[{"OA_type":"closed access","publication_status":"published","page":"522-532","year":"2024","date_updated":"2025-09-08T14:27:08Z","oa_version":"None","scopus_import":"1","date_created":"2024-10-27T23:01:45Z","abstract":[{"lang":"eng","text":"This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a shift to a vector x0 ∈ \r\nRn. The goal is to find t0 and x0. In the special case of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev center and the Chebyshev radius of A. This paper focuses on the case in which A and B are defined with their black-box support functions. An algorithm for solving such problems efficiently is suggested. The algorithm has a superlinear convergence rate, and it can solve hundred-dimensional test problems in a reasonable time, but some additional conditions on A and B are required to guarantee the presence of convergence. Additionally, the behavior of the algorithm for a simple special case is investigated, which leads to a number of theoretical results. Perturbations of this special case are also studied."}],"_id":"18482","status":"public","title":"An algorithm for finding the generalized Chebyshev center of sets defined via their support functions","isi":1,"corr_author":"1","article_processing_charge":"No","date_published":"2024-06-01T00:00:00Z","day":"01","intvolume":" 85","issue":"6","citation":{"ama":"Arkhipov P. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 2024;85(6):522-532. doi:10.1134/S0005117924060031","ieee":"P. Arkhipov, “An algorithm for finding the generalized Chebyshev center of sets defined via their support functions,” Automation and Remote Control, vol. 85, no. 6. Springer Nature, pp. 522–532, 2024.","chicago":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” Automation and Remote Control. Springer Nature, 2024. https://doi.org/10.1134/S0005117924060031.","ista":"Arkhipov P. 2024. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 85(6), 522–532.","short":"P. Arkhipov, Automation and Remote Control 85 (2024) 522–532.","mla":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” Automation and Remote Control, vol. 85, no. 6, Springer Nature, 2024, pp. 522–32, doi:10.1134/S0005117924060031.","apa":"Arkhipov, P. (2024). An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. Springer Nature. https://doi.org/10.1134/S0005117924060031"},"publisher":"Springer Nature","language":[{"iso":"eng"}],"publication":"Automation and Remote Control","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"GradSch"}],"acknowledgement":"The author is grateful to Maxim Balashov for setting the problem, providing useful literature, important discussions and text review. Also, I thank Dmitry Tsarev and Kseniia Petukhova for meaningful talks and support.","author":[{"full_name":"Arkhipov, Pavel","last_name":"Arkhipov","first_name":"Pavel","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f"}],"article_type":"original","month":"06","quality_controlled":"1","publication_identifier":{"issn":["0005-1179"],"eissn":["1608-3032"]},"volume":85,"doi":"10.1134/S0005117924060031","external_id":{"isi":["001338721700007"]},"type":"journal_article"},{"publication_identifier":{"issn":["1016-443X"],"eissn":["1420-8970"]},"month":"12","quality_controlled":"1","article_type":"original","external_id":{"arxiv":["2306.12301"],"isi":["001329804200001"]},"type":"journal_article","has_accepted_license":"1","volume":34,"doi":"10.1007/s00039-024-00695-6","citation":{"short":"V. Kaloshin, E. Koudjinan, K. Zhang, Geometric and Functional Analysis 34 (2024) 1973–2007.","ama":"Kaloshin V, Koudjinan E, Zhang K. Birkhoff conjecture for nearly centrally symmetric domains. Geometric and Functional Analysis. 2024;34:1973-2007. doi:10.1007/s00039-024-00695-6","chicago":"Kaloshin, Vadim, Edmond Koudjinan, and Ke Zhang. “Birkhoff Conjecture for Nearly Centrally Symmetric Domains.” Geometric and Functional Analysis. Springer Nature, 2024. https://doi.org/10.1007/s00039-024-00695-6.","ieee":"V. Kaloshin, E. Koudjinan, and K. Zhang, “Birkhoff conjecture for nearly centrally symmetric domains,” Geometric and Functional Analysis, vol. 34. Springer Nature, pp. 1973–2007, 2024.","ista":"Kaloshin V, Koudjinan E, Zhang K. 2024. Birkhoff conjecture for nearly centrally symmetric domains. Geometric and Functional Analysis. 34, 1973–2007.","mla":"Kaloshin, Vadim, et al. “Birkhoff Conjecture for Nearly Centrally Symmetric Domains.” Geometric and Functional Analysis, vol. 34, Springer Nature, 2024, pp. 1973–2007, doi:10.1007/s00039-024-00695-6.","apa":"Kaloshin, V., Koudjinan, E., & Zhang, K. (2024). Birkhoff conjecture for nearly centrally symmetric domains. Geometric and Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-024-00695-6"},"file":[{"relation":"main_file","checksum":"e7fcd9f78beb40408c7d858ac0625e27","success":1,"date_updated":"2025-01-13T09:14:24Z","content_type":"application/pdf","access_level":"open_access","file_size":2260980,"file_name":"2024_GeometricFunctionalAnalysis_Kaloshin.pdf","creator":"dernst","file_id":"18833","date_created":"2025-01-13T09:14:24Z"}],"publisher":"Springer Nature","intvolume":" 34","file_date_updated":"2025-01-13T09:14:24Z","article_processing_charge":"Yes (via OA deal)","date_published":"2024-12-01T00:00:00Z","day":"01","OA_place":"publisher","ec_funded":1,"author":[{"last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Koudjinan","first_name":"Edmond","full_name":"Koudjinan, Edmond","orcid":"0000-0003-2640-4049","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E"},{"full_name":"Zhang, Ke","last_name":"Zhang","first_name":"Ke"}],"department":[{"_id":"VaKa"}],"acknowledgement":"We are grateful to the anonymous referee for their careful reading and valuable remarks and comments which helped to improve significantly the paper. Open access funding provided by Institute of Science and Technology (IST Austria). V.K. and C.E.K. gratefully acknowledge support from the European Research Council (ERC) through the Advanced Grant “SPERIG” (#885 707).","arxiv":1,"language":[{"iso":"eng"}],"publication":"Geometric and Functional Analysis","ddc":["510"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Birkhoff conjecture for nearly centrally symmetric domains","_id":"18483","status":"public","oa":1,"date_created":"2024-10-27T23:01:45Z","abstract":[{"lang":"eng","text":"In this paper we prove a perturbative version of a remarkable Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) result. They prove non perturbative Birkhoff conjecture for centrally-symmetric convex domains, namely, a centrally-symmetric convex domain with integrable billiard is ellipse. We combine techniques from Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) with a local result by Kaloshin–Sorrentino (Ann. Math. 188(1):315–380, 2018) and show that a domain close enough to a centrally symmetric one with integrable billiard is ellipse. To combine these results we derive a slight extension of Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) by proving that a notion of rational integrability is equivalent to the C0-integrability condition used in their paper."}],"isi":1,"corr_author":"1","project":[{"call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707"}],"year":"2024","OA_type":"hybrid","publication_status":"published","page":"1973-2007","oa_version":"Published Version","scopus_import":"1","date_updated":"2025-09-08T14:27:45Z"},{"doi":"10.1103/prxquantum.5.040311","has_accepted_license":"1","volume":5,"type":"journal_article","external_id":{"arxiv":["2403.12325"],"isi":["001346198800001"]},"DOAJ_listed":"1","article_type":"original","quality_controlled":"1","month":"10","publication_identifier":{"eissn":["2691-3399"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530"],"language":[{"iso":"eng"}],"publication":"PRX Quantum","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"acknowledgement":"We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions. This research was funded in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1, 10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This work was performed in part at the Aspen Center for Physics, which is supported by National Science Foundation Grant PHY-2210452. This research was supported in part by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).","department":[{"_id":"MaSe"}],"author":[{"last_name":"Ljubotina","first_name":"Marko","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"full_name":"Petrova, Elena","last_name":"Petrova","first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede"},{"first_name":"Norbert","last_name":"Schuch","full_name":"Schuch, Norbert"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"ec_funded":1,"OA_place":"publisher","day":"23","date_published":"2024-10-23T00:00:00Z","article_processing_charge":"Yes","article_number":"040311","file_date_updated":"2024-10-30T08:59:09Z","issue":"4","intvolume":" 5","publisher":"American Physical Society","file":[{"date_created":"2024-10-30T08:59:09Z","creator":"dernst","file_name":"2024_PRXQuantum_Ljubotina.pdf","file_id":"18489","file_size":1151431,"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2024-10-30T08:59:09Z","checksum":"2e057ba021744d0a74602517935326b3","relation":"main_file"}],"citation":{"apa":"Ljubotina, M., Petrova, E., Schuch, N., & Serbyn, M. (2024). Tangent space generators of matrix product states and exact floquet quantum scars. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.5.040311","mla":"Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” PRX Quantum, vol. 5, no. 4, 040311, American Physical Society, 2024, doi:10.1103/prxquantum.5.040311.","ista":"Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.","ieee":"M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators of matrix product states and exact floquet quantum scars,” PRX Quantum, vol. 5, no. 4. American Physical Society, 2024.","chicago":"Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” PRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.040311.","ama":"Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix product states and exact floquet quantum scars. PRX Quantum. 2024;5(4). doi:10.1103/prxquantum.5.040311","short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024)."},"corr_author":"1","isi":1,"abstract":[{"text":"The advancement of quantum simulators motivates the development of a theoretical framework to assist with efficient state preparation in quantum many-body systems. Generally, preparing a target entangled state via unitary evolution with time-dependent couplings is a challenging task and very little is known about the existence of solutions and their properties. In this work we develop a constructive approach for preparing matrix product states (MPS) via continuous unitary evolution. We provide an explicit construction of the operator that exactly implements the evolution of a given MPS along a specified direction in its tangent space. This operator can be written as a sum of local terms of finite range, yet it is in general non-Hermitian. Relying on the explicit construction of the non-Hermitian generator of the dynamics, we demonstrate the existence of a Hermitian sequence of operators that implements the desired MPS evolution with an error that decreases exponentially with the operator range. The construction is benchmarked on an explicit periodic trajectory in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary generating the dynamics over one period of the trajectory features an approximate MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results show that our construction is not only useful for state preparation and control of many-body systems, but also provides a generic route towards Floquet scars—periodically driven models with quasilocal generators of dynamics that have exact MPS eigenstates in their spectrum.","lang":"eng"}],"date_created":"2024-10-29T16:04:05Z","oa":1,"_id":"18488","status":"public","title":"Tangent space generators of matrix product states and exact floquet quantum scars","date_updated":"2025-09-08T14:26:29Z","scopus_import":"1","oa_version":"Published Version","APC_amount":"3711,01 EUR","publication_status":"published","OA_type":"gold","year":"2024","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}]},{"ddc":["510"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"publication":"Journal of the London Mathematical Society","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","author":[{"orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo"},{"full_name":"Herry, Ronan","first_name":"Ronan","last_name":"Herry"},{"full_name":"Kopfer, Eva","first_name":"Eva","last_name":"Kopfer"},{"last_name":"Sturm","first_name":"Karl Theodor","full_name":"Sturm, Karl Theodor"}],"ec_funded":1,"department":[{"_id":"JaMa"}],"acknowledgement":"The authors are grateful to Masha Gordina for helpful references, and to Nathanaël Berestycki, Baptiste Cerclé, and Ewain Gwynne for valuable comments on the first circulated version of this paper. They also would like to thank Sebastian Andres, Peter Friz, and Yizheng Yuan for pointing out an erroneous formulation in the previous version of Theorem 5.7. Moreover, KTS would liketo express his thanks to Sebastian Andres, Matthias Erbar, Martin Huesmann, and Jan Mass for stimulating discussions on previous attempts to this project. LDS gratefully acknowledges financial support from the European Research Council (grant agreement No 716117, awarded to J. Maas), from the Austrian Science Fund (FWF) project 10.55776/ESP208, and from the Austrian Science Fund (FWF) project 10.55776/F65.RH, EK, and KTS gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through the project “Random Riemannian Geometry” within the SPP 2265 “Random Geomet-ric Systems,” through the Hausdorff Center for Mathematics (project ID 390685813), and through project B03 within the CRC 1060 (project ID 211504053). RH and KTS also gratefully acknowledge financial support from the European Research Council through the ERC AdG “RicciBounds”(grant agreement 694405).Data sharing not applicable to this article as no datasets were generated or analyzed during the current study. Open access funding enabled and organized by Projekt DEAL.","file_date_updated":"2024-11-04T08:54:26Z","article_number":"e70003","article_processing_charge":"Yes (via OA deal)","date_published":"2024-11-01T00:00:00Z","day":"01","citation":{"short":"L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Journal of the London Mathematical Society 110 (2024).","ama":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. Journal of the London Mathematical Society. 2024;110(5). doi:10.1112/jlms.70003","ieee":"L. Dello Schiavo, R. Herry, E. Kopfer, and K. T. Sturm, “Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension,” Journal of the London Mathematical Society, vol. 110, no. 5. London Mathematical Society, 2024.","ista":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. 2024. Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. Journal of the London Mathematical Society. 110(5), e70003.","chicago":"Dello Schiavo, Lorenzo, Ronan Herry, Eva Kopfer, and Karl Theodor Sturm. “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” Journal of the London Mathematical Society. London Mathematical Society, 2024. https://doi.org/10.1112/jlms.70003.","mla":"Dello Schiavo, Lorenzo, et al. “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” Journal of the London Mathematical Society, vol. 110, no. 5, e70003, London Mathematical Society, 2024, doi:10.1112/jlms.70003.","apa":"Dello Schiavo, L., Herry, R., Kopfer, E., & Sturm, K. T. (2024). Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. Journal of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/jlms.70003"},"publisher":"London Mathematical Society","file":[{"date_created":"2024-11-04T08:54:26Z","creator":"dernst","file_name":"2024_JourLondonMathSoc_Schiavo.pdf","file_id":"18497","access_level":"open_access","file_size":911476,"date_updated":"2024-11-04T08:54:26Z","success":1,"content_type":"application/pdf","relation":"main_file","checksum":"143816823b5f43bd3748da8e3e91cef5"}],"intvolume":" 110","issue":"5","has_accepted_license":"1","volume":110,"doi":"10.1112/jlms.70003","external_id":{"isi":["001351918100029"]},"type":"journal_article","month":"11","quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"date_updated":"2025-09-08T14:29:45Z","scopus_import":"1","oa_version":"Published Version","OA_type":"hybrid","publication_status":"published","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"year":"2024","isi":1,"date_created":"2024-11-03T23:01:44Z","oa":1,"abstract":[{"lang":"eng","text":"For large classes of even-dimensional Riemannian manifolds (Formula presented.), we construct and analyze conformally invariant random fields. These centered Gaussian fields (Formula presented.), called co-polyharmonic Gaussian fields, are characterized by their covariance kernels k which exhibit a precise logarithmic divergence: (Formula presented.). They share a fundamental quasi-invariance property under conformal transformations. In terms of the co-polyharmonic Gaussian field (Formula presented.), we define the Liouville Quantum Gravity measure, a random measure on (Formula presented.), heuristically given as (Formula presented.) and rigorously obtained as almost sure weak limit of the right-hand side with (Formula presented.) replaced by suitable regular approximations (Formula presented.). In terms on the Liouville Quantum Gravity measure, we define the Liouville Brownian motion on (Formula presented.) and the random GJMS operators. Finally, we present an approach to a conformal field theory in arbitrary even dimension with an ansatz based on Branson's (Formula presented.) -curvature: we give a rigorous meaning to the Polyakov–Liouville measure (Formula presented.) and we derive the corresponding conformal anomaly. The set of admissible manifolds is conformally invariant. It includes all compact 2-dimensional Riemannian manifolds, all compact non-negatively curved Einstein manifolds of even dimension, and large classes of compact hyperbolic manifolds of even dimension. However, not every compact even-dimensional Riemannian manifold is admissible. Our results concerning the logarithmic divergence of the kernel (Formula presented.) rely on new sharp estimates for heat kernels and higher order Green kernels on arbitrary closed manifolds. "}],"title":"Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension","status":"public","_id":"18490"},{"publication_identifier":{"eissn":["2375-2548"]},"month":"10","quality_controlled":"1","article_type":"original","DOAJ_listed":"1","external_id":{"isi":["001354405400018"]},"type":"journal_article","volume":10,"has_accepted_license":"1","doi":"10.1126/sciadv.adp2102","citation":{"ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. Science Advances. 10(41), eadp2102.","ieee":"D. F. Garcia Castillo et al., “Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails,” Science Advances, vol. 10, no. 41. AAAS, 2024.","chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Science Advances. AAAS, 2024. https://doi.org/10.1126/sciadv.adp2102.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. Science Advances. 2024;10(41). doi:10.1126/sciadv.adp2102","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, Science Advances 10 (2024).","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adp2102","mla":"Garcia Castillo, Diego Fernando, et al. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Science Advances, vol. 10, no. 41, eadp2102, AAAS, 2024, doi:10.1126/sciadv.adp2102."},"publisher":"AAAS","file":[{"file_id":"18499","file_name":"2024_ScienceAdv_Castillo.pdf","creator":"dernst","date_created":"2024-11-04T09:35:49Z","relation":"main_file","checksum":"96aa0d3640fa9401975138e59054f84e","date_updated":"2024-11-04T09:35:49Z","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":1154107}],"intvolume":" 10","issue":"41","article_number":"eadp2102","file_date_updated":"2024-11-04T09:35:49Z","article_processing_charge":"Yes","day":"11","date_published":"2024-10-11T00:00:00Z","OA_place":"publisher","author":[{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","full_name":"Garcia Castillo, Diego Fernando","last_name":"Garcia Castillo","first_name":"Diego Fernando"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Larsson, Jenny","first_name":"Jenny","last_name":"Larsson"},{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram"}],"department":[{"_id":"NiBa"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"18498"},{"id":"20991","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://github.com/fernandoGarcia21/littorina_saxatilis_skerry","relation":"software"}]},"acknowledgement":"This work was received funding from the following: Norwegian Research Council RCN project 315287 (A.M.W.), Swedish Research Council 2021-04191 (K.J.), European Research Council grant 101055327 HaplotypeStructure (N.B.), Austrian Science Fund FWF; P 32166-B32 Snapdragon Speciation (N.B.), European Research Council (R.B.), and Portuguese Foundation for Science and Technology FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021 (R.F.).","ddc":["570"],"publication":"Science Advances","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","PlanS_conform":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails","_id":"18491","status":"public","oa":1,"date_created":"2024-11-03T23:01:44Z","abstract":[{"lang":"eng","text":"Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations."}],"isi":1,"corr_author":"1","project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"},{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"year":"2024","OA_type":"gold","publication_status":"published","APC_amount":"4569,23 EUR","scopus_import":"1","oa_version":"Published Version","date_updated":"2026-04-07T11:42:09Z"},{"department":[{"_id":"JoMa"}],"acknowledgement":"The authors would like to thank the anonymous referee for the thoughtful comments, which significantly improved our manuscript, and Jan-Torge Schindler, Jiamu Huang, and Feige Wang for helpful discussions.\r\n\r\nJ.F.H. and E.P. acknowledge support from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation program (grant agreement No. 885301). J.M. acknowledges support from the European Union (ERC, AGENTS, 101076224).\r\n\r\nThis work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The JWST data presented in this article 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. The specific observations analyzed are associated with program #1243 and can be accessed via doi:10.17909/m5mp-5v90.\r\n\r\nThis work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Directors Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded DiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure.\r\n\r\nWe thank the Instituto de Astrofisica de Andalucia (IAA-CSIC), Centro de Supercomputacion de Galicia (CESGA), and Spanish Academic and Research Network (RedIRIS) in Spain for hosting Uchuu DR1, DR2, and DR3 in the Skies & Universes site for cosmological simulations. The Uchuu simulations were carried out on the Aterui II supercomputer at the Center for Computational Astrophysics, CfCA, of the National Astronomical Observatory of Japan, and the K computer at the RIKEN Advanced Institute for Computational Science. The Uchuu Data Releases efforts have made use of the skunIAA_RedIRIS and skun6IAA computer facilities managed by the IAA-CSIC in Spain (MICINN EU-Feder grant EQC2018-004366-P).","OA_place":"publisher","author":[{"last_name":"Eilers","first_name":"Anna Christina","full_name":"Eilers, Anna Christina"},{"full_name":"Mackenzie, Ruari","first_name":"Ruari","last_name":"Mackenzie"},{"first_name":"Elia","last_name":"Pizzati","full_name":"Pizzati, Elia"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee"},{"first_name":"Joseph F.","last_name":"Hennawi","full_name":"Hennawi, Joseph F."},{"first_name":"Haowen","last_name":"Zhang","full_name":"Zhang, Haowen"},{"full_name":"Bordoloi, Rongmon","first_name":"Rongmon","last_name":"Bordoloi"},{"last_name":"Kashino","first_name":"Daichi","full_name":"Kashino, Daichi"},{"last_name":"Lilly","first_name":"Simon J.","full_name":"Lilly, Simon J."},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"full_name":"Simcoe, Robert A.","last_name":"Simcoe","first_name":"Robert A."},{"first_name":"Minghao","last_name":"Yue","full_name":"Yue, Minghao"},{"first_name":"Carlos S.","last_name":"Frenk","full_name":"Frenk, Carlos S."},{"full_name":"Helly, John C.","first_name":"John C.","last_name":"Helly"},{"last_name":"Schaller","first_name":"Matthieu","full_name":"Schaller, Matthieu"},{"first_name":"Joop","last_name":"Schaye","full_name":"Schaye, Joop"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["520"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"publication":"Astrophysical Journal","intvolume":" 974","issue":"2","citation":{"apa":"Eilers, A. C., Mackenzie, R., Pizzati, E., Matthee, J. J., Hennawi, J. F., Zhang, H., … Schaye, J. (2024). EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad778b","mla":"Eilers, Anna Christina, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” Astrophysical Journal, vol. 974, no. 2, 275, IOP Publishing, 2024, doi:10.3847/1538-4357/ad778b.","short":"A.C. Eilers, R. Mackenzie, E. Pizzati, J.J. Matthee, J.F. Hennawi, H. Zhang, R. Bordoloi, D. Kashino, S.J. Lilly, R.P. Naidu, R.A. Simcoe, M. Yue, C.S. Frenk, J.C. Helly, M. Schaller, J. Schaye, Astrophysical Journal 974 (2024).","ista":"Eilers AC, Mackenzie R, Pizzati E, Matthee JJ, Hennawi JF, Zhang H, Bordoloi R, Kashino D, Lilly SJ, Naidu RP, Simcoe RA, Yue M, Frenk CS, Helly JC, Schaller M, Schaye J. 2024. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. 974(2), 275.","chicago":"Eilers, Anna Christina, Ruari Mackenzie, Elia Pizzati, Jorryt J Matthee, Joseph F. Hennawi, Haowen Zhang, Rongmon Bordoloi, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad778b.","ieee":"A. C. Eilers et al., “EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6,” Astrophysical Journal, vol. 974, no. 2. IOP Publishing, 2024.","ama":"Eilers AC, Mackenzie R, Pizzati E, et al. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. 2024;974(2). doi:10.3847/1538-4357/ad778b"},"publisher":"IOP Publishing","file":[{"date_updated":"2024-11-04T08:42:23Z","content_type":"application/pdf","success":1,"file_size":1042470,"access_level":"open_access","checksum":"1fcac3d11d01d91cf2bb4963b6e10b22","relation":"main_file","date_created":"2024-11-04T08:42:23Z","file_id":"18496","file_name":"2024_AstrophysicalJour_Eilers.pdf","creator":"dernst"}],"article_processing_charge":"Yes","day":"01","date_published":"2024-10-01T00:00:00Z","article_number":"275","file_date_updated":"2024-11-04T08:42:23Z","external_id":{"isi":["001338877100001"]},"type":"journal_article","DOAJ_listed":"1","has_accepted_license":"1","volume":974,"doi":"10.3847/1538-4357/ad778b","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"article_type":"original","month":"10","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","date_updated":"2025-09-08T14:29:05Z","year":"2024","project":[{"_id":"bd9b2118-d553-11ed-ba76-db24564edfea","name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224"}],"OA_type":"gold","publication_status":"published","isi":1,"status":"public","_id":"18494","title":"EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6","date_created":"2024-11-03T23:01:45Z","oa":1,"abstract":[{"lang":"eng","text":"We expect luminous (M 1450 ≲ −26.5) high-redshift quasars to trace the highest-density peaks in the early Universe. Here, we present observations of four z ≳ 6 quasar fields using JWST/NIRCam in the imaging and wide-field slitless spectroscopy mode and report a wide range in the number of detected [O iii]-emitting galaxies in the quasars’ environments, ranging between a density enhancement of δ ≈ 65 within a 2 cMpc radius—one of the largest protoclusters during the Epoch of Reionization discovered to date—to a density contrast consistent with zero, indicating the presence of a UV-luminous quasar in a region comparable to the average density of the Universe. By measuring the two-point cross-correlation function of quasars and their surrounding galaxies, as well as the galaxy autocorrelation function, we infer a correlation length of quasars at 〈z〉 = 6.25 of r 0 QQ = 22.0 − 2.9 + 3.0 cMpc h − 1 , while we obtain a correlation length of the [O iii]-emitting galaxies of r 0 GG = 4.1 ± 0.3 cMpc h − 1 . By comparing the correlation functions to dark-matter-only simulations we estimate the minimum mass of the quasars’ host dark matter halos to be log 10 ( M halo , min / M ⊙ ) = 12.43 − 0.15 + 0.13 (and log 10 ( M halo , min [ OIII ] / M ⊙ ) = 10.56 − 0.03 + 0.05 for the [O iii] emitters), indicating that (a) luminous quasars do not necessarily reside within the most overdense regions in the early Universe, and that (b) the UV-luminous duty cycle of quasar activity at these redshifts is f duty ≪ 1. Such short quasar activity timescales challenge our understanding of early supermassive black hole growth and provide evidence for highly dust-obscured growth phases or episodic, radiatively inefficient accretion rates."}]},{"doi":"10.5281/ZENODO.12159343","corr_author":"1","has_accepted_license":"1","type":"research_data_reference","abstract":[{"text":"Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715","lang":"eng"}],"date_created":"2024-11-04T09:33:17Z","month":"06","oa":1,"status":"public","_id":"18498","title":"Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2026-04-16T12:20:37Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20991"},{"id":"18491","relation":"used_in_publication","status":"public"}]},"department":[{"_id":"NiBa"}],"author":[{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Larsson, Jenny","first_name":"Jenny","last_name":"Larsson"},{"last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M"}],"oa_version":"Published Version","OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.12159344","open_access":"1"}],"day":"19","date_published":"2024-06-19T00:00:00Z","article_processing_charge":"No","year":"2024","publisher":"Zenodo","citation":{"chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.12159343.","ieee":"D. F. Garcia Castillo et al., “Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails.” Zenodo, 2024.","ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails, Zenodo, 10.5281/ZENODO.12159343.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. 2024. doi:10.5281/ZENODO.12159343","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, (2024).","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.12159343","mla":"Garcia Castillo, Diego Fernando, et al. Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails. Zenodo, 2024, doi:10.5281/ZENODO.12159343."}},{"corr_author":"1","abstract":[{"text":"In 1996, Karger [Kar96] gave a startling randomized algorithm that finds a minimum-cut in a (weighted) graph in time O(m log3 n) which he termed near-linear time meaning linear (in the size of the input) times a polylogarthmic factor. In this paper, we give the first deterministic algorithm which runs in near-linear time for weighted graphs.\r\nPreviously, the breakthrough results of Kawarabayashi and Thorup [KT19] gave a near-linear time algorithm for simple graphs (which was improved to have running time O(m log2 n log log n) in [HRW20].) The main technique here is a clustering procedure that perfectly preserves minimum cuts. Recently, Li [Li21] gave an m1+o(1) deterministic minimum-cut algorithm for weighted graphs; this form of running time has been termed “almost-linear”. Li uses almost-linear time deterministic expander decompositions which do not perfectly preserve minimum cuts, but he can use these clusterings to, in a sense, “derandomize” the methods of Karger.\r\nIn terms of techniques, we provide a structural theorem that says there exists a sparse clustering that preserves minimum cuts in a weighted graph with o(1) error. In addition, we construct it deterministically in near linear time. This was done exactly for simple graphs in [KT19, HRW20] and with polylogarithmic error for weighted graphs in [Li21]. Extending the techniques in [KT19, HRW20] to weighted graphs presents significant challenges, and moreover, the algorithm can only polylogarithmically approximately preserve minimum cuts. A remaining challenge is to reduce the polylogarithmic-approximate clusterings to 1 + o(1/ log n)-approximate so that they can be applied recursively as in [Li21] over O(log n) many levels. This is an additional challenge that requires building on properties of tree-packings in the presence of a wide range of edge weights to, for example, find sources for local flow computations which identify minimum cuts that cross clusters.","lang":"eng"}],"date_created":"2024-11-04T10:54:21Z","oa":1,"status":"public","_id":"18503","title":"Deterministic near-linear time minimum cut in weighted graphs","conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2024-01-10","start_date":"2024-01-07","location":"Alexandria, VA, United States"},"date_updated":"2025-06-24T12:09:26Z","scopus_import":"1","oa_version":"Preprint","page":"3089-3139","publication_status":"published","OA_type":"free access","year":"2024","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422","name":"Efficient algorithms"},{"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"}],"doi":"10.1137/1.9781611977912.111","type":"conference","external_id":{"arxiv":["2401.05627"]},"quality_controlled":"1","month":"01","publication_identifier":{"eisbn":["9781611977912"]},"language":[{"iso":"eng"}],"publication":"35th Annual ACM-SIAM Symposium on Discrete Algorithms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"acknowledgement":"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 (MoDyn-Struct)” and the Austrian Science Fund (FWF) project Z 422-N, project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","department":[{"_id":"MoHe"}],"author":[{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Li, Jason","last_name":"Li","first_name":"Jason"},{"full_name":"Rao, Satish","last_name":"Rao","first_name":"Satish"},{"last_name":"Wang","first_name":"Di","full_name":"Wang, Di"}],"ec_funded":1,"OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2401.05627","open_access":"1"}],"date_published":"2024-01-04T00:00:00Z","day":"04","article_processing_charge":"No","publisher":"Society for Industrial and Applied Mathematics","citation":{"mla":"Henzinger, Monika, et al. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” 35th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 3089–139, doi:10.1137/1.9781611977912.111.","apa":"Henzinger, M., Li, J., Rao, S., & Wang, D. (2024). Deterministic near-linear time minimum cut in weighted graphs. In 35th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 3089–3139). Alexandria, VA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.111","short":"M. Henzinger, J. Li, S. Rao, D. Wang, in:, 35th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 3089–3139.","ama":"Henzinger M, Li J, Rao S, Wang D. Deterministic near-linear time minimum cut in weighted graphs. In: 35th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2024:3089-3139. doi:10.1137/1.9781611977912.111","ista":"Henzinger M, Li J, Rao S, Wang D. 2024. Deterministic near-linear time minimum cut in weighted graphs. 35th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 3089–3139.","chicago":"Henzinger, Monika, Jason Li, Satish Rao, and Di Wang. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” In 35th Annual ACM-SIAM Symposium on Discrete Algorithms, 3089–3139. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.111.","ieee":"M. Henzinger, J. Li, S. Rao, and D. Wang, “Deterministic near-linear time minimum cut in weighted graphs,” in 35th Annual ACM-SIAM Symposium on Discrete Algorithms, Alexandria, VA, United States, 2024, pp. 3089–3139."}},{"citation":{"apa":"Surendranadh, P. (2024). Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18515","mla":"Surendranadh, Parvathy. Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18515.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18515.","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:10.15479/at:ista:18515","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024."},"file":[{"date_updated":"2024-11-07T10:59:29Z","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":37019760,"checksum":"c32cf7bc75748d9c551d8eb70178bbec","relation":"main_file","date_created":"2024-11-07T10:59:29Z","file_id":"18519","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","creator":"psurendr"},{"checksum":"4417e02d54084d89e75734e18caaa96d","relation":"source_file","access_level":"closed","file_size":41198857,"content_type":"application/zip","date_updated":"2024-11-07T10:59:42Z","creator":"psurendr","file_name":"PhD Thesis- Parvathy_071124.zip","file_id":"18520","date_created":"2024-11-07T10:59:42Z"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-11-07T10:59:42Z","article_processing_charge":"No","day":"07","date_published":"2024-11-07T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"OA_place":"publisher","author":[{"orcid":"0000-0001-6395-386X","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["576"],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"month":"11","type":"dissertation","has_accepted_license":"1","doi":"10.15479/at:ista:18515","project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"year":"2024","OA_type":"gold","page":"219","publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","date_updated":"2026-04-07T12:56:52Z","title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","_id":"18515","status":"public","oa":1,"date_created":"2024-11-06T21:25:37Z","abstract":[{"lang":"eng","text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations."}],"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"corr_author":"1"},{"scopus_import":"1","oa_version":"Published Version","conference":{"start_date":"2024-10-15","location":"Istanbul, Turkey","name":"RV: Conference on Runtime Verification","end_date":"2024-10-17"},"date_updated":"2026-05-20T08:43:20Z","year":"2024","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"APC_amount":"2748 EUR","publication_status":"published","page":"282-301","OA_type":"hybrid","corr_author":"1","isi":1,"_id":"18521","status":"public","title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","abstract":[{"lang":"eng","text":"In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples."}],"oa":1,"date_created":"2024-11-10T23:01:58Z","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. This work is sponsored in part by the United States NSF CCF-2118356 award. This research was partially funded by A-IQ Ready (Chips JU, grant agreement No. 101096658).","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"author":[{"full_name":"Bonakdarpour, Borzoo","first_name":"Borzoo","last_name":"Bonakdarpour"},{"first_name":"Anik","last_name":"Momtaz","full_name":"Momtaz, Anik"},{"last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac"}],"ec_funded":1,"OA_place":"publisher","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publication":"24th International Conference on Runtime Verification","language":[{"iso":"eng"}],"arxiv":1,"intvolume":" 15191","publisher":"Springer Nature","file":[{"date_created":"2024-11-11T09:42:28Z","file_id":"18539","creator":"dernst","file_name":"2024_LNCS_Bonakdarpour.pdf","access_level":"open_access","file_size":1897101,"content_type":"application/pdf","date_updated":"2024-11-11T09:42:28Z","success":1,"checksum":"7b8ca21b8c19ab796fa445b0e54003ca","relation":"main_file"}],"citation":{"ama":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy. In: 24th International Conference on Runtime Verification. Vol 15191. Springer Nature; 2024:282-301. doi:10.1007/978-3-031-74234-7_18","ista":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. 2024. Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy. 24th International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 15191, 282–301.","chicago":"Bonakdarpour, Borzoo, Anik Momtaz, Dejan Nickovic, and Naci E Sarac. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed & Accuracy.” In 24th International Conference on Runtime Verification, 15191:282–301. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-74234-7_18.","ieee":"B. Bonakdarpour, A. Momtaz, D. Nickovic, and N. E. Sarac, “Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy,” in 24th International Conference on Runtime Verification, Istanbul, Turkey, 2024, vol. 15191, pp. 282–301.","short":"B. Bonakdarpour, A. Momtaz, D. Nickovic, N.E. Sarac, in:, 24th International Conference on Runtime Verification, Springer Nature, 2024, pp. 282–301.","mla":"Bonakdarpour, Borzoo, et al. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed & Accuracy.” 24th International Conference on Runtime Verification, vol. 15191, Springer Nature, 2024, pp. 282–301, doi:10.1007/978-3-031-74234-7_18.","apa":"Bonakdarpour, B., Momtaz, A., Nickovic, D., & Sarac, N. E. (2024). Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy. In 24th International Conference on Runtime Verification (Vol. 15191, pp. 282–301). Istanbul, Turkey: Springer Nature. https://doi.org/10.1007/978-3-031-74234-7_18"},"date_published":"2024-10-12T00:00:00Z","day":"12","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-11-11T09:42:28Z","type":"conference","external_id":{"arxiv":["2408.05033"],"isi":["001420093700018"]},"doi":"10.1007/978-3-031-74234-7_18","volume":15191,"has_accepted_license":"1","alternative_title":["LNCS"],"publication_identifier":{"isbn":["9783031742330"],"eissn":["1611-3349"],"issn":["0302-9743"]},"quality_controlled":"1","month":"10"},{"publication_status":"published","OA_type":"gold","year":"2024","pmid":1,"date_updated":"2026-03-05T11:20:12Z","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex uses its rhomboid pseudo-protease subunit, Dsc2, to assess the hydrophobic length of α-helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex likely interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation. Some Dsc substrates will be extracted by Cdc48 for endosome and Golgi associated proteasomal degradation (EGAD), while others will undergo ESCRT dependent vacuolar degradation. Some substrates are degraded by both, EGAD- or ESCRT pathways. The accumulation of Dsc substrates entails a specific increase in glycerophospholipids with shorter and asymmetric fatty acyl chains. Hence, the Dsc complex mediates the selective degradation of orphaned proteins at the sorting center of cells, which prevents their spreading across other organelles and thereby preserves cellular membrane protein and lipid composition."}],"oa":1,"date_created":"2024-11-10T23:01:58Z","status":"public","_id":"18522","title":"The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi","isi":1,"day":"01","date_published":"2024-12-01T00:00:00Z","article_processing_charge":"Yes","article_number":"9257","file_date_updated":"2025-01-22T14:36:33Z","intvolume":" 15","file":[{"success":1,"date_updated":"2025-01-22T14:36:33Z","content_type":"application/pdf","file_size":5634494,"access_level":"open_access","checksum":"32c986fc3babec999c03a5c043310f40","relation":"main_file","date_created":"2025-01-22T14:36:33Z","file_name":"2024_NatureComm_Weyer.pdf","creator":"dernst","file_id":"18870"}],"publisher":"Springer Nature","citation":{"mla":"Weyer, Yannick, et al. “The Dsc Ubiquitin Ligase Complex Identifies Transmembrane Degrons to Degrade Orphaned Proteins at the Golgi.” Nature Communications, vol. 15, 9257, Springer Nature, 2024, doi:10.1038/s41467-024-53676-6.","apa":"Weyer, Y., Schwabl, S. I., Tang, X., Purwar, A., Siegmann, K., Ruepp, A., … Teis, D. (2024). The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-53676-6","ama":"Weyer Y, Schwabl SI, Tang X, et al. The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. Nature Communications. 2024;15. doi:10.1038/s41467-024-53676-6","chicago":"Weyer, Yannick, Sinead I. Schwabl, Xuechen Tang, Astha Purwar, Konstantin Siegmann, Angela Ruepp, Theresia Dunzendorfer-Matt, et al. “The Dsc Ubiquitin Ligase Complex Identifies Transmembrane Degrons to Degrade Orphaned Proteins at the Golgi.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53676-6.","ieee":"Y. Weyer et al., “The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi,” Nature Communications, vol. 15. Springer Nature, 2024.","ista":"Weyer Y, Schwabl SI, Tang X, Purwar A, Siegmann K, Ruepp A, Dunzendorfer-Matt T, Widerin MA, Niedrist V, Mutsters NJM, Tettamanti MG, Weys S, Sarg B, Kremser L, Liedl KR, Schmidt O, Teis D. 2024. The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. Nature Communications. 15, 9257.","short":"Y. Weyer, S.I. Schwabl, X. Tang, A. Purwar, K. Siegmann, A. Ruepp, T. Dunzendorfer-Matt, M.A. Widerin, V. Niedrist, N.J.M. Mutsters, M.G. Tettamanti, S. Weys, B. Sarg, L. Kremser, K.R. Liedl, O. Schmidt, D. Teis, Nature Communications 15 (2024)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Nature Communications","ddc":["570"],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Snezhana Oliferenko, Hesso Farhan, Chris Dunworth, and Lukas A Huber for critically reading the manuscript, Ming Li, Peter Espenshade, Sebastien Leon, and Scott Emr for reagents, Bob Kaufmann for help in characterizing the Dsc2 L1 loop mutant. This research was funded in part by the Austrian Science Fund (FWF) (10.55776/P32161, 10.55776/P34907, 10.55776/DOC82 to DT, and 10.55776/P36187 to OS), by a Lipotype lipidomics excellence award (LEA 2019) to OS, by a Luxembourg National Research Fund (FNR): Grant #13571826 to YW, and by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 847681 (to KRL). For open access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission.","author":[{"last_name":"Weyer","first_name":"Yannick","full_name":"Weyer, Yannick"},{"first_name":"Sinead I.","last_name":"Schwabl","full_name":"Schwabl, Sinead I."},{"full_name":"Tang, Xuechen","last_name":"Tang","first_name":"Xuechen"},{"first_name":"Astha","last_name":"Purwar","full_name":"Purwar, Astha"},{"full_name":"Siegmann, Konstantin","first_name":"Konstantin","last_name":"Siegmann"},{"last_name":"Ruepp","first_name":"Angela","full_name":"Ruepp, Angela"},{"first_name":"Theresia","last_name":"Dunzendorfer-Matt","full_name":"Dunzendorfer-Matt, Theresia"},{"full_name":"Widerin, Michael A.","last_name":"Widerin","first_name":"Michael A."},{"first_name":"Veronika","last_name":"Niedrist","full_name":"Niedrist, Veronika"},{"last_name":"Mutsters","first_name":"Noa J.M.","full_name":"Mutsters, Noa J.M."},{"first_name":"Maria G.","last_name":"Tettamanti","full_name":"Tettamanti, Maria G."},{"full_name":"Weys, Sabine","last_name":"Weys","first_name":"Sabine","id":"caffa136-9669-11ed-9092-ceac12ac9c05"},{"full_name":"Sarg, Bettina","first_name":"Bettina","last_name":"Sarg"},{"full_name":"Kremser, Leopold","last_name":"Kremser","first_name":"Leopold"},{"full_name":"Liedl, Klaus R.","last_name":"Liedl","first_name":"Klaus R."},{"full_name":"Schmidt, Oliver","last_name":"Schmidt","first_name":"Oliver"},{"last_name":"Teis","first_name":"David","full_name":"Teis, David"}],"OA_place":"publisher","article_type":"original","quality_controlled":"1","month":"12","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-024-53676-6","volume":15,"has_accepted_license":"1","type":"journal_article","external_id":{"isi":["001345548100007"],"pmid":["39461958"]},"DOAJ_listed":"1"},{"article_processing_charge":"Yes","date_published":"2024-11-01T00:00:00Z","day":"01","file_date_updated":"2024-11-12T07:17:26Z","intvolume":" 534","issue":"4","citation":{"short":"E. Pizzati, J.F. Hennawi, J. Schaye, M. Schaller, A.C. Eilers, F. Wang, C.S. Frenk, W. Elbers, J.C. Helly, R. Mackenzie, J.J. Matthee, R. Bordoloi, D. Kashino, R.P. Naidu, M. Yue, Monthly Notices of the Royal Astronomical Society 534 (2024) 3155–3175.","chicago":"Pizzati, Elia, Joseph F. Hennawi, Joop Schaye, Matthieu Schaller, Anna Christina Eilers, Feige Wang, Carlos S. Frenk, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stae2307.","ieee":"E. Pizzati et al., “A unified model for the clustering of quasars and galaxies at z ≈ 6,” Monthly Notices of the Royal Astronomical Society, vol. 534, no. 4. Oxford University Press, pp. 3155–3175, 2024.","ista":"Pizzati E, Hennawi JF, Schaye J, Schaller M, Eilers AC, Wang F, Frenk CS, Elbers W, Helly JC, Mackenzie R, Matthee JJ, Bordoloi R, Kashino D, Naidu RP, Yue M. 2024. A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. 534(4), 3155–3175.","ama":"Pizzati E, Hennawi JF, Schaye J, et al. A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. 2024;534(4):3155-3175. doi:10.1093/mnras/stae2307","apa":"Pizzati, E., Hennawi, J. F., Schaye, J., Schaller, M., Eilers, A. C., Wang, F., … Yue, M. (2024). A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae2307","mla":"Pizzati, Elia, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” Monthly Notices of the Royal Astronomical Society, vol. 534, no. 4, Oxford University Press, 2024, pp. 3155–75, doi:10.1093/mnras/stae2307."},"publisher":"Oxford University Press","file":[{"file_id":"18542","creator":"dernst","file_name":"2024_MonthlyNRoyalAstronSoc_Pizzati.pdf","date_created":"2024-11-12T07:17:26Z","checksum":"9ea6285dd1d04d7a9e7b40a4c9e11edb","relation":"main_file","access_level":"open_access","file_size":2954312,"date_updated":"2024-11-12T07:17:26Z","success":1,"content_type":"application/pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Monthly Notices of the Royal Astronomical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"ddc":["520"],"department":[{"_id":"JoMa"}],"acknowledgement":"We are grateful to Junya Arita and the SHELLQs team for sharing their data on the quasar autocorrelation function and to Jan-Torge Schindler for discussion on the QLF. We acknowledge helpful conversations with the ENIGMA group at UC Santa Barbara and Leiden University. EP is grateful to Rob McGibbon and Victor Forouhar Moreno for help with the simulation outputs, and to Timo Kist, Jiamu Huang, and Vikram Khaire for comments on an early version of the manuscript. JFH and EP acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 885301). This work is partly supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 860744 (BiD4BESt). FW acknowledges support from NSF grant AST-2308258. This work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Director’s Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded\r\nDiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University, and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure.","OA_place":"publisher","author":[{"last_name":"Pizzati","first_name":"Elia","full_name":"Pizzati, Elia"},{"full_name":"Hennawi, Joseph F.","first_name":"Joseph F.","last_name":"Hennawi"},{"full_name":"Schaye, Joop","first_name":"Joop","last_name":"Schaye"},{"last_name":"Schaller","first_name":"Matthieu","full_name":"Schaller, Matthieu"},{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"first_name":"Feige","last_name":"Wang","full_name":"Wang, Feige"},{"last_name":"Frenk","first_name":"Carlos S.","full_name":"Frenk, Carlos S."},{"full_name":"Elbers, Willem","last_name":"Elbers","first_name":"Willem"},{"first_name":"John C.","last_name":"Helly","full_name":"Helly, John C."},{"full_name":"Mackenzie, Ruari","last_name":"Mackenzie","first_name":"Ruari"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee"},{"full_name":"Bordoloi, Rongmon","first_name":"Rongmon","last_name":"Bordoloi"},{"last_name":"Kashino","first_name":"Daichi","full_name":"Kashino, Daichi"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"full_name":"Yue, Minghao","first_name":"Minghao","last_name":"Yue"}],"article_type":"original","month":"11","quality_controlled":"1","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"has_accepted_license":"1","volume":534,"doi":"10.1093/mnras/stae2307","external_id":{"isi":["001335663900008"]},"type":"journal_article","DOAJ_listed":"1","OA_type":"gold","publication_status":"published","page":"3155-3175","year":"2024","date_updated":"2025-09-08T14:40:22Z","oa_version":"Published Version","scopus_import":"1","oa":1,"date_created":"2024-11-10T23:01:58Z","abstract":[{"text":"Recent observations from the EIGER JWST program have measured for the first time the quasar–galaxy cross-correlation function at z ≈ 6. The autocorrelation function of faint z ≈ 6 quasars was also recently estimated. These measurements provide key insights into the properties of quasars and galaxies at high redshift and their relation with the host dark matter haloes. In this work, we interpret these data building upon an empirical quasar population model that has been applied successfully to quasar clustering and demographic measurements at z ≈ 2–4. We use a new, large-volume N-body simulation with more than a trillion particles, FLAMINGO-10k, to model quasars and galaxies simultaneously. We successfully reproduce observations of z ≈ 6 quasars and galaxies (i.e. their clustering properties and luminosity functions), and infer key quantities such as their luminosity–halo mass relation, the mass function of their host haloes, and their duty cycle/occupation fraction. Our key findings\r\nare (i) quasars reside on average in ≈ 1012.5 M haloes (corresponding to ≈ 5σ fluctuations in the initial conditions of the linear density field), but the distribution of host halo masses is quite broad; (ii) the duty cycle of (UV-bright) quasar activity is relatively low (≈ 1 per cent); (iii) galaxies (that are bright in [O III]) live in much smaller haloes (≈ 1010.9 M) and have a larger duty cycle (occupation fraction) of ≈ 13 per cent. Finally, we focus on the inferred properties of quasars and present a homogeneous analysis of their evolution with redshift. The picture that emerges reveals a strong evolution of the host halo mass and duty cycle of quasars at z ≈ 2–6, and calls for new investigations of the role of quasar activity across cosmic time.","lang":"eng"}],"_id":"18523","status":"public","title":"A unified model for the clustering of quasars and galaxies at z ≈ 6","isi":1},{"day":"01","date_published":"2024-11-01T00:00:00Z","article_processing_charge":"No","article_number":"29","file_date_updated":"2024-11-11T09:20:45Z","intvolume":" 975","publisher":"IOP Publishing","file":[{"file_name":"2024_AstrophysicalJour_Grady.pdf","creator":"dernst","file_id":"18535","date_created":"2024-11-11T09:20:45Z","relation":"main_file","checksum":"0e9bb88b5048ecc782ac27953c84b8ce","success":1,"content_type":"application/pdf","date_updated":"2024-11-11T09:20:45Z","file_size":34634395,"access_level":"open_access"}],"citation":{"mla":"O’Grady, Anna J. G., et al. “Binary Yellow Supergiants in the Magellanic Clouds. I. Photometric Candidate Identification.” Astrophysical Journal, vol. 975, 29, IOP Publishing, 2024, doi:10.3847/1538-4357/ad778a.","apa":"O’Grady, A. J. G., Drout, M. R., Neugent, K. F., Ludwig, B., Götberg, Y. L. L., & Gaensler, B. M. (2024). Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad778a","ama":"O’Grady AJG, Drout MR, Neugent KF, Ludwig B, Götberg YLL, Gaensler BM. Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification. Astrophysical Journal. 2024;975. doi:10.3847/1538-4357/ad778a","ieee":"A. J. G. O’Grady, M. R. Drout, K. F. Neugent, B. Ludwig, Y. L. L. Götberg, and B. M. Gaensler, “Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification,” Astrophysical Journal, vol. 975. IOP Publishing, 2024.","chicago":"O’Grady, Anna J.G., Maria R. Drout, Kathryn F. Neugent, Bethany Ludwig, Ylva Louise Linsdotter Götberg, and B. M. Gaensler. “Binary Yellow Supergiants in the Magellanic Clouds. I. Photometric Candidate Identification.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad778a.","ista":"O’Grady AJG, Drout MR, Neugent KF, Ludwig B, Götberg YLL, Gaensler BM. 2024. Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification. Astrophysical Journal. 975, 29.","short":"A.J.G. O’Grady, M.R. Drout, K.F. Neugent, B. Ludwig, Y.L.L. Götberg, B.M. Gaensler, Astrophysical Journal 975 (2024)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["520"],"publication":"Astrophysical Journal","arxiv":1,"acknowledgement":"The authors thank Aaron Tohuvavohu, Katie Breivik, Marten van Kerkwijk, Jakub Klencki, Eva Laplace, and Dae-Sik Moon for helpful discussions, and Adiv Paradise for helpful edits. The authors also thank the anonymous reviewer for a helpful and constructive referee report.\r\nThe authors at the University of Toronto acknowledge that the land on which the University of Toronto operates is the traditional territory of the Huron–Wendat, the Seneca, and the Mississaugas of the Credit River. They are grateful to have the opportunity to work on this land.\r\nThe Dunlap Institute is funded through an endowment established by the David Dunlap family and the University of Toronto.\r\nA.J.G.O. is supported by a McWilliams Fellowship at Carnegie Mellon University. M.R.D. acknowledges support from the NSERC through grant RGPIN-2019-06186, the Canada Research Chairs Program, and the Dunlap Institute at the University of Toronto. B.M.G. acknowledges the support of the Natural Sciences and Engineering Research Council of Canada (NSERC) through grant RGPIN-2022-03163, and of the Canada Research Chairs program. Support for this work was provided by NASA through the NASA Hubble Fellowship Program grant Nos. HST-HF2-51457.001-A and HST-HF2-51516 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555.\r\nThis research has made use of the SIMBAD database (M. Wenger et al. 2000), operated at CDS, Strasbourg, France, and the SVO Filter Profile Service 13 supported by the Spanish MINECO through grant AYA2017-84089 (C. Rodrigo et al. 2012, 2020).\r\nThis research has made use of the following software: astropy (Astropy Collaboration et al. 2013, 2018, 2022), IRAF (D. Tody 1986, 1993), and TOPCAT (M. B. Taylor 2005).","department":[{"_id":"YlGo"}],"author":[{"last_name":"O’Grady","first_name":"Anna J.G.","full_name":"O’Grady, Anna J.G."},{"last_name":"Drout","first_name":"Maria R.","full_name":"Drout, Maria R."},{"last_name":"Neugent","first_name":"Kathryn F.","full_name":"Neugent, Kathryn F."},{"full_name":"Ludwig, Bethany","first_name":"Bethany","last_name":"Ludwig"},{"first_name":"Ylva Louise Linsdotter","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"last_name":"Gaensler","first_name":"B. M.","full_name":"Gaensler, B. M."}],"OA_place":"publisher","article_type":"original","quality_controlled":"1","month":"11","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"doi":"10.3847/1538-4357/ad778a","has_accepted_license":"1","volume":975,"type":"journal_article","external_id":{"arxiv":["2406.17177"],"isi":["001339486900001"]},"DOAJ_listed":"1","publication_status":"published","OA_type":"gold","year":"2024","date_updated":"2025-09-08T14:37:18Z","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Recent works have constrained the binary fraction of evolved populations of massive stars in local galaxies such as red supergiants and Wolf–Rayet stars, but the binary fraction of yellow supergiants (YSGs) in the Hertzsprung gap remains unconstrained. Binary evolution theory predicts that the Hertzsprung gap is home to multiple populations of binary systems with varied evolutionary histories. In this paper, we develop a method to distinguish single YSGs from YSG plus O- or B-type main-sequence binaries using optical and ultraviolet photometry, and then apply this method to identify candidate YSG binaries in the Magellanic Clouds. After constructing a set of combined stellar atmosphere models, we find that optical photometry is, given typical measurement and reddening uncertainties, sufficient to discern single YSGs from YSG+OB binaries if the OB-star is at least ∼5M⊙ for Teff,YSG ∼ 4000 K, but requires a ∼20M⊙ OB star for YSGs up to Teff,YSG ∼ 9000 K. For these hotter YSG temperatures, ultraviolet photometry allows binaries with OB companions as small as ∼7M⊙ to be identified. We use color–color spaces developed from these models to search for evidence of excess blue or ultraviolet light in a set of ∼1000 YSG candidates in the Magellanic Clouds. We identify hundreds of candidate YSG binary systems and report a preliminary fraction of YSGs that show a blue/UV color excess of 20%–60%. Spectroscopic follow-up is now required to confirm the true nature of this population."}],"date_created":"2024-11-10T23:01:59Z","oa":1,"_id":"18524","status":"public","title":"Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification","isi":1},{"publication_status":"published","OA_type":"hybrid","pmid":1,"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"year":"2024","date_updated":"2025-09-08T14:38:35Z","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets.","lang":"eng"}],"oa":1,"date_created":"2024-11-10T23:01:59Z","title":"Endosomal membrane budding patterns in plants","_id":"18526","status":"public","isi":1,"article_number":"e2409407121","file_date_updated":"2024-11-11T09:35:15Z","day":"29","date_published":"2024-10-29T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","file":[{"content_type":"application/pdf","success":1,"date_updated":"2024-11-11T09:35:15Z","file_size":5268074,"access_level":"open_access","relation":"main_file","checksum":"21c82d2ab58ff99b2bd0489797be42e5","date_created":"2024-11-11T09:35:15Z","creator":"dernst","file_name":"2024_PNAS_Weiner.pdf","file_id":"18538"}],"publisher":"National Academy of Sciences","citation":{"short":"E. Weiner, E. Berryman, F.F. Frey, A.G. Solís, A. Leier, T.M. Lago, A. Šarić, M.S. Otegui, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Weiner E, Berryman E, Frey FF, Solís AG, Leier A, Lago TM, Šarić A, Otegui MS. 2024. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2409407121.","ieee":"E. Weiner et al., “Endosomal membrane budding patterns in plants,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44. National Academy of Sciences, 2024.","chicago":"Weiner, Ethan, Elizabeth Berryman, Felix F Frey, Ariadna González Solís, André Leier, Tatiana Marquez Lago, Anđela Šarić, and Marisa S. Otegui. “Endosomal Membrane Budding Patterns in Plants.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2409407121.","ama":"Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(44). doi:10.1073/pnas.2409407121","apa":"Weiner, E., Berryman, E., Frey, F. F., Solís, A. G., Leier, A., Lago, T. M., … Otegui, M. S. (2024). Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2409407121","mla":"Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:10.1073/pnas.2409407121."},"issue":"44","intvolume":" 121","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Proceedings of the National Academy of Sciences of the United States of America","language":[{"iso":"eng"}],"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"author":[{"full_name":"Weiner, Ethan","last_name":"Weiner","first_name":"Ethan"},{"full_name":"Berryman, Elizabeth","first_name":"Elizabeth","last_name":"Berryman"},{"orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F","last_name":"Frey","full_name":"Frey, Felix F"},{"full_name":"Solís, Ariadna González","first_name":"Ariadna González","last_name":"Solís"},{"first_name":"André","last_name":"Leier","full_name":"Leier, André"},{"first_name":"Tatiana Marquez","last_name":"Lago","full_name":"Lago, Tatiana Marquez"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Otegui, Marisa S.","first_name":"Marisa S.","last_name":"Otegui"}],"ec_funded":1,"OA_place":"publisher","acknowledgement":"We would like to thank Janice Pennington for her support with electron tomography data collection, Dr. Ingrid Jordon-Thaden, director of the Botany Garden and Greenhouse of University of Wisconsin Madison, for her invaluable assistance collecting plant materials, Dr. Marie Trest for providing Chara specimens, and Dr. Nicholas Keuler for his advice on statistical analyses. We thank Charlie Hamilton for exploring the initial computational model. This work was supported by grant NSF MCB 2114603 and NIH 1S10OD026769-01 to M.S.O. F.F acknowledges support as a NOMIS Fellow from the NOMIS Foundation. A.Š. acknowledges ERC Starting Grant “NEPA” 802960.","department":[{"_id":"AnSa"}],"quality_controlled":"1","month":"10","article_type":"original","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2409407121","volume":121,"has_accepted_license":"1","type":"journal_article","external_id":{"isi":["001349500800007"],"pmid":["39441629"]}},{"author":[{"full_name":"Degtev, Dmitrii","last_name":"Degtev","first_name":"Dmitrii"},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","first_name":"Jack Peter Kelly"},{"full_name":"Emmanouilidi, Aikaterini","last_name":"Emmanouilidi","first_name":"Aikaterini"},{"full_name":"Zdravković, Aleksandar","last_name":"Zdravković","first_name":"Aleksandar"},{"last_name":"Choong","first_name":"Oi Kuan","full_name":"Choong, Oi Kuan"},{"last_name":"Liz Touza","first_name":"Julia","full_name":"Liz Touza, Julia"},{"full_name":"Selfjord, Niklas","first_name":"Niklas","last_name":"Selfjord"},{"full_name":"Weisheit, Isabel","first_name":"Isabel","last_name":"Weisheit"},{"full_name":"Francescatto, Margherita","last_name":"Francescatto","first_name":"Margherita"},{"full_name":"Akcakaya, Pinar","last_name":"Akcakaya","first_name":"Pinar"},{"full_name":"Porritt, Michelle","first_name":"Michelle","last_name":"Porritt"},{"full_name":"Maresca, Marcello","last_name":"Maresca","first_name":"Marcello"},{"first_name":"David","last_name":"Taylor","full_name":"Taylor, David"},{"last_name":"Sienski","first_name":"Grzegorz","full_name":"Sienski, Grzegorz"}],"OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"language":[{"iso":"eng"}],"publication":"Nature Communications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["572"],"intvolume":" 15","publisher":"Springer Nature","file":[{"date_created":"2024-11-12T10:18:32Z","file_id":"18546","creator":"jbravo","file_name":"s41467-024-53418-8.pdf","success":1,"date_updated":"2024-11-12T10:18:32Z","content_type":"application/pdf","access_level":"open_access","file_size":2967001,"checksum":"dcfadc806f4144d065eb8e2032554782","relation":"main_file"}],"citation":{"mla":"Degtev, Dmitrii, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.” Nature Communications, vol. 15, 9173, Springer Nature, 2024, doi:10.1038/s41467-024-53418-8.","apa":"Degtev, D., Bravo, J. P. K., Emmanouilidi, A., Zdravković, A., Choong, O. K., Liz Touza, J., … Sienski, G. (2024). Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-53418-8","short":"D. Degtev, J.P.K. Bravo, A. Emmanouilidi, A. Zdravković, O.K. Choong, J. Liz Touza, N. Selfjord, I. Weisheit, M. Francescatto, P. Akcakaya, M. Porritt, M. Maresca, D. Taylor, G. Sienski, Nature Communications 15 (2024).","ama":"Degtev D, Bravo JPK, Emmanouilidi A, et al. Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. Nature Communications. 2024;15. doi:10.1038/s41467-024-53418-8","ista":"Degtev D, Bravo JPK, Emmanouilidi A, Zdravković A, Choong OK, Liz Touza J, Selfjord N, Weisheit I, Francescatto M, Akcakaya P, Porritt M, Maresca M, Taylor D, Sienski G. 2024. Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. Nature Communications. 15, 9173.","ieee":"D. Degtev et al., “Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles,” Nature Communications, vol. 15. Springer Nature, 2024.","chicago":"Degtev, Dmitrii, Jack Peter Kelly Bravo, Aikaterini Emmanouilidi, Aleksandar Zdravković, Oi Kuan Choong, Julia Liz Touza, Niklas Selfjord, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53418-8."},"day":"07","date_published":"2024-11-07T00:00:00Z","article_processing_charge":"Yes","article_number":"9173","file_date_updated":"2024-11-12T10:18:32Z","type":"journal_article","DOAJ_listed":"1","doi":"10.1038/s41467-024-53418-8","volume":15,"has_accepted_license":"1","publication_identifier":{"issn":["2041-1723"]},"article_type":"original","quality_controlled":"1","month":"11","scopus_import":"1","oa_version":"Published Version","date_updated":"2024-11-13T08:19:50Z","year":"2024","publication_status":"published","OA_type":"gold","_id":"18545","status":"public","title":"Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles","extern":"1","abstract":[{"text":"Clinical implementation of therapeutic genome editing relies on efficient in vivo delivery and the safety of CRISPR-Cas tools. Previously, we identified PsCas9 as a Type II-B family enzyme capable of editing mouse liver genome upon adenoviral delivery without detectable off-targets and reduced chromosomal translocations. Yet, its efficacy remains insufficient with non-viral delivery, a common challenge for many Cas9 orthologues. Here, we sought to redesign PsCas9 for in vivo editing using lipid nanoparticles. We solve the PsCas9 ribonucleoprotein structure with cryo-EM and characterize it biochemically, providing a basis for its rational engineering. Screening over numerous guide RNA and protein variants lead us to develop engineered PsCas9 (ePsCas9) with up to 20-fold increased activity across various targets and preserved safety advantages. We apply the same design principles to boost the activity of FnCas9, an enzyme phylogenetically relevant to PsCas9. Remarkably, a single administration of mRNA encoding ePsCas9 and its guide formulated with lipid nanoparticles results in high levels of editing in the Pcsk9 gene in mouse liver, a clinically relevant target for hypercholesterolemia treatment. Collectively, our findings introduce ePsCas9 as a highly efficient, and precise tool for therapeutic genome editing, in addition to the engineering strategy applicable to other Cas9 orthologues.","lang":"eng"}],"oa":1,"date_created":"2024-11-12T10:18:04Z"},{"date_updated":"2025-09-08T14:42:50Z","scopus_import":"1","oa_version":"Published Version","page":"4740-4757.e12","publication_status":"published","OA_type":"hybrid","year":"2024","pmid":1,"isi":1,"abstract":[{"text":"Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component.","lang":"eng"}],"oa":1,"date_created":"2024-11-15T12:12:54Z","status":"public","_id":"18553","title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"publication":"Molecular Cell","language":[{"iso":"eng"}],"acknowledgement":"We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF) and the Preclinical Facility (PCF). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer Institute is supported by institutional grants of the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI (VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for Scientific Research.","department":[{"_id":"CaBe"}],"author":[{"last_name":"Ramadhin","first_name":"Anisha R.","full_name":"Ramadhin, Anisha R."},{"first_name":"Shun-Hsiao","last_name":"Lee","full_name":"Lee, Shun-Hsiao"},{"first_name":"Di","last_name":"Zhou","full_name":"Zhou, Di"},{"last_name":"Testa Salmazo","first_name":"Anita P","full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gonzalo-Hansen, Camila","first_name":"Camila","last_name":"Gonzalo-Hansen"},{"full_name":"van Sluis, Marjolein","first_name":"Marjolein","last_name":"van Sluis"},{"full_name":"Blom, Cindy M.A.","last_name":"Blom","first_name":"Cindy M.A."},{"full_name":"Janssens, Roel C.","last_name":"Janssens","first_name":"Roel C."},{"last_name":"Raams","first_name":"Anja","full_name":"Raams, Anja"},{"last_name":"Dekkers","first_name":"Dick","full_name":"Dekkers, Dick"},{"full_name":"Bezstarosti, Karel","last_name":"Bezstarosti","first_name":"Karel"},{"full_name":"Slade, Dea","first_name":"Dea","last_name":"Slade"},{"full_name":"Vermeulen, Wim","first_name":"Wim","last_name":"Vermeulen"},{"first_name":"Alex","last_name":"Pines","full_name":"Pines, Alex"},{"full_name":"Demmers, Jeroen A.A.","first_name":"Jeroen A.A.","last_name":"Demmers"},{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","full_name":"Bernecky, Carrie A"},{"full_name":"Sixma, Titia K.","first_name":"Titia K.","last_name":"Sixma"},{"full_name":"Marteijn, Jurgen A.","last_name":"Marteijn","first_name":"Jurgen A."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"OA_place":"publisher","day":"19","date_published":"2024-12-19T00:00:00Z","article_processing_charge":"No","file_date_updated":"2025-01-13T11:17:35Z","issue":"24","intvolume":" 84","publisher":"Elsevier","file":[{"file_id":"18844","file_name":"2024_MolecularCell_Ramadhin.pdf","creator":"dernst","date_created":"2025-01-13T11:17:35Z","checksum":"e051e2766b2d424983778f742cb7c5ed","relation":"main_file","file_size":25071994,"access_level":"open_access","date_updated":"2025-01-13T11:17:35Z","success":1,"content_type":"application/pdf"}],"citation":{"mla":"Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” Molecular Cell, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:10.1016/j.molcel.2024.10.030.","apa":"Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen, C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2024.10.030","short":"A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen, M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti, D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A. Marteijn, Molecular Cell 84 (2024) 4740–4757.e12.","ama":"Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. 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Ramadhin et al., “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” Molecular Cell, vol. 84, no. 24. 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As the main technical ingredient, we prove rank-uniform optimal local laws for one and two resolvents of a Wigner-type matrix with regular observables. Our results hold under very general conditions on the variance profile, even allowing many vanishing entries, demonstrating that Eigenstate Thermalization occurs robustly across a diverse class of random matrix ensembles, for which the underlying quantum system has a non-trivial spatial structure."}],"title":"Eigenstate Thermalization Hypothesis for Wigner-type matrices","_id":"18554","status":"public","isi":1,"corr_author":"1","OA_type":"hybrid","publication_status":"published","pmid":1,"year":"2024","date_updated":"2026-04-07T12:32:19Z","oa_version":"Published Version","scopus_import":"1"},{"ddc":["510"],"language":[{"iso":"eng"}],"publication":"32nd International Symposium on Graph Drawing and Network Visualization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano","last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832"},{"orcid":"0000-0003-0464-3823","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov","first_name":"Ondrej","full_name":"Draganov, Ondrej"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"ec_funded":1,"OA_place":"publisher","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, \"Discretization in Geometry and Dynamics\", Austrian Science Fund (FWF), grant no. I 02979-N35.","department":[{"_id":"HeEd"}],"article_number":"3","file_date_updated":"2024-11-18T07:49:25Z","day":"28","date_published":"2024-10-28T00:00:00Z","article_processing_charge":"Yes","file":[{"relation":"main_file","checksum":"5f9b35e115c3d375e99be78da9054cb4","access_level":"open_access","file_size":908541,"success":1,"date_updated":"2024-11-18T07:49:25Z","content_type":"application/pdf","file_name":"2024_LIPIcs_CultreradiMontesano.pdf","creator":"dernst","file_id":"18560","date_created":"2024-11-18T07:49:25Z"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. The Euclidean MST-ratio for bi-colored lattices. In: 32nd International Symposium on Graph Drawing and Network Visualization. Vol 320. 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Edelsbrunner, M. Saghafian, in:, 32nd International Symposium on Graph Drawing and Network Visualization, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Cultrera di Montesano, Sebastiano, et al. “The Euclidean MST-Ratio for Bi-Colored Lattices.” 32nd International Symposium on Graph Drawing and Network Visualization, vol. 320, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.GD.2024.3.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (2024). The Euclidean MST-ratio for bi-colored lattices. In 32nd International Symposium on Graph Drawing and Network Visualization (Vol. 320). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.GD.2024.3"},"intvolume":" 320","doi":"10.4230/LIPIcs.GD.2024.3","has_accepted_license":"1","volume":320,"type":"conference","external_id":{"arxiv":["2403.10204"],"isi":["001540278400001"]},"quality_controlled":"1","month":"10","publication_identifier":{"isbn":["9783959773430"],"issn":["1868-8969"]},"alternative_title":["LIPIcs"],"date_updated":"2025-12-02T13:50:50Z","conference":{"end_date":"2024-09-20","name":"GD: Graph Drawing and Network Visualization","start_date":"2024-09-18","location":"Vienna, Austria"},"oa_version":"Published Version","scopus_import":"1","publication_status":"published","OA_type":"gold","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"name":"Mathematics, Computer Science","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"year":"2024","corr_author":"1","isi":1,"abstract":[{"lang":"eng","text":"Given a finite set, A ⊆ ℝ², and a subset, B ⊆ A, the MST-ratio is the combined length of the minimum spanning trees of B and A⧵B divided by the length of the minimum spanning tree of A. The question of the supremum, over all sets A, of the maximum, over all subsets B, is related to the Steiner ratio, and we prove this sup-max is between 2.154 and 2.427. Restricting ourselves to 2-dimensional lattices, we prove that the sup-max is 2, while the inf-max is 1.25. By some margin the most difficult of these results is the upper bound for the inf-max, which we prove by showing that the hexagonal lattice cannot have MST-ratio larger than 1.25."}],"oa":1,"date_created":"2024-11-17T23:01:47Z","title":"The Euclidean MST-ratio for bi-colored lattices","_id":"18556","status":"public"},{"publication":"Annals of Mathematics","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"acknowledgement":"Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE1745302. Sah was supported by the PD Soros Fellowship. 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The selection of contributions in this essay reflects primarily my personal involvement rather than any measure of importance.","author":[{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"month":"10","quality_controlled":"1","series_title":"LNCS","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031737503"],"eisbn":["9783031737510"]},"alternative_title":["LNCS"],"volume":15230,"doi":"10.1007/978-3-031-73751-0_12","type":"book_chapter"}]