[{"DOAJ_listed":"1","title":"Tangent space generators of matrix product states and exact floquet quantum scars","intvolume":"         5","oa":1,"file_date_updated":"2024-10-30T08:59:09Z","status":"public","arxiv":1,"volume":5,"citation":{"ama":"Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>","mla":"Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>, vol. 5, no. 4, 040311, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>.","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.","apa":"Ljubotina, M., Petrova, E., Schuch, N., &#38; Serbyn, M. (2024). Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>","short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).","ieee":"M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators of matrix product states and exact floquet quantum scars,” <i>PRX Quantum</i>, 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.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>."},"date_created":"2024-10-29T16:04:05Z","article_processing_charge":"Yes","APC_amount":"3711,01 EUR","publisher":"American Physical Society","article_type":"original","_id":"18488","external_id":{"arxiv":["2403.12325"],"isi":["001346198800001"]},"has_accepted_license":"1","OA_type":"gold","issue":"4","month":"10","isi":1,"department":[{"_id":"MaSe"}],"date_updated":"2025-09-08T14:26:29Z","article_number":"040311","ddc":["530"],"year":"2024","oa_version":"Published Version","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).","author":[{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","first_name":"Marko"},{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","last_name":"Petrova","full_name":"Petrova, Elena","first_name":"Elena"},{"first_name":"Norbert","last_name":"Schuch","full_name":"Schuch, Norbert"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"publication_identifier":{"eissn":["2691-3399"]},"corr_author":"1","fulldoi":"https://doi.org/10.1103/prxquantum.5.040311","ec_funded":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"}],"day":"23","OA_place":"publisher","date_published":"2024-10-23T00:00:00Z","file":[{"file_name":"2024_PRXQuantum_Ljubotina.pdf","relation":"main_file","content_type":"application/pdf","file_size":1151431,"success":1,"creator":"dernst","date_created":"2024-10-30T08:59:09Z","date_updated":"2024-10-30T08:59:09Z","checksum":"2e057ba021744d0a74602517935326b3","file_id":"18489","access_level":"open_access"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1103/prxquantum.5.040311","scopus_import":"1","quality_controlled":"1","type":"journal_article","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication":"PRX Quantum"},{"issue":"5","OA_type":"hybrid","has_accepted_license":"1","department":[{"_id":"JaMa"}],"isi":1,"month":"11","ddc":["510"],"article_number":"e70003","date_updated":"2025-09-08T14:29:45Z","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.","author":[{"last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo","orcid":"0000-0002-9881-6870"},{"full_name":"Herry, Ronan","last_name":"Herry","first_name":"Ronan"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"full_name":"Sturm, Karl Theodor","last_name":"Sturm","first_name":"Karl Theodor"}],"oa_version":"Published Version","year":"2024","oa":1,"intvolume":"       110","title":"Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension","status":"public","file_date_updated":"2024-11-04T08:54:26Z","publisher":"London Mathematical Society","citation":{"apa":"Dello Schiavo, L., Herry, R., Kopfer, E., &#38; Sturm, K. T. (2024). Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension. <i>Journal of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/jlms.70003\">https://doi.org/10.1112/jlms.70003</a>","short":"L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Journal of the London Mathematical Society 110 (2024).","mla":"Dello Schiavo, Lorenzo, et al. “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 5, e70003, London Mathematical Society, 2024, doi:<a href=\"https://doi.org/10.1112/jlms.70003\">10.1112/jlms.70003</a>.","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. <i>Journal of the London Mathematical Society</i>. 2024;110(5). doi:<a href=\"https://doi.org/10.1112/jlms.70003\">10.1112/jlms.70003</a>","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.” <i>Journal of the London Mathematical Society</i>. London Mathematical Society, 2024. <a href=\"https://doi.org/10.1112/jlms.70003\">https://doi.org/10.1112/jlms.70003</a>.","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,” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 5. London Mathematical Society, 2024."},"article_processing_charge":"Yes (via OA deal)","volume":110,"date_created":"2024-11-03T23:01:44Z","external_id":{"isi":["001351918100029"]},"_id":"18490","article_type":"original","scopus_import":"1","doi":"10.1112/jlms.70003","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","type":"journal_article","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication":"Journal of the London Mathematical Society","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"fulldoi":"https://doi.org/10.1112/jlms.70003","ec_funded":1,"OA_place":"publisher","day":"01","abstract":[{"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. ","lang":"eng"}],"date_published":"2024-11-01T00:00:00Z","file":[{"checksum":"143816823b5f43bd3748da8e3e91cef5","access_level":"open_access","file_id":"18497","date_updated":"2024-11-04T08:54:26Z","date_created":"2024-11-04T08:54:26Z","success":1,"creator":"dernst","file_name":"2024_JourLondonMathSoc_Schiavo.pdf","relation":"main_file","file_size":911476,"content_type":"application/pdf"}]},{"_id":"18494","article_type":"original","external_id":{"isi":["001338877100001"]},"date_created":"2024-11-03T23:01:45Z","article_processing_charge":"Yes","citation":{"ieee":"A. C. Eilers <i>et al.</i>, “EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6,” <i>Astrophysical Journal</i>, vol. 974, no. 2. IOP Publishing, 2024.","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.” <i>Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad778b\">https://doi.org/10.3847/1538-4357/ad778b</a>.","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. <i>Astrophysical Journal</i>. 2024;974(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778b\">10.3847/1538-4357/ad778b</a>","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.","mla":"Eilers, Anna Christina, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” <i>Astrophysical Journal</i>, vol. 974, no. 2, 275, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad778b\">10.3847/1538-4357/ad778b</a>.","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).","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. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad778b\">https://doi.org/10.3847/1538-4357/ad778b</a>"},"volume":974,"publisher":"IOP Publishing","file_date_updated":"2024-11-04T08:42:23Z","status":"public","oa":1,"title":"EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6","intvolume":"       974","DOAJ_listed":"1","oa_version":"Published Version","year":"2024","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).","author":[{"last_name":"Eilers","full_name":"Eilers, Anna Christina","first_name":"Anna Christina"},{"full_name":"Mackenzie, Ruari","last_name":"Mackenzie","first_name":"Ruari"},{"first_name":"Elia","full_name":"Pizzati, Elia","last_name":"Pizzati"},{"first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee"},{"full_name":"Hennawi, Joseph F.","last_name":"Hennawi","first_name":"Joseph F."},{"first_name":"Haowen","last_name":"Zhang","full_name":"Zhang, Haowen"},{"first_name":"Rongmon","full_name":"Bordoloi, Rongmon","last_name":"Bordoloi"},{"first_name":"Daichi","last_name":"Kashino","full_name":"Kashino, Daichi"},{"full_name":"Lilly, Simon J.","last_name":"Lilly","first_name":"Simon J."},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"first_name":"Robert A.","last_name":"Simcoe","full_name":"Simcoe, Robert A."},{"last_name":"Yue","full_name":"Yue, Minghao","first_name":"Minghao"},{"last_name":"Frenk","full_name":"Frenk, Carlos S.","first_name":"Carlos S."},{"full_name":"Helly, John C.","last_name":"Helly","first_name":"John C."},{"first_name":"Matthieu","last_name":"Schaller","full_name":"Schaller, Matthieu"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"}],"article_number":"275","date_updated":"2025-09-08T14:29:05Z","ddc":["520"],"isi":1,"month":"10","department":[{"_id":"JoMa"}],"OA_type":"gold","has_accepted_license":"1","issue":"2","date_published":"2024-10-01T00:00:00Z","file":[{"date_updated":"2024-11-04T08:42:23Z","date_created":"2024-11-04T08:42:23Z","checksum":"1fcac3d11d01d91cf2bb4963b6e10b22","access_level":"open_access","file_id":"18496","file_name":"2024_AstrophysicalJour_Eilers.pdf","relation":"main_file","file_size":1042470,"content_type":"application/pdf","success":1,"creator":"dernst"}],"abstract":[{"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.","lang":"eng"}],"OA_place":"publisher","day":"01","fulldoi":"https://doi.org/10.3847/1538-4357/ad778b","project":[{"name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224","_id":"bd9b2118-d553-11ed-ba76-db24564edfea"}],"publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"publication":"Astrophysical Journal","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_status":"published","type":"journal_article","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","doi":"10.3847/1538-4357/ad778b"},{"author":[{"first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando","last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Larsson, Jenny","last_name":"Larsson","first_name":"Jenny"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","oa_version":"Published Version","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"20991","relation":"used_in_publication"},{"status":"public","id":"18491","relation":"used_in_publication"}]},"date_updated":"2026-04-16T12:20:37Z","department":[{"_id":"NiBa"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.12159344","open_access":"1"}],"type":"research_data_reference","month":"06","doi":"10.5281/ZENODO.12159343","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","date_published":"2024-06-19T00:00:00Z","_id":"18498","day":"19","publisher":"Zenodo","OA_place":"repository","abstract":[{"lang":"eng","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"}],"article_processing_charge":"No","date_created":"2024-11-04T09:33:17Z","citation":{"mla":"Garcia Castillo, Diego Fernando, et al. <i>Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","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, <a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","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:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>","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. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>","ieee":"D. F. Garcia Castillo <i>et al.</i>, “Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails.” Zenodo, 2024.","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. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>."},"status":"public","fulldoi":"https://doi.org/10.5281/ZENODO.12159343","corr_author":"1","title":"Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails","oa":1},{"publication":"35th Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","type":"conference","scopus_import":"1","doi":"10.1137/1.9781611977912.111","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-01-04T00:00:00Z","page":"3089-3139","OA_place":"repository","conference":{"location":"Alexandria, VA,  United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2024-01-10","start_date":"2024-01-07"},"day":"04","abstract":[{"lang":"eng","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."}],"ec_funded":1,"fulldoi":"https://doi.org/10.1137/1.9781611977912.111","corr_author":"1","publication_identifier":{"eisbn":["9781611977912"]},"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"Z00422","name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"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.","author":[{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"last_name":"Li","full_name":"Li, Jason","first_name":"Jason"},{"first_name":"Satish","last_name":"Rao","full_name":"Rao, Satish"},{"first_name":"Di","last_name":"Wang","full_name":"Wang, Di"}],"oa_version":"Preprint","year":"2024","date_updated":"2025-06-24T12:09:26Z","department":[{"_id":"MoHe"}],"month":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2401.05627","open_access":"1"}],"OA_type":"free access","external_id":{"arxiv":["2401.05627"]},"_id":"18503","publisher":"Society for Industrial and Applied Mathematics","article_processing_charge":"No","citation":{"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.","mla":"Henzinger, Monika, et al. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2024, pp. 3089–139, doi:<a href=\"https://doi.org/10.1137/1.9781611977912.111\">10.1137/1.9781611977912.111</a>.","ama":"Henzinger M, Li J, Rao S, Wang D. Deterministic near-linear time minimum cut in weighted graphs. In: <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2024:3089-3139. doi:<a href=\"https://doi.org/10.1137/1.9781611977912.111\">10.1137/1.9781611977912.111</a>","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.","apa":"Henzinger, M., Li, J., Rao, S., &#38; Wang, D. (2024). Deterministic near-linear time minimum cut in weighted graphs. In <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 3089–3139). Alexandria, VA,  United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977912.111\">https://doi.org/10.1137/1.9781611977912.111</a>","ieee":"M. Henzinger, J. Li, S. Rao, and D. Wang, “Deterministic near-linear time minimum cut in weighted graphs,” in <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Alexandria, VA,  United States, 2024, pp. 3089–3139.","chicago":"Henzinger, Monika, Jason Li, Satish Rao, and Di Wang. “Deterministic Near-Linear Time Minimum Cut in Weighted Graphs.” In <i>35th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 3089–3139. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/1.9781611977912.111\">https://doi.org/10.1137/1.9781611977912.111</a>."},"date_created":"2024-11-04T10:54:21Z","arxiv":1,"status":"public","oa":1,"title":"Deterministic near-linear time minimum cut in weighted graphs"},{"year":"2024","oa_version":"Published Version","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.","author":[{"orcid":"0000-0001-6395-386X","first_name":"Parvathy","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T12:56:52Z","ddc":["576"],"month":"11","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"OA_type":"gold","degree_awarded":"PhD","_id":"18515","date_created":"2024-11-06T21:25:37Z","article_processing_charge":"No","citation":{"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. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024."},"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-11-07T10:59:42Z","status":"public","title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","oa":1,"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"type":"dissertation","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:18515","page":"219","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"date_created":"2024-11-07T10:59:29Z","date_updated":"2024-11-07T10:59:29Z","file_id":"18519","access_level":"open_access","checksum":"c32cf7bc75748d9c551d8eb70178bbec","content_type":"application/pdf","file_size":37019760,"file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","relation":"main_file","creator":"psurendr","success":1},{"checksum":"4417e02d54084d89e75734e18caaa96d","access_level":"closed","file_id":"18520","date_updated":"2024-11-07T10:59:42Z","date_created":"2024-11-07T10:59:42Z","creator":"psurendr","relation":"source_file","file_name":"PhD Thesis- Parvathy_071124.zip","file_size":41198857,"content_type":"application/zip"}],"date_published":"2024-11-07T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"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."}],"day":"07","OA_place":"publisher","supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"fulldoi":"https://doi.org/10.15479/at:ista:18515","corr_author":"1","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"publication_identifier":{"issn":["2663-337X"]}},{"fulldoi":"https://doi.org/10.1007/978-3-031-74234-7_18","ec_funded":1,"corr_author":"1","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"publication_identifier":{"isbn":["9783031742330"],"eissn":["1611-3349"],"issn":["0302-9743"]},"page":"282-301","file":[{"relation":"main_file","file_name":"2024_LNCS_Bonakdarpour.pdf","content_type":"application/pdf","file_size":1897101,"success":1,"creator":"dernst","date_created":"2024-11-11T09:42:28Z","date_updated":"2024-11-11T09:42:28Z","checksum":"7b8ca21b8c19ab796fa445b0e54003ca","file_id":"18539","access_level":"open_access"}],"date_published":"2024-10-12T00:00:00Z","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."}],"conference":{"name":"RV: Conference on Runtime Verification","end_date":"2024-10-17","start_date":"2024-10-15","location":"Istanbul, Turkey"},"OA_place":"publisher","day":"12","publication_status":"published","type":"conference","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1007/978-3-031-74234-7_18","publication":"24th International Conference on Runtime Verification","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"file_date_updated":"2024-11-11T09:42:28Z","arxiv":1,"status":"public","oa":1,"intvolume":"     15191","title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","_id":"18521","external_id":{"arxiv":["2408.05033"],"isi":["001420093700018"]},"article_processing_charge":"Yes (in subscription journal)","citation":{"apa":"Bonakdarpour, B., Momtaz, A., Nickovic, D., &#38; Sarac, N. E. (2024). Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In <i>24th International Conference on Runtime Verification</i> (Vol. 15191, pp. 282–301). Istanbul, Turkey: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>","short":"B. Bonakdarpour, A. Momtaz, D. Nickovic, N.E. Sarac, in:, 24th International Conference on Runtime Verification, Springer Nature, 2024, pp. 282–301.","ama":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In: <i>24th International Conference on Runtime Verification</i>. Vol 15191. Springer Nature; 2024:282-301. doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>","ista":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. 2024. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. 24th International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 15191, 282–301.","mla":"Bonakdarpour, Borzoo, et al. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” <i>24th International Conference on Runtime Verification</i>, vol. 15191, Springer Nature, 2024, pp. 282–301, doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>.","chicago":"Bonakdarpour, Borzoo, Anik Momtaz, Dejan Nickovic, and Naci E Sarac. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” In <i>24th International Conference on Runtime Verification</i>, 15191:282–301. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>.","ieee":"B. Bonakdarpour, A. Momtaz, D. Nickovic, and N. E. Sarac, “Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy,” in <i>24th International Conference on Runtime Verification</i>, Istanbul, Turkey, 2024, vol. 15191, pp. 282–301."},"date_created":"2024-11-10T23:01:58Z","volume":15191,"APC_amount":"2748 EUR","publisher":"Springer Nature","isi":1,"month":"10","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"OA_type":"hybrid","alternative_title":["LNCS"],"has_accepted_license":"1","oa_version":"Published Version","year":"2024","author":[{"full_name":"Bonakdarpour, Borzoo","last_name":"Bonakdarpour","first_name":"Borzoo"},{"first_name":"Anik","last_name":"Momtaz","full_name":"Momtaz, Anik"},{"first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"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).","date_updated":"2026-05-20T08:43:20Z","ddc":["000"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41467-024-53676-6","scopus_import":"1","type":"journal_article","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"fulldoi":"https://doi.org/10.1038/s41467-024-53676-6","abstract":[{"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.","lang":"eng"}],"day":"01","OA_place":"publisher","file":[{"date_created":"2025-01-22T14:36:33Z","date_updated":"2025-01-22T14:36:33Z","checksum":"32c986fc3babec999c03a5c043310f40","file_id":"18870","access_level":"open_access","file_name":"2024_NatureComm_Weyer.pdf","relation":"main_file","content_type":"application/pdf","file_size":5634494,"success":1,"creator":"dernst"}],"date_published":"2024-12-01T00:00:00Z","has_accepted_license":"1","OA_type":"gold","month":"12","isi":1,"date_updated":"2026-03-05T11:20:12Z","article_number":"9257","ddc":["570"],"oa_version":"Published Version","year":"2024","author":[{"first_name":"Yannick","last_name":"Weyer","full_name":"Weyer, Yannick"},{"last_name":"Schwabl","full_name":"Schwabl, Sinead I.","first_name":"Sinead I."},{"first_name":"Xuechen","last_name":"Tang","full_name":"Tang, Xuechen"},{"last_name":"Purwar","full_name":"Purwar, Astha","first_name":"Astha"},{"first_name":"Konstantin","last_name":"Siegmann","full_name":"Siegmann, Konstantin"},{"first_name":"Angela","full_name":"Ruepp, Angela","last_name":"Ruepp"},{"first_name":"Theresia","full_name":"Dunzendorfer-Matt, Theresia","last_name":"Dunzendorfer-Matt"},{"last_name":"Widerin","full_name":"Widerin, Michael A.","first_name":"Michael A."},{"full_name":"Niedrist, Veronika","last_name":"Niedrist","first_name":"Veronika"},{"first_name":"Noa J.M.","full_name":"Mutsters, Noa J.M.","last_name":"Mutsters"},{"full_name":"Tettamanti, Maria G.","last_name":"Tettamanti","first_name":"Maria G."},{"first_name":"Sabine","id":"caffa136-9669-11ed-9092-ceac12ac9c05","last_name":"Weys","full_name":"Weys, Sabine"},{"full_name":"Sarg, Bettina","last_name":"Sarg","first_name":"Bettina"},{"full_name":"Kremser, Leopold","last_name":"Kremser","first_name":"Leopold"},{"full_name":"Liedl, Klaus R.","last_name":"Liedl","first_name":"Klaus R."},{"last_name":"Schmidt","full_name":"Schmidt, Oliver","first_name":"Oliver"},{"first_name":"David","last_name":"Teis","full_name":"Teis, David"}],"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.","title":"The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi","DOAJ_listed":"1","intvolume":"        15","oa":1,"pmid":1,"file_date_updated":"2025-01-22T14:36:33Z","status":"public","citation":{"ieee":"Y. Weyer <i>et al.</i>, “The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","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.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53676-6\">https://doi.org/10.1038/s41467-024-53676-6</a>.","ama":"Weyer Y, Schwabl SI, Tang X, et al. The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53676-6\">10.1038/s41467-024-53676-6</a>","mla":"Weyer, Yannick, et al. “The Dsc Ubiquitin Ligase Complex Identifies Transmembrane Degrons to Degrade Orphaned Proteins at the Golgi.” <i>Nature Communications</i>, vol. 15, 9257, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53676-6\">10.1038/s41467-024-53676-6</a>.","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.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53676-6\">https://doi.org/10.1038/s41467-024-53676-6</a>","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)."},"volume":15,"date_created":"2024-11-10T23:01:58Z","article_processing_charge":"Yes","publisher":"Springer Nature","article_type":"original","_id":"18522","external_id":{"isi":["001345548100007"],"pmid":["39461958"]}},{"abstract":[{"lang":"eng","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."}],"day":"01","OA_place":"publisher","page":"3155-3175","file":[{"content_type":"application/pdf","file_size":2954312,"relation":"main_file","file_name":"2024_MonthlyNRoyalAstronSoc_Pizzati.pdf","creator":"dernst","success":1,"date_created":"2024-11-12T07:17:26Z","date_updated":"2024-11-12T07:17:26Z","file_id":"18542","access_level":"open_access","checksum":"9ea6285dd1d04d7a9e7b40a4c9e11edb"}],"date_published":"2024-11-01T00:00:00Z","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"fulldoi":"https://doi.org/10.1093/mnras/stae2307","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication":"Monthly Notices of the Royal Astronomical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1093/mnras/stae2307","scopus_import":"1","type":"journal_article","quality_controlled":"1","publication_status":"published","date_created":"2024-11-10T23:01:58Z","volume":534,"article_processing_charge":"Yes","citation":{"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.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stae2307\">https://doi.org/10.1093/mnras/stae2307</a>.","ieee":"E. Pizzati <i>et al.</i>, “A unified model for the clustering of quasars and galaxies at z ≈ 6,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 4. Oxford University Press, pp. 3155–3175, 2024.","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.","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. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stae2307\">https://doi.org/10.1093/mnras/stae2307</a>","ama":"Pizzati E, Hennawi JF, Schaye J, et al. A unified model for the clustering of quasars and galaxies at z ≈ 6. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;534(4):3155-3175. doi:<a href=\"https://doi.org/10.1093/mnras/stae2307\">10.1093/mnras/stae2307</a>","mla":"Pizzati, Elia, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 4, Oxford University Press, 2024, pp. 3155–75, doi:<a href=\"https://doi.org/10.1093/mnras/stae2307\">10.1093/mnras/stae2307</a>.","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."},"publisher":"Oxford University Press","article_type":"original","_id":"18523","external_id":{"isi":["001335663900008"]},"intvolume":"       534","DOAJ_listed":"1","title":"A unified model for the clustering of quasars and galaxies at z ≈ 6","oa":1,"file_date_updated":"2024-11-12T07:17:26Z","status":"public","date_updated":"2025-09-08T14:40:22Z","ddc":["520"],"oa_version":"Published Version","year":"2024","author":[{"full_name":"Pizzati, Elia","last_name":"Pizzati","first_name":"Elia"},{"first_name":"Joseph F.","full_name":"Hennawi, Joseph F.","last_name":"Hennawi"},{"first_name":"Joop","last_name":"Schaye","full_name":"Schaye, Joop"},{"first_name":"Matthieu","full_name":"Schaller, Matthieu","last_name":"Schaller"},{"full_name":"Eilers, Anna Christina","last_name":"Eilers","first_name":"Anna Christina"},{"full_name":"Wang, Feige","last_name":"Wang","first_name":"Feige"},{"first_name":"Carlos S.","full_name":"Frenk, Carlos S.","last_name":"Frenk"},{"full_name":"Elbers, Willem","last_name":"Elbers","first_name":"Willem"},{"last_name":"Helly","full_name":"Helly, John C.","first_name":"John C."},{"last_name":"Mackenzie","full_name":"Mackenzie, Ruari","first_name":"Ruari"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"first_name":"Rongmon","last_name":"Bordoloi","full_name":"Bordoloi, Rongmon"},{"last_name":"Kashino","full_name":"Kashino, Daichi","first_name":"Daichi"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"first_name":"Minghao","full_name":"Yue, Minghao","last_name":"Yue"}],"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.","has_accepted_license":"1","OA_type":"gold","issue":"4","month":"11","isi":1,"department":[{"_id":"JoMa"}]},{"publication":"Nature Communications","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication_status":"published","type":"journal_article","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1038/s41467-024-53418-8","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2024-11-07T00:00:00Z","file":[{"checksum":"dcfadc806f4144d065eb8e2032554782","access_level":"open_access","file_id":"18546","date_updated":"2024-11-12T10:18:32Z","date_created":"2024-11-12T10:18:32Z","success":1,"creator":"jbravo","relation":"main_file","file_name":"s41467-024-53418-8.pdf","file_size":2967001,"content_type":"application/pdf"}],"abstract":[{"lang":"eng","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."}],"OA_place":"publisher","day":"07","fulldoi":"https://doi.org/10.1038/s41467-024-53418-8","publication_identifier":{"issn":["2041-1723"]},"year":"2024","oa_version":"Published Version","author":[{"first_name":"Dmitrii","last_name":"Degtev","full_name":"Degtev, Dmitrii"},{"full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly"},{"first_name":"Aikaterini","last_name":"Emmanouilidi","full_name":"Emmanouilidi, Aikaterini"},{"full_name":"Zdravković, Aleksandar","last_name":"Zdravković","first_name":"Aleksandar"},{"first_name":"Oi Kuan","last_name":"Choong","full_name":"Choong, Oi Kuan"},{"full_name":"Liz Touza, Julia","last_name":"Liz Touza","first_name":"Julia"},{"first_name":"Niklas","last_name":"Selfjord","full_name":"Selfjord, Niklas"},{"full_name":"Weisheit, Isabel","last_name":"Weisheit","first_name":"Isabel"},{"first_name":"Margherita","full_name":"Francescatto, Margherita","last_name":"Francescatto"},{"full_name":"Akcakaya, Pinar","last_name":"Akcakaya","first_name":"Pinar"},{"full_name":"Porritt, Michelle","last_name":"Porritt","first_name":"Michelle"},{"first_name":"Marcello","full_name":"Maresca, Marcello","last_name":"Maresca"},{"first_name":"David","full_name":"Taylor, David","last_name":"Taylor"},{"first_name":"Grzegorz","full_name":"Sienski, Grzegorz","last_name":"Sienski"}],"article_number":"9173","date_updated":"2024-11-13T08:19:50Z","ddc":["572"],"month":"11","extern":"1","OA_type":"gold","has_accepted_license":"1","_id":"18545","article_type":"original","volume":15,"citation":{"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.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53418-8\">https://doi.org/10.1038/s41467-024-53418-8</a>.","ieee":"D. Degtev <i>et al.</i>, “Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53418-8\">https://doi.org/10.1038/s41467-024-53418-8</a>","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. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53418-8\">10.1038/s41467-024-53418-8</a>","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.","mla":"Degtev, Dmitrii, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.” <i>Nature Communications</i>, vol. 15, 9173, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53418-8\">10.1038/s41467-024-53418-8</a>."},"date_created":"2024-11-12T10:18:04Z","article_processing_charge":"Yes","publisher":"Springer Nature","file_date_updated":"2024-11-12T10:18:32Z","status":"public","oa":1,"DOAJ_listed":"1","title":"Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles","intvolume":"        15"},{"author":[{"full_name":"Ramadhin, Anisha R.","last_name":"Ramadhin","first_name":"Anisha R."},{"first_name":"Shun-Hsiao","full_name":"Lee, Shun-Hsiao","last_name":"Lee"},{"first_name":"Di","last_name":"Zhou","full_name":"Zhou, Di"},{"full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","first_name":"Anita P"},{"first_name":"Camila","full_name":"Gonzalo-Hansen, Camila","last_name":"Gonzalo-Hansen"},{"first_name":"Marjolein","last_name":"van Sluis","full_name":"van Sluis, Marjolein"},{"last_name":"Blom","full_name":"Blom, Cindy M.A.","first_name":"Cindy M.A."},{"last_name":"Janssens","full_name":"Janssens, Roel C.","first_name":"Roel C."},{"full_name":"Raams, Anja","last_name":"Raams","first_name":"Anja"},{"full_name":"Dekkers, Dick","last_name":"Dekkers","first_name":"Dick"},{"last_name":"Bezstarosti","full_name":"Bezstarosti, Karel","first_name":"Karel"},{"full_name":"Slade, Dea","last_name":"Slade","first_name":"Dea"},{"first_name":"Wim","last_name":"Vermeulen","full_name":"Vermeulen, Wim"},{"last_name":"Pines","full_name":"Pines, Alex","first_name":"Alex"},{"last_name":"Demmers","full_name":"Demmers, Jeroen A.A.","first_name":"Jeroen A.A."},{"first_name":"Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"full_name":"Sixma, Titia K.","last_name":"Sixma","first_name":"Titia K."},{"first_name":"Jurgen A.","last_name":"Marteijn","full_name":"Marteijn, Jurgen A."}],"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.","year":"2024","oa_version":"Published Version","ddc":["570"],"date_updated":"2025-09-08T14:42:50Z","department":[{"_id":"CaBe"}],"isi":1,"month":"12","issue":"24","OA_type":"hybrid","has_accepted_license":"1","external_id":{"isi":["001395711300001"],"pmid":["39547223"]},"_id":"18553","article_type":"original","publisher":"Elsevier","article_processing_charge":"No","date_created":"2024-11-15T12:12:54Z","volume":84,"citation":{"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. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>","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.","mla":"Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>.","ista":"Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 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. <i>Molecular Cell</i>. 2024;84(24):4740-4757.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>","chicago":"Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>.","ieee":"A. R. Ramadhin <i>et al.</i>, “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” <i>Molecular Cell</i>, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024."},"status":"public","file_date_updated":"2025-01-13T11:17:35Z","pmid":1,"oa":1,"title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","intvolume":"        84","publication":"Molecular Cell","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_status":"published","quality_controlled":"1","type":"journal_article","scopus_import":"1","doi":"10.1016/j.molcel.2024.10.030","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"creator":"dernst","success":1,"content_type":"application/pdf","file_size":25071994,"file_name":"2024_MolecularCell_Ramadhin.pdf","relation":"main_file","file_id":"18844","access_level":"open_access","checksum":"e051e2766b2d424983778f742cb7c5ed","date_created":"2025-01-13T11:17:35Z","date_updated":"2025-01-13T11:17:35Z"}],"date_published":"2024-12-19T00:00:00Z","page":"4740-4757.e12","OA_place":"publisher","day":"19","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"fulldoi":"https://doi.org/10.1016/j.molcel.2024.10.030","publication_identifier":{"issn":["1097-2765"]}},{"type":"journal_article","quality_controlled":"1","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/s00220-024-05143-y","scopus_import":"1","publication":"Communications in Mathematical Physics","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"dissertation_contains","id":"20575","status":"public"}]},"language":[{"iso":"eng"}],"corr_author":"1","fulldoi":"https://doi.org/10.1007/s00220-024-05143-y","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"date_published":"2024-12-01T00:00:00Z","file":[{"date_created":"2024-11-18T08:15:07Z","date_updated":"2024-11-18T08:15:07Z","file_id":"18562","access_level":"open_access","checksum":"c9ae0ea195bd39b8b3a630d492fb00dc","content_type":"application/pdf","file_size":1426046,"relation":"main_file","file_name":"2024_CommMathPhysics_Erdoes.pdf","creator":"dernst","success":1}],"abstract":[{"text":"We prove the Eigenstate Thermalization Hypothesis for general Wigner-type matrices in the bulk of the self-consistent spectrum, with optimal control on the fluctuations for obs ervables of arbitrary rank. 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.","lang":"eng"}],"day":"01","OA_place":"publisher","month":"12","isi":1,"department":[{"_id":"LaEr"}],"has_accepted_license":"1","OA_type":"hybrid","issue":"12","oa_version":"Published Version","year":"2024","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","author":[{"orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"},{"id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","last_name":"Riabov","full_name":"Riabov, Volodymyr","first_name":"Volodymyr"}],"date_updated":"2026-04-07T12:32:19Z","article_number":"282","ddc":["510"],"pmid":1,"file_date_updated":"2024-11-18T08:15:07Z","status":"public","arxiv":1,"intvolume":"       405","title":"Eigenstate Thermalization Hypothesis for Wigner-type matrices","oa":1,"article_type":"original","_id":"18554","external_id":{"arxiv":["2403.10359"],"pmid":["39526190"],"isi":["001348943900004"]},"volume":405,"article_processing_charge":"Yes (via OA deal)","date_created":"2024-11-17T23:01:46Z","citation":{"ieee":"L. Erdös and V. Riabov, “Eigenstate Thermalization Hypothesis for Wigner-type matrices,” <i>Communications in Mathematical Physics</i>, vol. 405, no. 12. Springer Nature, 2024.","chicago":"Erdös, László, and Volodymyr Riabov. “Eigenstate Thermalization Hypothesis for Wigner-Type Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00220-024-05143-y\">https://doi.org/10.1007/s00220-024-05143-y</a>.","ista":"Erdös L, Riabov V. 2024. Eigenstate Thermalization Hypothesis for Wigner-type matrices. Communications in Mathematical Physics. 405(12), 282.","ama":"Erdös L, Riabov V. Eigenstate Thermalization Hypothesis for Wigner-type matrices. <i>Communications in Mathematical Physics</i>. 2024;405(12). doi:<a href=\"https://doi.org/10.1007/s00220-024-05143-y\">10.1007/s00220-024-05143-y</a>","mla":"Erdös, László, and Volodymyr Riabov. “Eigenstate Thermalization Hypothesis for Wigner-Type Matrices.” <i>Communications in Mathematical Physics</i>, vol. 405, no. 12, 282, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00220-024-05143-y\">10.1007/s00220-024-05143-y</a>.","apa":"Erdös, L., &#38; Riabov, V. (2024). Eigenstate Thermalization Hypothesis for Wigner-type matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-024-05143-y\">https://doi.org/10.1007/s00220-024-05143-y</a>","short":"L. Erdös, V. Riabov, Communications in Mathematical Physics 405 (2024)."},"publisher":"Springer Nature"},{"volume":320,"date_created":"2024-11-17T23:01:47Z","article_processing_charge":"Yes","citation":{"ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. The Euclidean MST-ratio for bi-colored lattices. In: <i>32nd International Symposium on Graph Drawing and Network Visualization</i>. Vol 320. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">10.4230/LIPIcs.GD.2024.3</a>","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. 2024. The Euclidean MST-ratio for bi-colored lattices. 32nd International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LIPIcs, vol. 320, 3.","mla":"Cultrera di Montesano, Sebastiano, et al. “The Euclidean MST-Ratio for Bi-Colored Lattices.” <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, vol. 320, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">10.4230/LIPIcs.GD.2024.3</a>.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (2024). The Euclidean MST-ratio for bi-colored lattices. In <i>32nd International Symposium on Graph Drawing and Network Visualization</i> (Vol. 320). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">https://doi.org/10.4230/LIPIcs.GD.2024.3</a>","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, in:, 32nd International Symposium on Graph Drawing and Network Visualization, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “The Euclidean MST-ratio for bi-colored lattices,” in <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, Vienna, Austria, 2024, vol. 320.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “The Euclidean MST-Ratio for Bi-Colored Lattices.” In <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, Vol. 320. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">https://doi.org/10.4230/LIPIcs.GD.2024.3</a>."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"18556","external_id":{"arxiv":["2403.10204"],"isi":["001540278400001"]},"intvolume":"       320","title":"The Euclidean MST-ratio for bi-colored lattices","oa":1,"file_date_updated":"2024-11-18T07:49:25Z","status":"public","arxiv":1,"date_updated":"2025-12-02T13:50:50Z","article_number":"3","ddc":["510"],"oa_version":"Published Version","year":"2024","author":[{"full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832"},{"last_name":"Draganov","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","full_name":"Draganov, Ondrej","first_name":"Ondrej","orcid":"0000-0003-0464-3823"},{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","last_name":"Saghafian","first_name":"Morteza"}],"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.","has_accepted_license":"1","alternative_title":["LIPIcs"],"OA_type":"gold","month":"10","isi":1,"department":[{"_id":"HeEd"}],"abstract":[{"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.","lang":"eng"}],"day":"28","OA_place":"publisher","conference":{"start_date":"2024-09-18","name":"GD: Graph Drawing and Network Visualization","end_date":"2024-09-20","location":"Vienna, Austria"},"file":[{"date_updated":"2024-11-18T07:49:25Z","date_created":"2024-11-18T07:49:25Z","access_level":"open_access","file_id":"18560","checksum":"5f9b35e115c3d375e99be78da9054cb4","file_size":908541,"content_type":"application/pdf","relation":"main_file","file_name":"2024_LIPIcs_CultreradiMontesano.pdf","creator":"dernst","success":1}],"date_published":"2024-10-28T00:00:00Z","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773430"]},"fulldoi":"https://doi.org/10.4230/LIPIcs.GD.2024.3","ec_funded":1,"corr_author":"1","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"32nd International Symposium on Graph Drawing and Network Visualization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.4230/LIPIcs.GD.2024.3","scopus_import":"1","quality_controlled":"1","type":"conference","publication_status":"published"},{"oa":1,"intvolume":"       200","title":"High-girth Steiner triple systems","arxiv":1,"status":"public","publisher":"Princeton University","date_created":"2024-11-17T23:01:48Z","citation":{"chicago":"Kwan, Matthew Alan, Ashwin Sah, Mehtaab Sawhney, and Michael Simkin. “High-Girth Steiner Triple Systems.” <i>Annals of Mathematics</i>. Princeton University, 2024. <a href=\"https://doi.org/10.4007/annals.2024.200.3.4\">https://doi.org/10.4007/annals.2024.200.3.4</a>.","ieee":"M. A. Kwan, A. Sah, M. Sawhney, and M. Simkin, “High-girth Steiner triple systems,” <i>Annals of Mathematics</i>, vol. 200, no. 3. Princeton University, pp. 1059–1156, 2024.","short":"M.A. Kwan, A. Sah, M. Sawhney, M. Simkin, Annals of Mathematics 200 (2024) 1059–1156.","apa":"Kwan, M. A., Sah, A., Sawhney, M., &#38; Simkin, M. (2024). High-girth Steiner triple systems. <i>Annals of Mathematics</i>. Princeton University. <a href=\"https://doi.org/10.4007/annals.2024.200.3.4\">https://doi.org/10.4007/annals.2024.200.3.4</a>","mla":"Kwan, Matthew Alan, et al. “High-Girth Steiner Triple Systems.” <i>Annals of Mathematics</i>, vol. 200, no. 3, Princeton University, 2024, pp. 1059–156, doi:<a href=\"https://doi.org/10.4007/annals.2024.200.3.4\">10.4007/annals.2024.200.3.4</a>.","ista":"Kwan MA, Sah A, Sawhney M, Simkin M. 2024. High-girth Steiner triple systems. Annals of Mathematics. 200(3), 1059–1156.","ama":"Kwan MA, Sah A, Sawhney M, Simkin M. High-girth Steiner triple systems. <i>Annals of Mathematics</i>. 2024;200(3):1059-1156. doi:<a href=\"https://doi.org/10.4007/annals.2024.200.3.4\">10.4007/annals.2024.200.3.4</a>"},"volume":200,"article_processing_charge":"No","external_id":{"isi":["001366233800004"],"arxiv":["2201.04554"]},"_id":"18559","article_type":"original","issue":"3","OA_type":"green","department":[{"_id":"MaKw"}],"isi":1,"month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.04554"}],"date_updated":"2025-09-08T14:40:55Z","author":[{"orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sah","full_name":"Sah, Ashwin","first_name":"Ashwin"},{"first_name":"Mehtaab","full_name":"Sawhney, Mehtaab","last_name":"Sawhney"},{"last_name":"Simkin","full_name":"Simkin, Michael","first_name":"Michael"}],"acknowledgement":"Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE1745302. Sah was supported by the PD Soros Fellowship. Simkin was supported by the Center of Mathematical Sciences and Applications at Harvard University.","oa_version":"Preprint","year":"2024","publication_identifier":{"eissn":["1939-8980"],"issn":["0003-486X"]},"fulldoi":"https://doi.org/10.4007/annals.2024.200.3.4","corr_author":"1","OA_place":"repository","day":"01","abstract":[{"lang":"eng","text":"We prove a 1973 conjecture due to Erdős on the existence of Steiner triple systems with arbitrarily high girth."}],"date_published":"2024-11-01T00:00:00Z","page":"1059-1156","scopus_import":"1","doi":"10.4007/annals.2024.200.3.4","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publication":"Annals of Mathematics"},{"day":"23","abstract":[{"text":"I give a personal account about the wave of new research activities that rose in the 1990s on the specification, verification, and control of real-time systems.","lang":"eng"}],"date_published":"2024-10-23T00:00:00Z","page":"154-164","publication_identifier":{"eisbn":["9783031737510"],"isbn":["9783031737503"],"eissn":["1611-3349"],"issn":["0302-9743"]},"series_title":"LNCS","corr_author":"1","fulldoi":"https://doi.org/10.1007/978-3-031-73751-0_12","language":[{"iso":"eng"}],"place":"Cham","publication":"Real Time and Such","scopus_import":"1","doi":"10.1007/978-3-031-73751-0_12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"book_chapter","quality_controlled":"1","publisher":"Springer Nature","volume":15230,"citation":{"mla":"Henzinger, Thomas A. “Reminiscences of a Real-Time Researcher.” <i>Real Time and Such</i>, edited by Susanne Graf et al., vol. 15230, Springer Nature, 2024, pp. 154–64, doi:<a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">10.1007/978-3-031-73751-0_12</a>.","ista":"Henzinger TA. 2024.Reminiscences of a Real-Time Researcher. In: Real Time and Such. LNCS, vol. 15230, 154–164.","ama":"Henzinger TA. Reminiscences of a Real-Time Researcher. In: Graf S, Pettersson P, Steffen B, eds. <i>Real Time and Such</i>. Vol 15230. LNCS. Cham: Springer Nature; 2024:154-164. doi:<a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">10.1007/978-3-031-73751-0_12</a>","short":"T.A. Henzinger, in:, S. Graf, P. Pettersson, B. Steffen (Eds.), Real Time and Such, Springer Nature, Cham, 2024, pp. 154–164.","apa":"Henzinger, T. A. (2024). Reminiscences of a Real-Time Researcher. In S. Graf, P. Pettersson, &#38; B. Steffen (Eds.), <i>Real Time and Such</i> (Vol. 15230, pp. 154–164). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">https://doi.org/10.1007/978-3-031-73751-0_12</a>","ieee":"T. A. Henzinger, “Reminiscences of a Real-Time Researcher,” in <i>Real Time and Such</i>, vol. 15230, S. Graf, P. Pettersson, and B. Steffen, Eds. Cham: Springer Nature, 2024, pp. 154–164.","chicago":"Henzinger, Thomas A. “Reminiscences of a Real-Time Researcher.” In <i>Real Time and Such</i>, edited by Susanne Graf, Paul Pettersson, and Bernhard Steffen, 15230:154–64. LNCS. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">https://doi.org/10.1007/978-3-031-73751-0_12</a>."},"article_processing_charge":"No","date_created":"2024-11-18T09:10:06Z","_id":"18563","title":"Reminiscences of a Real-Time Researcher","intvolume":"     15230","status":"public","editor":[{"first_name":"Susanne","full_name":"Graf, Susanne","last_name":"Graf"},{"first_name":"Paul","last_name":"Pettersson","full_name":"Pettersson, Paul"},{"full_name":"Steffen, Bernhard","last_name":"Steffen","first_name":"Bernhard"}],"date_updated":"2025-08-05T12:19:50Z","acknowledgement":"I thank all my collaborators over the years. None of the mentioned contributions would have been possible without them. I also apologize for all omissions. The selection of contributions in this essay reflects primarily my personal involvement rather than any measure of importance.","author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"year":"2024","oa_version":"None","OA_type":"closed access","alternative_title":["LNCS"],"department":[{"_id":"ToHe"}],"month":"10"},{"day":"20","OA_place":"publisher","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Locomotion is ubiquitous in the animal kingdom because an animal's survival depends on its ability to navigate its environment to find food, avoid predators and locate potential mates. These behaviours require control mechanisms that can extract information from the environment, particularly visual cues. Selective evolutionary pressures have thus refined such visuomotor transformations in a species-specific manner to meet the specific ecological and ethological challenges of each organism. However, a common challenge across organisms as visual information processing\r\nbecomes increasingly detailed is the mechanisms required to synthesise disparate pieces of information into a coherent percept or unified picture of the world. In this thesis, I investigate how disparate visual information is combined in the brain of Drosophila melanogaster to effectively guide locomotion.\r\nFor this, I first designed and built a behavioural setup to record locomotion and present visual stimuli to freely-walking fruit flies in a closed-loop manner. This setup allowed the investigation of innate visually-guided behaviours, including the optomotor reflex and courtship.\r\nSecond, taking advantage of my system I investigated the optomotor response, a reflexive visual stabilisation behaviour in which flies turn in the direction of global motion to minimise retinal slip. This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs); a complex network of optic-flow-sensitive neurons essential for self-motion estimation. Using a novel genetic mutant, I demonstrate that electrical coupling between two LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between smooth optomotor turning and saccadic anti-optomotor responses. These findings underscore the critical role of binocular motion cue integration in guiding course control. Finally, I developed a novel behavioural paradigm in which a sexually aroused male fruit fly is presented with an optomotor distractor. This setup creates competition between two visual behaviours, courtship tracking and the  optomotor response, enabling me to explore how the visual system resolves this conflict. In this setting, males\r\nengaged in courtship selectively suppress their optomotor response based on the female's location. Furthermore, when this experiment is replicated with an “artificial female”, optogenetically aroused males alternate between tracking and optomotor responses. The probability and dynamics of this switching are determined by the relative strengths of the two competing stimuli. In summary, the results presented in this thesis explore two mechanisms – integration and competition - through which visual information is combined in the brain of the fruit fly to drive locomotion.","lang":"eng"}],"file":[{"content_type":"application/pdf","file_size":10960975,"relation":"main_file","file_name":"Roshan PhD thesis-Final.pdf","creator":"rsatapat","success":1,"date_created":"2024-11-19T12:39:55Z","date_updated":"2024-11-19T12:39:55Z","file_id":"18570","access_level":"open_access","checksum":"340f2bfe882c8a85e11ec0687ca15f5e"},{"file_name":"Roshan PhD thesis-Final.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":36695917,"creator":"rsatapat","date_created":"2024-11-19T12:46:47Z","date_updated":"2024-12-13T10:27:25Z","checksum":"0f846fce60d6ea511e07f77eff59a6a1","file_id":"18571","access_level":"closed"}],"date_published":"2024-11-20T00:00:00Z","page":"114","license":"https://creativecommons.org/licenses/by-sa/4.0/","publication_identifier":{"isbn":["978-3-99078-047-3"],"issn":["2663-337X"]},"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:18568","corr_author":"1","related_material":{"record":[{"id":"18444","relation":"part_of_dissertation","status":"public"}]},"tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)"},"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:18568","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","publication_status":"published","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"ieee":"R. K. Satapathy, “Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster,” Institute of Science and Technology Austria, 2024.","chicago":"Satapathy, Roshan K. “Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>.","ama":"Satapathy RK. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>","mla":"Satapathy, Roshan K. <i>Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>.","ista":"Satapathy RK. 2024. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. Institute of Science and Technology Austria.","short":"R.K. Satapathy, Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster, Institute of Science and Technology Austria, 2024.","apa":"Satapathy, R. K. (2024). <i>Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>"},"date_created":"2024-11-19T12:34:30Z","degree_awarded":"PhD","_id":"18568","title":"Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster","oa":1,"status":"public","file_date_updated":"2024-12-13T10:27:25Z","ddc":["573"],"date_updated":"2026-04-07T13:00:36Z","acknowledgement":"I am incredibly thankful for the outstanding support provided by ISTA, especially the Machine Shop team, who made conducting research much easier and more efficient. I am also grateful for the funding provided by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme (665385) and The German Research Foundation grant DFG (SPP2205) “Evolutionary optimization of neuronal processing”.","author":[{"orcid":"0009-0006-2974-5075","first_name":"Roshan K","last_name":"Satapathy","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","full_name":"Satapathy, Roshan K"}],"year":"2024","oa_version":"Published Version","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"month":"11"},{"year":"2024","oa_version":"Published Version","acknowledgement":"Freyja Lange, Michael Schunn, and Todor Asenov","author":[{"last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A"},{"orcid":"0000-0002-4792-1881","first_name":"Anton L","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser"},{"full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","first_name":"Olga","orcid":"0000-0003-2012-9947"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter"},{"first_name":"Florian","last_name":"Schmidt","id":"A2EF226A-AF19-11E9-924C-0525E6697425","full_name":"Schmidt, Florian"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"}],"date_updated":"2026-06-18T18:12:08Z","ddc":["570"],"month":"12","department":[{"_id":"MaJö"}],"has_accepted_license":"1","_id":"18579","date_created":"2024-11-22T13:48:12Z","article_processing_charge":"No","citation":{"chicago":"Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>.","ieee":"T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024.","apa":"Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., &#38; Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>","short":"T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024).","ista":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","ama":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>","mla":"Vega Zuniga, Tomas A., et al. <i>A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>."},"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-12-09T12:54:55Z","status":"public","title":"A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"id":"19076","relation":"used_in_publication","status":"public"}]},"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:18579","date_published":"2024-12-09T00:00:00Z","file":[{"checksum":"8b13990ca1a458ae3f3ae54c2e888564","file_id":"18625","access_level":"open_access","date_created":"2024-12-06T13:28:18Z","date_updated":"2024-12-09T10:24:25Z","creator":"symonova","relation":"main_file","file_name":"electro_physiology_data.zip","content_type":"application/x-zip-compressed","file_size":800647957},{"success":1,"creator":"symonova","relation":"main_file","file_name":"NN_vLGN_Ca_data.zip","content_type":"application/x-zip-compressed","file_size":828410832,"checksum":"c5a4d71c5f29c009c3d96a3244532afa","file_id":"18636","access_level":"open_access","date_created":"2024-12-09T10:21:10Z","date_updated":"2024-12-09T10:21:10Z"},{"file_id":"18637","access_level":"open_access","checksum":"63651df0186196969553dc48b467f6ab","date_created":"2024-12-09T12:54:55Z","date_updated":"2024-12-09T12:54:55Z","creator":"symonova","success":1,"content_type":"text/plain","file_size":505,"file_name":"readme.txt","relation":"main_file"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al.  Relevant information can be found in the 'README.txt' files. ","lang":"eng"}],"day":"09","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/AT:ISTA:18579","ec_funded":1,"corr_author":"1","project":[{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"},{"_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256"},{"call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"grant_number":"101086580","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540"}]},{"ddc":["570"],"date_updated":"2025-09-09T11:41:12Z","article_number":"434","author":[{"last_name":"Marolt Presen","full_name":"Marolt Presen, Darja","first_name":"Darja"},{"first_name":"Vanessa","full_name":"Goeschl, Vanessa","last_name":"Goeschl"},{"first_name":"Dominik","last_name":"Hanetseder","full_name":"Hanetseder, Dominik"},{"first_name":"Laura","full_name":"Ogrin, Laura","last_name":"Ogrin"},{"first_name":"Alexandra Larissa","full_name":"Stetco, Alexandra Larissa","last_name":"Stetco"},{"first_name":"Anja","last_name":"Tansek","full_name":"Tansek, Anja"},{"first_name":"Laura","full_name":"Pozenel, Laura","last_name":"Pozenel"},{"first_name":"Bella","last_name":"Bruszel","id":"70abbbb3-88ea-11ec-8e0a-e8c939944834","full_name":"Bruszel, Bella"},{"first_name":"Goran","last_name":"Mitulovic","full_name":"Mitulovic, Goran"},{"full_name":"Oesterreicher, Johannes","last_name":"Oesterreicher","first_name":"Johannes"},{"first_name":"Johannes","full_name":"Zipperle, Johannes","last_name":"Zipperle"},{"first_name":"Barbara","full_name":"Schaedl, Barbara","last_name":"Schaedl"},{"full_name":"Holnthoner, Wolfgang","last_name":"Holnthoner","first_name":"Wolfgang"},{"first_name":"Johannes","last_name":"Grillari","full_name":"Grillari, Johannes"},{"first_name":"Heinz","last_name":"Redl","full_name":"Redl, Heinz"}],"acknowledgement":"We thank the personnel of the Lorenz-Böhler-Unfallkrankenhaus for providing the human tissue waste for primary cell isolation and the New York Stem Cell Foundation Research Institute for providing the human induced pluripotent stem cell line 1013 A and its mesenchymal progenitors. We also thank all our colleagues at the Ludwig Boltzmann Institute for Traumatology for their suggestions and ongoing support of the project. InstaText writing tool (https://instatext.io) was used to edit the English language of the final manuscript.\r\nThis work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie actions (grant agreement No. 657716) and the Transforming European Industry call H2020-NMBP-TRIND-2020 (grant agreement No. 953134), as well as by the FFG Industrienahe Dissertation program (grant agreement No. 867803 and 853056), the FEMtech Praktika program (grant agreement No. 852154, 868917 and 877951) and the Production of the Future program (grant agreement No. 877452).","oa_version":"Published Version","year":"2024","has_accepted_license":"1","OA_type":"gold","department":[{"_id":"LifeSc"}],"month":"12","isi":1,"publisher":"Springer Nature","citation":{"ista":"Marolt Presen D, Goeschl V, Hanetseder D, Ogrin L, Stetco AL, Tansek A, Pozenel L, Bruszel B, Mitulovic G, Oesterreicher J, Zipperle J, Schaedl B, Holnthoner W, Grillari J, Redl H. 2024. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. 15, 434.","mla":"Marolt Presen, Darja, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” <i>Stem Cell Research and Therapy</i>, vol. 15, 434, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s13287-024-03960-5\">10.1186/s13287-024-03960-5</a>.","ama":"Marolt Presen D, Goeschl V, Hanetseder D, et al. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. <i>Stem Cell Research and Therapy</i>. 2024;15. doi:<a href=\"https://doi.org/10.1186/s13287-024-03960-5\">10.1186/s13287-024-03960-5</a>","short":"D. Marolt Presen, V. Goeschl, D. Hanetseder, L. Ogrin, A.L. Stetco, A. Tansek, L. Pozenel, B. Bruszel, G. Mitulovic, J. Oesterreicher, J. Zipperle, B. Schaedl, W. Holnthoner, J. Grillari, H. Redl, Stem Cell Research and Therapy 15 (2024).","apa":"Marolt Presen, D., Goeschl, V., Hanetseder, D., Ogrin, L., Stetco, A. L., Tansek, A., … Redl, H. (2024). Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. <i>Stem Cell Research and Therapy</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13287-024-03960-5\">https://doi.org/10.1186/s13287-024-03960-5</a>","ieee":"D. Marolt Presen <i>et al.</i>, “Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium,” <i>Stem Cell Research and Therapy</i>, vol. 15. Springer Nature, 2024.","chicago":"Marolt Presen, Darja, Vanessa Goeschl, Dominik Hanetseder, Laura Ogrin, Alexandra Larissa Stetco, Anja Tansek, Laura Pozenel, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” <i>Stem Cell Research and Therapy</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s13287-024-03960-5\">https://doi.org/10.1186/s13287-024-03960-5</a>."},"article_processing_charge":"Yes","volume":15,"date_created":"2024-11-24T23:01:47Z","external_id":{"isi":["001356479400001"],"pmid":["39551765"]},"article_type":"original","_id":"18581","DOAJ_listed":"1","intvolume":"        15","title":"Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium","oa":1,"status":"public","file_date_updated":"2024-12-10T08:28:17Z","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"publication":"Stem Cell Research and Therapy","doi":"10.1186/s13287-024-03960-5","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","type":"journal_article","publication_status":"published","day":"01","OA_place":"publisher","abstract":[{"lang":"eng","text":"Background: Human induced pluripotent stem cells represent a scalable source of youthful tissue progenitors and secretomes for regenerative therapies. The aim of our study was to investigate the potential of conditioned medium (CM) from hiPSC-mesenchymal progenitors (hiPSC-MPs) to stimulate osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (MSCs). We also investigated whether prolonged cultivation or osteogenic pre-differentiation of hiPSC-MPs could enhance the stimulatory activity of CM.\r\nMethods: MSCs were isolated from 13 donors (age 20–90 years). CM derived from hiPSC-MPs was added to the MSC cultures and the effects on proliferation and osteogenic differentiation were examined after 14 days and 6 weeks. The stimulatory activity of hiPSC-MP-CM was compared with the activity of MSC-derived CM and with the activity of CM prepared from hiPSC-MPs pre-cultured in growth or osteogenic medium for 14 days. Comparative proteomic analysis of CM was performed to gain insight into the molecular components responsible for the stimulatory activity.\r\nResults: Primary bone marrow-derived MSC exhibited variability, with a tendency towards lower proliferation and tri-lineage differentiation in older donors. hiPSC-MP-CM increased the proliferation and alkaline phosphatase activity of MSC from several adult/aged donors after 14 days of continuous supplementation under osteogenic conditions. However, CM supplementation failed to improve the mineralization of MSC pellets after 6 weeks under osteogenic conditions. hiPSC-MP-CM showed greater enhancement of proliferation and ALP activity than CM derived from bone marrow-derived MSCs. Moreover, 14-day cultivation but not osteogenic pre-differentiation of hiPSC-MPs strongly enhanced CM stimulatory activity. Quantitative proteomic analysis of d14-CM revealed a distinct profile of components that formed a highly interconnected associations network with two clusters, one functionally associated with binding and organization of actin/cytoskeletal components and the other with structural constituents of the extracellular matrix, collagen, and growth factor binding. Several hub proteins were identified that were reported to have functions in cell-extracellular matrix interaction, osteogenic differentiation and development.\r\nConclusions: Our data show that hiPSC-MP-CM enhances early osteogenic differentiation of human bone marrow-derived MSCs and that prolonged cultivation of hiPSC-MPs enhances CM-stimulatory activity. Proteomic analysis of the upregulated protein components provides the basis for further optimization of hiPSC-MP-CM for bone regenerative therapies."}],"file":[{"date_updated":"2024-12-10T08:28:17Z","date_created":"2024-12-10T08:28:17Z","access_level":"open_access","file_id":"18641","checksum":"91edba8edde30d781dce89fdd5cadc39","file_size":6690494,"content_type":"application/pdf","relation":"main_file","file_name":"2024_StemCellResearch_Presen.pdf","creator":"dernst","success":1}],"date_published":"2024-12-01T00:00:00Z","publication_identifier":{"eissn":["1757-6512"]},"fulldoi":"https://doi.org/10.1186/s13287-024-03960-5"},{"publisher":"Springer Nature","citation":{"mla":"Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” <i>Nature Communications</i>, vol. 15, 9904, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-54240-y\">10.1038/s41467-024-54240-y</a>.","ista":"Luschnig C, Friml J. 2024. Over 25 years of decrypting PIN-mediated plant development. Nature Communications. 15, 9904.","ama":"Luschnig C, Friml J. Over 25 years of decrypting PIN-mediated plant development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-54240-y\">10.1038/s41467-024-54240-y</a>","apa":"Luschnig, C., &#38; Friml, J. (2024). Over 25 years of decrypting PIN-mediated plant development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-54240-y\">https://doi.org/10.1038/s41467-024-54240-y</a>","short":"C. Luschnig, J. Friml, Nature Communications 15 (2024).","ieee":"C. Luschnig and J. Friml, “Over 25 years of decrypting PIN-mediated plant development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-54240-y\">https://doi.org/10.1038/s41467-024-54240-y</a>."},"date_created":"2024-11-24T23:01:48Z","article_processing_charge":"Yes","volume":15,"external_id":{"pmid":["39548100"],"isi":["001356232600004"]},"article_type":"original","_id":"18582","intvolume":"        15","title":"Over 25 years of decrypting PIN-mediated plant development","DOAJ_listed":"1","oa":1,"status":"public","file_date_updated":"2024-12-03T14:10:54Z","pmid":1,"ddc":["580"],"date_updated":"2025-09-08T14:53:48Z","article_number":"9904","author":[{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"acknowledgement":"We gratefully acknowledge Leo Gälweiler for authorizing his PIN1 story. We would like to thank Yuanrong Pei for invaluable help with preparing figures. Work in the lab of C.L. is supported by grants from the Austrian Science Fund (PAT 8419423) and by the Gesellschaft für Forschungsförderung Niederösterreich m.b.H. (FTI19-008). The lab of J.F. is supported by the Austrian Science Fund (I 6123-B and P 37051-B).","year":"2024","oa_version":"Published Version","has_accepted_license":"1","OA_type":"gold","department":[{"_id":"JiFr"}],"month":"12","isi":1,"day":"01","OA_place":"publisher","abstract":[{"text":"Identification of PIN exporters for auxin, the major coordinative signal in plants, some 25 years ago, signifies a landmark in our understanding of plant-specific mechanisms underlying development and adaptation. Auxin is directionally transported throughout the plant body; a unique feature already envisioned by Darwin and solidified by PINs’ discovery and characterization. The PIN-based auxin distribution network with its complex regulations of PIN expression, localization and activity turned out to underlie a remarkable multitude of developmental processes and represents means to integrate endogenous and environmental signals. Given the recent anniversary, we here summarize past and current developments in this exciting field.","lang":"eng"}],"file":[{"file_name":"2024_NatureComm_Luschnig.pdf","relation":"main_file","file_size":1426555,"content_type":"application/pdf","success":1,"creator":"dernst","date_updated":"2024-12-03T14:10:54Z","date_created":"2024-12-03T14:10:54Z","checksum":"3a31af06f52100d287f1e9d9c2aa1d40","access_level":"open_access","file_id":"18615"}],"date_published":"2024-12-01T00:00:00Z","publication_identifier":{"eissn":["2041-1723"]},"project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"}],"corr_author":"1","fulldoi":"https://doi.org/10.1038/s41467-024-54240-y","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication":"Nature Communications","doi":"10.1038/s41467-024-54240-y","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","quality_controlled":"1","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1112/jlms.70010","publication_status":"published","type":"journal_article","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication":"Journal of the London Mathematical Society","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"name":"Randomness and structure in combinatorics","grant_number":"101076777","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"}],"publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"corr_author":"1","fulldoi":"https://doi.org/10.1112/jlms.70010","ec_funded":1,"abstract":[{"text":"There are a number of well-known problems and conjectures about partitioning graphs to satisfy local constraints. For example, the majority colouring conjecture of Kreutzer, Oum, Seymour, van der Zypen and Wood states that every directed graph has a 3-colouring such that for every vertex v, at most half of the out-neighbours of v have the same colour as \r\n. As another example, the internal partition conjecture, due to DeVos and to Ban and Linial, states that for every d, all but finitely many d-regular graphs have a partition into two non-empty parts such that for every vertex v, at least half of the neighbours of v lie in the same part as v. We prove several results in this spirit: in particular, two of our results are that the majority colouring conjecture holds for Erdős–Rényi random directed graphs (of any density), and that the internal partition conjecture holds if we permit a tiny number of ‘exceptional vertices’. Our proofs involve a variety of techniques, including several different methods to analyse random recolouring processes. One highlight is a personality-changing scheme: we ‘forget’ certain information based on the state of a Markov chain, giving us more independence to work with.","lang":"eng"}],"OA_place":"publisher","day":"01","date_published":"2024-12-01T00:00:00Z","file":[{"checksum":"98e301e0565d75e3fb50e10e982a5018","access_level":"open_access","file_id":"18639","date_updated":"2024-12-10T08:10:39Z","date_created":"2024-12-10T08:10:39Z","success":1,"creator":"dernst","file_name":"2024_JournLondonMathSoc_Anastos.pdf","relation":"main_file","file_size":539891,"content_type":"application/pdf"}],"OA_type":"hybrid","has_accepted_license":"1","issue":"6","isi":1,"month":"12","department":[{"_id":"MaKw"}],"article_number":"e70010","date_updated":"2025-12-02T13:52:26Z","ddc":["510"],"oa_version":"Published Version","year":"2024","acknowledgement":"We are grateful to the anonymous referees for their thorough reading of the paper, and for many suggestions which have improved the exposition throughout.\r\n\r\nMichael Anastos was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101034413. Matthew Kwan was supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777, also funded by the European Union image. Mihyun Kang was supported in part by the Austrian Science Fund (FWF) [10.55776/I6502]. For the purpose of open access, the authors have applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","author":[{"full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","first_name":"Michael"},{"full_name":"Cooley, Oliver","last_name":"Cooley","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","first_name":"Oliver"},{"first_name":"Mihyun","last_name":"Kang","full_name":"Kang, Mihyun"},{"orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan"}],"oa":1,"title":"Partitioning problems via random processes","intvolume":"       110","file_date_updated":"2024-12-10T08:10:39Z","arxiv":1,"status":"public","citation":{"ieee":"M. Anastos, O. Cooley, M. Kang, and M. A. Kwan, “Partitioning problems via random processes,” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 6. Wiley, 2024.","chicago":"Anastos, Michael, Oliver Cooley, Mihyun Kang, and Matthew Alan Kwan. “Partitioning Problems via Random Processes.” <i>Journal of the London Mathematical Society</i>. Wiley, 2024. <a href=\"https://doi.org/10.1112/jlms.70010\">https://doi.org/10.1112/jlms.70010</a>.","ama":"Anastos M, Cooley O, Kang M, Kwan MA. Partitioning problems via random processes. <i>Journal of the London Mathematical Society</i>. 2024;110(6). doi:<a href=\"https://doi.org/10.1112/jlms.70010\">10.1112/jlms.70010</a>","mla":"Anastos, Michael, et al. “Partitioning Problems via Random Processes.” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 6, e70010, Wiley, 2024, doi:<a href=\"https://doi.org/10.1112/jlms.70010\">10.1112/jlms.70010</a>.","ista":"Anastos M, Cooley O, Kang M, Kwan MA. 2024. Partitioning problems via random processes. Journal of the London Mathematical Society. 110(6), e70010.","short":"M. Anastos, O. Cooley, M. Kang, M.A. Kwan, Journal of the London Mathematical Society 110 (2024).","apa":"Anastos, M., Cooley, O., Kang, M., &#38; Kwan, M. A. (2024). Partitioning problems via random processes. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.70010\">https://doi.org/10.1112/jlms.70010</a>"},"article_processing_charge":"Yes (via OA deal)","date_created":"2024-11-24T23:01:48Z","volume":110,"publisher":"Wiley","_id":"18583","article_type":"original","external_id":{"arxiv":["2307.06453"],"isi":["001374738100001"]}}]