Engineering","has_accepted_license":"1","year":"2023","date_published":"2023-04-20T00:00:00Z","doi":"10.1007/978-3-031-30826-0_15","date_created":"2023-04-20T08:29:42Z","page":"260-281","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281."},"title":"Vamos: Middleware for best-effort third-party monitoring","author":[{"last_name":"Chalupa","full_name":"Chalupa, Marek","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","last_name":"Mühlböck"},{"first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"article_processing_charge":"No","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}]},{"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407","mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407."},"title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","article_processing_charge":"No","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"last_name":"Mühlböck","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"27","year":"2023","has_accepted_license":"1","date_created":"2023-01-27T03:18:08Z","date_published":"2023-01-27T00:00:00Z","doi":"10.15479/AT:ISTA:12407","page":"38","_id":"12407","keyword":["runtime monitoring","best effort","third party"],"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":"technical_report","ddc":["005"],"date_updated":"2023-04-25T07:19:06Z","file_date_updated":"2023-01-27T03:18:34Z","department":[{"_id":"ToHe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"month":"01","alternative_title":["IST Austria Technical Report"],"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"55426e463fdeafe9777fc3ff635154c7","file_id":"12408","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"main.pdf","date_created":"2023-01-27T03:18:34Z","creator":"fmuehlbo","file_size":662409,"date_updated":"2023-01-27T03:18:34Z"}],"publication_status":"published","publication_identifier":{"eissn":["2664-1690"]},"ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"12856","status":"public"}]}},{"article_processing_charge":"No","external_id":{"pmid":["36639687"]},"author":[{"last_name":"Zhao","full_name":"Zhao, Long","first_name":"Long"},{"last_name":"Yang","full_name":"Yang, Yiman","first_name":"Yiman"},{"last_name":"Chen","full_name":"Chen, Jinchao","first_name":"Jinchao"},{"first_name":"Xuelei","full_name":"Lin, Xuelei","last_name":"Lin"},{"first_name":"Hao","full_name":"Zhang, Hao","last_name":"Zhang"},{"full_name":"Wang, Hao","last_name":"Wang","first_name":"Hao"},{"last_name":"Wang","full_name":"Wang, Hongzhe","first_name":"Hongzhe"},{"last_name":"Bie","full_name":"Bie, Xiaomin","first_name":"Xiaomin"},{"full_name":"Jiang, Jiafu","last_name":"Jiang","first_name":"Jiafu"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Xiangdong","last_name":"Fu","full_name":"Fu, Xiangdong"},{"last_name":"Zhang","full_name":"Zhang, Xiansheng","first_name":"Xiansheng"},{"first_name":"Zhuo","last_name":"Du","full_name":"Du, Zhuo"},{"full_name":"Xiao, Jun","last_name":"Xiao","first_name":"Jun"}],"title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","citation":{"ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"7","date_created":"2023-02-23T09:13:49Z","doi":"10.1186/s13059-022-02844-2","date_published":"2023-01-13T00:00:00Z","year":"2023","publication":"Genome Biology","day":"13","oa":1,"publisher":"Springer Nature","quality_controlled":"1","department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:52:49Z","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"12668","volume":24,"publication_status":"published","publication_identifier":{"issn":["1474-760X"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1186/s13059-022-02844-2","open_access":"1"}],"scopus_import":"1","intvolume":" 24","month":"01","abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"pmid":1,"oa_version":"Published Version"},{"publisher":"Wiley","quality_controlled":"1","oa":1,"doi":"10.1002/chem.202202967","date_published":"2023-01-18T00:00:00Z","date_created":"2023-05-08T08:25:34Z","day":"18","publication":"Chemistry – A European Journal","year":"2023","article_number":"e202202967","title":"Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts","author":[{"last_name":"Traxler","full_name":"Traxler, Michael","first_name":"Michael"},{"last_name":"Reischauer","full_name":"Reischauer, Susanne","first_name":"Susanne"},{"last_name":"Vogl","full_name":"Vogl, Sarah","first_name":"Sarah"},{"first_name":"Jérôme","full_name":"Roeser, Jérôme","last_name":"Roeser"},{"last_name":"Rabeah","full_name":"Rabeah, Jabor","first_name":"Jabor"},{"first_name":"Christopher","last_name":"Penschke","full_name":"Penschke, Christopher"},{"first_name":"Peter","full_name":"Saalfrank, Peter","last_name":"Saalfrank"},{"last_name":"Pieber","full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus"},{"full_name":"Thomas, Arne","last_name":"Thomas","first_name":"Arne"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Traxler, Michael, et al. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal, vol. 29, no. 4, e202202967, Wiley, 2023, doi:10.1002/chem.202202967.","short":"M. Traxler, S. Reischauer, S. Vogl, J. Roeser, J. Rabeah, C. Penschke, P. Saalfrank, B. Pieber, A. Thomas, Chemistry – A European Journal 29 (2023).","ieee":"M. Traxler et al., “Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts,” Chemistry – A European Journal, vol. 29, no. 4. Wiley, 2023.","ama":"Traxler M, Reischauer S, Vogl S, et al. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 2023;29(4). doi:10.1002/chem.202202967","apa":"Traxler, M., Reischauer, S., Vogl, S., Roeser, J., Rabeah, J., Penschke, C., … Thomas, A. (2023). Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. Wiley. https://doi.org/10.1002/chem.202202967","chicago":"Traxler, Michael, Susanne Reischauer, Sarah Vogl, Jérôme Roeser, Jabor Rabeah, Christopher Penschke, Peter Saalfrank, Bartholomäus Pieber, and Arne Thomas. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal. Wiley, 2023. https://doi.org/10.1002/chem.202202967.","ista":"Traxler M, Reischauer S, Vogl S, Roeser J, Rabeah J, Penschke C, Saalfrank P, Pieber B, Thomas A. 2023. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 29(4), e202202967."},"month":"01","intvolume":" 29","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/chem.202202967"}],"oa_version":"Published Version","abstract":[{"text":"The multicomponent approach allows to incorporate several functionalities into a single covalent organic framework (COF) and consequently allows the construction of bifunctional materials for cooperative catalysis. The well-defined structure of such multicomponent COFs is furthermore ideally suited for structure-activity relationship studies. We report a series of multicomponent COFs that contain acridine- and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives. The acridine motif is responsible for broad light absorption, while the bipyridine unit enables complexation of nickel catalysts. These features enable the usage of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings. Variation of the node units shows that the catalytic activity correlates to the keto-enamine tautomer isomerism. This allows switching between high charge-carrier mobility and persistent, localized charge-separated species depending on the nodes, a tool to tailor the materials for specific reactions. Moreover, nickel-loaded COFs are recyclable and catalyze cross-couplings even using red light irradiation.","lang":"eng"}],"volume":29,"issue":"4","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0947-6539"],"eissn":["1521-3765"]},"publication_status":"published","status":"public","keyword":["General Chemistry","Catalysis","Organic Chemistry"],"type":"journal_article","article_type":"original","_id":"12920","extern":"1","date_updated":"2023-05-15T08:39:24Z"}]