[{"publication":"Proceedings of the 27th International Conference on Artificial Intelligence and Statistics","status":"public","page":"3448-3456","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"language":[{"iso":"eng"}],"intvolume":"       238","title":"Communication-efficient federated learning with data and client heterogeneity","article_processing_charge":"No","publication_status":"published","author":[{"full_name":"Zakerinia, Hossein","last_name":"Zakerinia","id":"653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4","first_name":"Hossein"},{"first_name":"Shayan","last_name":"Talaei","full_name":"Talaei, Shayan"},{"first_name":"Giorgi","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"volume":238,"date_published":"2024-05-01T00:00:00Z","conference":{"location":"Valencia, Spain","name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2024-05-02","end_date":"2024-05-04"},"quality_controlled":"1","abstract":[{"text":"Federated Learning (FL) enables large-scale distributed training of machine learning models, while still allowing individual nodes to maintain data locally. However, executing FL at scale comes with inherent practical challenges: 1) heterogeneity of the local node data distributions, 2) heterogeneity of node computational speeds (asynchrony), but also 3) constraints in the amount of communication between the clients and the server. In this work, we present the first variant of the classic federated averaging (FedAvg) algorithm which, at the same time, supports data heterogeneity, partial client asynchrony, and communication compression. Our algorithm comes with a novel, rigorous analysis showing that, in spite of these system relaxations, it can provide similar convergence to FedAvg in interesting parameter regimes. Experimental results in the rigorous LEAF benchmark on setups of up to 300 nodes show that our algorithm ensures fast convergence for standard federated tasks, improving upon prior quantized and asynchronous approaches.","lang":"eng"}],"day":"01","_id":"17093","publisher":"ML Research Press","date_updated":"2024-10-09T21:08:57Z","date_created":"2024-06-02T22:00:57Z","arxiv":1,"oa":1,"citation":{"chicago":"Zakerinia, Hossein, Shayan Talaei, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Communication-Efficient Federated Learning with Data and Client Heterogeneity.” In <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>, 238:3448–56. ML Research Press, 2024.","ieee":"H. Zakerinia, S. Talaei, G. Nadiradze, and D.-A. Alistarh, “Communication-efficient federated learning with data and client heterogeneity,” in <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>, Valencia, Spain, 2024, vol. 238, pp. 3448–3456.","mla":"Zakerinia, Hossein, et al. “Communication-Efficient Federated Learning with Data and Client Heterogeneity.” <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>, vol. 238, ML Research Press, 2024, pp. 3448–56.","apa":"Zakerinia, H., Talaei, S., Nadiradze, G., &#38; Alistarh, D.-A. (2024). Communication-efficient federated learning with data and client heterogeneity. In <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i> (Vol. 238, pp. 3448–3456). Valencia, Spain: ML Research Press.","ista":"Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. 2024. Communication-efficient federated learning with data and client heterogeneity. Proceedings of the 27th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 238, 3448–3456.","ama":"Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. Communication-efficient federated learning with data and client heterogeneity. In: <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>. Vol 238. ML Research Press; 2024:3448-3456.","short":"H. Zakerinia, S. Talaei, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 27th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2024, pp. 3448–3456."},"year":"2024","publication_identifier":{"eissn":["2640-3498"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","type":"conference","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.10032","open_access":"1"}],"scopus_import":"1","alternative_title":["PMLR"],"oa_version":"Preprint","external_id":{"arxiv":["2206.10032"]},"month":"05"},{"year":"2024","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"corr_author":"1","type":"conference","publication_identifier":{"isbn":["9798400706608"],"eissn":["1043-6871"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.02479"}],"month":"07","external_id":{"arxiv":["2405.02479"],"isi":["001275042100006"]},"isi":1,"date_updated":"2025-09-08T07:44:29Z","arxiv":1,"date_created":"2024-06-03T07:43:15Z","citation":{"ieee":"A. Asadi, K. Chatterjee, J. Svoboda, and R. J. Saona Urmeneta, “Deterministic sub-exponential algorithm for discounted-sum games with unary weights,” in <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Tallinn, Estonia, 2024.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Jakub Svoboda, and Raimundo J Saona Urmeneta. “Deterministic Sub-Exponential Algorithm for Discounted-Sum Games with Unary Weights.” In <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3661814.3662080\">https://doi.org/10.1145/3661814.3662080</a>.","short":"A. Asadi, K. Chatterjee, J. Svoboda, R.J. Saona Urmeneta, in:, 39th Annual ACM/IEEE Symposium on Logic in Computer Science, Association for Computing Machinery, 2024.","ama":"Asadi A, Chatterjee K, Svoboda J, Saona Urmeneta RJ. Deterministic sub-exponential algorithm for discounted-sum games with unary weights. In: <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3661814.3662080\">10.1145/3661814.3662080</a>","ista":"Asadi A, Chatterjee K, Svoboda J, Saona Urmeneta RJ. 2024. Deterministic sub-exponential algorithm for discounted-sum games with unary weights. 39th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6.","mla":"Asadi, Ali, et al. “Deterministic Sub-Exponential Algorithm for Discounted-Sum Games with Unary Weights.” <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 6, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3661814.3662080\">10.1145/3661814.3662080</a>.","apa":"Asadi, A., Chatterjee, K., Svoboda, J., &#38; Saona Urmeneta, R. J. (2024). Deterministic sub-exponential algorithm for discounted-sum games with unary weights. In <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Tallinn, Estonia: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3661814.3662080\">https://doi.org/10.1145/3661814.3662080</a>"},"oa":1,"fulldoi":"https://doi.org/10.1145/3661814.3662080","conference":{"end_date":"2024-07-11","start_date":"2024-07-08","name":"LICS: Logic in Computer Science","location":"Tallinn, Estonia"},"day":"08","abstract":[{"text":"Turn-based discounted-sum games are two-player zero-sum games played on finite directed graphs. The vertices of the graph are partitioned between player 1 and player 2. Plays are infinite walks on the graph where the next vertex is decided by a player that owns the current vertex. Each edge is assigned an integer weight and the payoff of a play is the discounted-sum of the weights of the play. The goal of player 1 is to maximize the discounted-sum payoff against the adversarial player 2. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class and the existence of a polynomial-time algorithm is a major open question. Since breaking the general exponential barrier has been a challenging problem, faster parameterized algorithms have been considered. If the discount factor is expressed in unary, then discounted-sum games can be solved in polynomial time. However, if the discount factor is arbitrary (or expressed in binary), but the weights are in unary, none of the existing approaches yield a sub-exponential bound. Our main result is a new analysis technique for a classical algorithm (namely, the strategy iteration algorithm) that present a new runtime bound which is [EQUATION] for game graphs with n vertices and absolute weights of at most W. In particular, our result yields a deterministic sub-exponential bound for games with weights that are constant or represented in unary.","lang":"eng"}],"quality_controlled":"1","_id":"17098","publisher":"Association for Computing Machinery","doi":"10.1145/3661814.3662080","department":[{"_id":"KrCh"}],"ec_funded":1,"status":"public","publication":"39th Annual ACM/IEEE Symposium on Logic in Computer Science","article_number":"6","language":[{"iso":"eng"}],"author":[{"first_name":"Ali","full_name":"Asadi, Ali","last_name":"Asadi","id":"02d96aae-000e-11ec-b801-cadd0a5eefbb"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Jakub","full_name":"Svoboda, Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267"},{"first_name":"Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"}],"publication_status":"published","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.\r\n","article_processing_charge":"No","title":"Deterministic sub-exponential algorithm for discounted-sum games with unary weights","date_published":"2024-07-08T00:00:00Z"},{"license":"https://creativecommons.org/licenses/by/4.0/","_id":"17099","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2025-01-08T09:49:31Z","doi":"10.4230/LIPIcs.FSTTCS.2024.5","OA_place":"publisher","has_accepted_license":"1","fulldoi":"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5","conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","start_date":"2024-12-16","end_date":"2024-12-18","location":"Gujarat, India"},"quality_controlled":"1","day":"05","abstract":[{"lang":"eng","text":"We study two-player zero-sum concurrent stochastic games with finite state and action space played for an infinite number of steps. In every step, the two players simultaneously and independently choose an action. Given the current state and the chosen actions, the next state is obtained according to a stochastic transition function. An objective is a measurable function on plays (or infinite trajectories) of the game, and the value for an objective is the maximal expectation that the player can guarantee against the adversarial player. We consider: (a) stateful-discounted objectives, which are similar to the classical discounted-sum objectives, but states are associated with different discount factors rather than a single discount factor; and (b) parity objectives, which are a canonical representation for ω-regular objectives. For stateful-discounted objectives, given an ordering of the discount factors, the limit value is the limit of the value of the stateful-discounted objectives, as the discount factors approach zero according to the given order.\r\nThe computational problem we consider is the approximation of the value within an arbitrary\r\nadditive error. The above problem is known to be in EXPSPACE for the limit value of statefuldiscounted objectives and in PSPACE for parity objectives. The best-known algorithms for both the above problems are at least exponential time, with an exponential dependence on the number of states and actions. Our main results for the value approximation problem for the limit value of stateful-discounted objectives and parity objectives are as follows: (a) we establish TFNP[NP] complexity; and (b) we present algorithms that improve the dependency on the number of actions in the exponent from linear to logarithmic. In particular, if the number of states is constant, our algorithms run in polynomial time."}],"OA_type":"gold","article_processing_charge":"No","acknowledgement":"This research was partially supported by ERC CoG 863818 (ForM-SMArt), Austrian\r\nScience Fund (FWF) 10.55776/COE12, and French Agence Nationale de la Recherche (ANR)\r\nANR-21-CE40-0020 (CONVERGENCE project)","title":"Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms","intvolume":"       323","author":[{"full_name":"Asadi, Ali","last_name":"Asadi","id":"02d96aae-000e-11ec-b801-cadd0a5eefbb","first_name":"Ali"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","orcid":"0000-0001-5103-038X","first_name":"Raimundo J"},{"first_name":"Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"}],"publication_status":"published","volume":323,"date_published":"2024-12-05T00:00:00Z","status":"public","article_number":"5","publication":"44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","department":[{"_id":"KrCh"}],"ec_funded":1,"language":[{"iso":"eng"}],"alternative_title":["LIPIcs"],"oa_version":"Published Version","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"arxiv":["2405.02486"],"isi":["001537516500005"]},"month":"12","year":"2024","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["9783959773553"],"issn":["1868-8969"]},"corr_author":"1","type":"conference","date_created":"2024-06-03T07:44:27Z","file":[{"file_name":"2024_LIPIcs_Asadi.pdf","file_id":"18777","date_updated":"2025-01-08T09:49:31Z","relation":"main_file","file_size":847960,"content_type":"application/pdf","access_level":"open_access","date_created":"2025-01-08T09:49:31Z","success":1,"creator":"dernst","checksum":"5b544ab4692b93300b404435c036ddd4"}],"arxiv":1,"citation":{"mla":"Asadi, Ali, et al. “Concurrent Stochastic Games with Stateful-Discounted and Parity Objectives: Complexity and Algorithms.” <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 323, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">10.4230/LIPIcs.FSTTCS.2024.5</a>.","apa":"Asadi, A., Chatterjee, K., Saona Urmeneta, R. J., &#38; Svoboda, J. (2024). Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms. In <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 323). Gujarat, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5</a>","ista":"Asadi A, Chatterjee K, Saona Urmeneta RJ, Svoboda J. 2024. Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms. 44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 323, 5.","ama":"Asadi A, Chatterjee K, Saona Urmeneta RJ, Svoboda J. Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms. In: <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 323. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">10.4230/LIPIcs.FSTTCS.2024.5</a>","short":"A. Asadi, K. Chatterjee, R.J. Saona Urmeneta, J. Svoboda, in:, 44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Concurrent Stochastic Games with Stateful-Discounted and Parity Objectives: Complexity and Algorithms.” In <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 323. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5</a>.","ieee":"A. Asadi, K. Chatterjee, R. J. Saona Urmeneta, and J. Svoboda, “Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms,” in <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Gujarat, India, 2024, vol. 323."},"oa":1,"date_updated":"2025-12-02T13:40:52Z","isi":1,"ddc":["000"]},{"department":[{"_id":"KrCh"}],"status":"public","date_updated":"2024-06-03T07:50:29Z","article_number":"2401.16252","publication":"arXiv","language":[{"iso":"eng"}],"publication_status":"submitted","arxiv":1,"author":[{"full_name":"Attia, Luc","last_name":"Attia","first_name":"Luc"},{"last_name":"Lichev","full_name":"Lichev, Lyuben","first_name":"Lyuben"},{"first_name":"Dieter","last_name":"Mitsche","full_name":"Mitsche, Dieter"},{"orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","first_name":"Raimundo J"},{"full_name":"Ziliotto, Bruno","last_name":"Ziliotto","first_name":"Bruno"}],"article_processing_charge":"No","acknowledgement":"This work was supported by the French Agence Nationale de la Recherche (ANR) under references ANR-21-CE40-0020 (CONVERGENCE project) and ANR-20-CE40-0002 (GrHyDy), and by Fondecyt grant 1220174. This collaboration was mainly conducted during a 1-year visit of Bruno Ziliotto to the Center for Mathematical Modeling (CMM) at University of Chile in 2023,\r\nunder the IRL program of CNRS.","date_created":"2024-06-03T07:45:22Z","title":"Zero-sum random games on directed graphs","citation":{"apa":"Attia, L., Lichev, L., Mitsche, D., Saona Urmeneta, R. J., &#38; Ziliotto, B. (n.d.). Zero-sum random games on directed graphs. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2401.16252\">https://doi.org/10.48550/arXiv.2401.16252</a>","mla":"Attia, Luc, et al. “Zero-Sum Random Games on Directed Graphs.” <i>ArXiv</i>, 2401.16252, doi:<a href=\"https://doi.org/10.48550/arXiv.2401.16252\">10.48550/arXiv.2401.16252</a>.","ista":"Attia L, Lichev L, Mitsche D, Saona Urmeneta RJ, Ziliotto B. Zero-sum random games on directed graphs. arXiv, 2401.16252.","ama":"Attia L, Lichev L, Mitsche D, Saona Urmeneta RJ, Ziliotto B. Zero-sum random games on directed graphs. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2401.16252\">10.48550/arXiv.2401.16252</a>","short":"L. Attia, L. Lichev, D. Mitsche, R.J. Saona Urmeneta, B. Ziliotto, ArXiv (n.d.).","chicago":"Attia, Luc, Lyuben Lichev, Dieter Mitsche, Raimundo J Saona Urmeneta, and Bruno Ziliotto. “Zero-Sum Random Games on Directed Graphs.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2401.16252\">https://doi.org/10.48550/arXiv.2401.16252</a>.","ieee":"L. Attia, L. Lichev, D. Mitsche, R. J. Saona Urmeneta, and B. Ziliotto, “Zero-sum random games on directed graphs,” <i>arXiv</i>. ."},"oa":1,"date_published":"2024-01-29T00:00:00Z","fulldoi":"https://doi.org/10.48550/arXiv.2401.16252","year":"2024","day":"29","abstract":[{"text":"This paper considers a class of two-player zero-sum games on directed graphs whose vertices are equipped with random payoffs of bounded support known by both players.\r\nStarting from a fixed vertex, players take turns to move a token along the edges of the graph.\r\nOn the one hand, for acyclic directed graphs of bounded degree and sub-exponential expansion, we show that the value of the game converges almost surely to a constant at an exponential rate dominated in terms of the expansion.\r\nOn the other hand, for the infinite d-ary tree that does not fall into the previous class of graphs, we show convergence at a double-exponential rate in terms of the expansion.","lang":"eng"}],"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","_id":"17101","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2401.16252","open_access":"1"}],"month":"01","external_id":{"arxiv":["2401.16252"]},"doi":"10.48550/arXiv.2401.16252"},{"author":[{"first_name":"Johannes C.","last_name":"Krämer","full_name":"Krämer, Johannes C."},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Gompper","full_name":"Gompper, Gerhard","first_name":"Gerhard"},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"}],"publication_status":"published","article_processing_charge":"No","acknowledgement":"JE and JK gratefully acknowledge financial support from the Initiative and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed with computing resources granted by RWTH Aachen University under project ‘rwth0475’.","intvolume":"        16","title":"Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells","volume":16,"date_published":"2024-04-08T00:00:00Z","department":[{"_id":"EdHa"}],"status":"public","article_number":"097","publication":"SciPost Physics","language":[{"iso":"eng"}],"_id":"17104","publisher":"SciPost Foundation","file_date_updated":"2024-06-03T11:18:51Z","doi":"10.21468/scipostphys.16.4.097","fulldoi":"https://doi.org/10.21468/scipostphys.16.4.097","issue":"4","has_accepted_license":"1","day":"08","abstract":[{"text":"The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth, the regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue steady-state are still poorly understood. Here, we develop a computational model that incorporates basic assumptions of stem cell renewal into distinct populations and mechanical interactions between cells. We find that the model generates unexpected dynamic features: stem cells repel each other in the bulk tissue and are thus found rather isolated, as in a number of in vivo contexts. By mapping the system onto a gas of passive Brownian particles with effective repulsive interactions, that arise from the generated flows of differentiated cells, we show that we can quantitatively describe such stem cell distribution in tissues. The interaction potential between a pair of stem cells decays exponentially with a characteristic length that spans several cell sizes, corresponding to the volume of cells generated per stem cell division. Our findings may help understanding the dynamics of normal and cancerous epithelial tissues.","lang":"eng"}],"quality_controlled":"1","arxiv":1,"file":[{"creator":"dernst","checksum":"6fdeecd21c166db8dedb927ecc2e6025","access_level":"open_access","content_type":"application/pdf","file_size":4973291,"success":1,"date_created":"2024-06-03T11:18:51Z","relation":"main_file","file_name":"2024_SciPostPhys_Kraemer.pdf","date_updated":"2024-06-03T11:18:51Z","file_id":"17109"}],"date_created":"2024-06-03T08:58:44Z","citation":{"chicago":"Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>. SciPost Foundation, 2024. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>.","ieee":"J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells,” <i>SciPost Physics</i>, vol. 16, no. 4. SciPost Foundation, 2024.","ista":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 16(4), 097.","mla":"Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>, vol. 16, no. 4, 097, SciPost Foundation, 2024, doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>.","apa":"Krämer, J. C., Hannezo, E. B., Gompper, G., &#38; Elgeti, J. (2024). Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>","ama":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. 2024;16(4). doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>","short":"J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024)."},"oa":1,"isi":1,"article_type":"original","date_updated":"2025-09-08T07:45:40Z","ddc":["530"],"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","month":"04","external_id":{"arxiv":["2310.04272"],"isi":["001202370200001"]},"year":"2024","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["2542-4653"]}},{"date_updated":"2025-01-13T11:03:41Z","article_type":"original","citation":{"chicago":"Kamatar, Advika, Jack Peter Kelly Bravo, Feng Yuan, Liping Wang, Eileen M. Lafer, David W. Taylor, Jeanne C. Stachowiak, and Sapun H. Parekh. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>.","ieee":"A. Kamatar <i>et al.</i>, “Lipid droplets as substrates for protein phase separation,” <i>Biophysical Journal</i>, vol. 123, no. 11. Elsevier, pp. 1494–1507, 2024.","ista":"Kamatar A, Bravo JPK, Yuan F, Wang L, Lafer EM, Taylor DW, Stachowiak JC, Parekh SH. 2024. Lipid droplets as substrates for protein phase separation. Biophysical Journal. 123(11), 1494–1507.","mla":"Kamatar, Advika, et al. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>, vol. 123, no. 11, Elsevier, 2024, pp. 1494–507, doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>.","apa":"Kamatar, A., Bravo, J. P. K., Yuan, F., Wang, L., Lafer, E. M., Taylor, D. W., … Parekh, S. H. (2024). Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>","ama":"Kamatar A, Bravo JPK, Yuan F, et al. Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. 2024;123(11):1494-1507. doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>","short":"A. Kamatar, J.P.K. Bravo, F. Yuan, L. Wang, E.M. Lafer, D.W. Taylor, J.C. Stachowiak, S.H. Parekh, Biophysical Journal 123 (2024) 1494–1507."},"date_created":"2024-06-04T06:41:03Z","publication_identifier":{"issn":["0006-3495"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","year":"2024","extern":"1","external_id":{"pmid":["38462838"]},"month":"06","scopus_import":"1","oa_version":"None","language":[{"iso":"eng"}],"publication":"Biophysical Journal","status":"public","page":"1494-1507","volume":123,"pmid":1,"date_published":"2024-06-04T00:00:00Z","title":"Lipid droplets as substrates for protein phase separation","intvolume":"       123","article_processing_charge":"No","author":[{"last_name":"Kamatar","full_name":"Kamatar, Advika","first_name":"Advika"},{"last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly"},{"last_name":"Yuan","full_name":"Yuan, Feng","first_name":"Feng"},{"last_name":"Wang","full_name":"Wang, Liping","first_name":"Liping"},{"full_name":"Lafer, Eileen M.","last_name":"Lafer","first_name":"Eileen M."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"},{"first_name":"Jeanne C.","full_name":"Stachowiak, Jeanne C.","last_name":"Stachowiak"},{"last_name":"Parekh","full_name":"Parekh, Sapun H.","first_name":"Sapun H."}],"publication_status":"published","quality_controlled":"1","abstract":[{"lang":"eng","text":"Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets."}],"day":"04","fulldoi":"https://doi.org/10.1016/j.bpj.2024.03.015","issue":"11","doi":"10.1016/j.bpj.2024.03.015","publisher":"Elsevier","_id":"17111"},{"publication":"Science","status":"public","page":"512-519","language":[{"iso":"eng"}],"intvolume":"       383","title":"Type III-B CRISPR-Cas cascade of proteolytic cleavages","OA_type":"green","article_processing_charge":"No","acknowledgement":"We thank R. Fregoso Ocampo for assistance with negative-stain EM imaging. This work was funded by Dutch Research Council (NWO) VIDI grant VI.Vidi.203.074 (R.H.J.S.), NWO Spinoza grant SPI 93-537 (J.v.d.O.), European Research Council (ERC) Advanced grant ERC-AdG-834279 (J.v.d.O.), ERC CoG grant 817834 (T.J.G.E.), NWO VICI grant VI.C.192.016 (T.J.G.E.), Volkswagen Foundation grant 96725 (T.J.G.E.), National Institute of General Medical Sciences of the National Institutes of Health grant R35GM138348 (D.W.T.), Welch Foundation research grant F-1938 (D.W.T.), a Robert J. Kleberg, Jr. And Helen C. Kleberg Foundation medical research grant (D.W.T.), and American Cancer Society Research Scholar grant RSG-21-050-01-DMC (D.W.T.).","publication_status":"published","author":[{"full_name":"Steens, Jurre A.","last_name":"Steens","first_name":"Jurre A."},{"first_name":"Jack Peter Kelly","last_name":"Bravo","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"last_name":"Salazar","full_name":"Salazar, Carl Raymund P.","first_name":"Carl Raymund P."},{"full_name":"Yildiz, Caglar","last_name":"Yildiz","first_name":"Caglar"},{"full_name":"Amieiro, Afonso M.","last_name":"Amieiro","first_name":"Afonso M."},{"first_name":"Stephan","full_name":"Köstlbacher, Stephan","last_name":"Köstlbacher"},{"first_name":"Stijn H.P.","full_name":"Prinsen, Stijn H.P.","last_name":"Prinsen"},{"full_name":"Patinios, Constantinos","last_name":"Patinios","first_name":"Constantinos"},{"first_name":"Andreas","last_name":"Bardis","full_name":"Bardis, Andreas"},{"first_name":"Arjan","full_name":"Barendregt, Arjan","last_name":"Barendregt"},{"full_name":"Scheltema, Richard A.","last_name":"Scheltema","first_name":"Richard A."},{"first_name":"Thijs J.G.","full_name":"Ettema, Thijs J.G.","last_name":"Ettema"},{"first_name":"John","full_name":"van der Oost, John","last_name":"van der Oost"},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"},{"first_name":"Raymond H.J.","full_name":"Staals, Raymond H.J.","last_name":"Staals"}],"volume":383,"pmid":1,"date_published":"2024-02-01T00:00:00Z","fulldoi":"https://doi.org/10.1126/science.adk0378","issue":"6682","quality_controlled":"1","abstract":[{"text":"The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide–based antiphage signaling system (CBASS). Cyclic tri–adenosine monophosphate (AMP)–induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas–based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities.","lang":"eng"}],"day":"01","_id":"17112","doi":"10.1126/science.adk0378","publisher":"American Association for the Advancement of Science","OA_place":"repository","date_updated":"2025-09-24T08:31:45Z","article_type":"original","date_created":"2024-06-04T06:41:26Z","oa":1,"citation":{"short":"J.A. Steens, J.P.K. Bravo, C.R.P. Salazar, C. Yildiz, A.M. Amieiro, S. Köstlbacher, S.H.P. Prinsen, C. Patinios, A. Bardis, A. Barendregt, R.A. Scheltema, T.J.G. Ettema, J. van der Oost, D.W. Taylor, R.H.J. Staals, Science 383 (2024) 512–519.","ama":"Steens JA, Bravo JPK, Salazar CRP, et al. Type III-B CRISPR-Cas cascade of proteolytic cleavages. <i>Science</i>. 2024;383(6682):512-519. doi:<a href=\"https://doi.org/10.1126/science.adk0378\">10.1126/science.adk0378</a>","ista":"Steens JA, Bravo JPK, Salazar CRP, Yildiz C, Amieiro AM, Köstlbacher S, Prinsen SHP, Patinios C, Bardis A, Barendregt A, Scheltema RA, Ettema TJG, van der Oost J, Taylor DW, Staals RHJ. 2024. Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science. 383(6682), 512–519.","apa":"Steens, J. A., Bravo, J. P. K., Salazar, C. R. P., Yildiz, C., Amieiro, A. M., Köstlbacher, S., … Staals, R. H. J. (2024). Type III-B CRISPR-Cas cascade of proteolytic cleavages. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adk0378\">https://doi.org/10.1126/science.adk0378</a>","mla":"Steens, Jurre A., et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” <i>Science</i>, vol. 383, no. 6682, American Association for the Advancement of Science, 2024, pp. 512–19, doi:<a href=\"https://doi.org/10.1126/science.adk0378\">10.1126/science.adk0378</a>.","ieee":"J. A. Steens <i>et al.</i>, “Type III-B CRISPR-Cas cascade of proteolytic cleavages,” <i>Science</i>, vol. 383, no. 6682. American Association for the Advancement of Science, pp. 512–519, 2024.","chicago":"Steens, Jurre A., Jack Peter Kelly Bravo, Carl Raymund P. Salazar, Caglar Yildiz, Afonso M. Amieiro, Stephan Köstlbacher, Stijn H.P. Prinsen, et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adk0378\">https://doi.org/10.1126/science.adk0378</a>."},"year":"2024","extern":"1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.06.23.546230"}],"scopus_import":"1","oa_version":"Preprint","external_id":{"pmid":["38301007"]},"month":"02"},{"extern":"1","year":"2024","type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-024-47830-3"}],"month":"04","external_id":{"pmid":["38688943"]},"article_type":"original","date_updated":"2024-10-14T12:34:26Z","date_created":"2024-06-04T06:42:07Z","citation":{"short":"G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J. Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).","ama":"Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>","apa":"Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang, H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>","mla":"Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>, vol. 15, 3663, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>.","ista":"Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. 15, 3663.","ieee":"G. N. Hibshman <i>et al.</i>, “Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L. Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>."},"oa":1,"fulldoi":"https://doi.org/10.1038/s41467-024-47830-3","day":"30","abstract":[{"lang":"eng","text":"CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for <jats:italic>Streptococcus pyogenes</jats:italic> Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing."}],"quality_controlled":"1","_id":"17113","publisher":"Springer Nature","doi":"10.1038/s41467-024-47830-3","status":"public","publication":"Nature Communications","article_number":"3663","language":[{"iso":"eng"}],"publication_status":"published","author":[{"last_name":"Hibshman","full_name":"Hibshman, Grace N.","first_name":"Grace N."},{"first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo"},{"first_name":"Matthew M.","full_name":"Hooper, Matthew M.","last_name":"Hooper"},{"first_name":"Tyler L.","last_name":"Dangerfield","full_name":"Dangerfield, Tyler L."},{"full_name":"Zhang, Hongshan","last_name":"Zhang","first_name":"Hongshan"},{"first_name":"Ilya J.","last_name":"Finkelstein","full_name":"Finkelstein, Ilya J."},{"first_name":"Kenneth A.","full_name":"Johnson, Kenneth A.","last_name":"Johnson"},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"article_processing_charge":"Yes","title":"Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9","intvolume":"        15","volume":15,"date_published":"2024-04-30T00:00:00Z","pmid":1},{"oa":1,"citation":{"ama":"Schwartz EA, Bravo JPK, Ahsan M, et al. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>","short":"E.A. Schwartz, J.P.K. Bravo, M. Ahsan, L.A. Macias, C.L. McCafferty, T.L. Dangerfield, J.N. Walker, J.S. Brodbelt, G. Palermo, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, Nature Communications 15 (2024).","mla":"Schwartz, Evan A., et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>, vol. 15, 3324, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>.","apa":"Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., … Taylor, D. W. (2024). RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>","ista":"Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. 2024. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. 15, 3324.","ieee":"E. A. Schwartz <i>et al.</i>, “RNA targeting and cleavage by the type III-Dv CRISPR effector complex,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Schwartz, Evan A., Jack Peter Kelly Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>."},"date_created":"2024-06-04T06:43:02Z","date_updated":"2024-06-04T07:05:26Z","article_type":"original","external_id":{"pmid":["38637512"]},"month":"04","main_file_link":[{"url":"https://doi.org/10.1038/s41467-024-47506-y","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2041-1723"]},"type":"journal_article","year":"2024","extern":"1","pmid":1,"volume":15,"date_published":"2024-04-18T00:00:00Z","intvolume":"        15","title":"RNA targeting and cleavage by the type III-Dv CRISPR effector complex","article_processing_charge":"Yes","author":[{"last_name":"Schwartz","full_name":"Schwartz, Evan A.","first_name":"Evan A."},{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly"},{"first_name":"Mohd","full_name":"Ahsan, Mohd","last_name":"Ahsan"},{"first_name":"Luis A.","last_name":"Macias","full_name":"Macias, Luis A."},{"full_name":"McCafferty, Caitlyn L.","last_name":"McCafferty","first_name":"Caitlyn L."},{"first_name":"Tyler L.","last_name":"Dangerfield","full_name":"Dangerfield, Tyler L."},{"first_name":"Jada N.","last_name":"Walker","full_name":"Walker, Jada N."},{"last_name":"Brodbelt","full_name":"Brodbelt, Jennifer S.","first_name":"Jennifer S."},{"first_name":"Giulia","last_name":"Palermo","full_name":"Palermo, Giulia"},{"full_name":"Fineran, Peter C.","last_name":"Fineran","first_name":"Peter C."},{"last_name":"Fagerlund","full_name":"Fagerlund, Robert D.","first_name":"Robert D."},{"first_name":"David W.","last_name":"Taylor","full_name":"Taylor, David W."}],"publication_status":"published","language":[{"iso":"eng"}],"publication":"Nature Communications","article_number":"3324","status":"public","doi":"10.1038/s41467-024-47506-y","publisher":"Springer Nature","_id":"17114","quality_controlled":"1","abstract":[{"lang":"eng","text":"CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction<jats:sup>1–5</jats:sup>. Target RNA cleavage at regular intervals is characteristic of type III effector complexes<jats:sup>6–8</jats:sup>. Here, we determine the structures of the <jats:italic>Synechocystis</jats:italic> type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors<jats:sup>9,10</jats:sup>, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes."}],"day":"18","fulldoi":"https://doi.org/10.1038/s41467-024-47506-y"},{"file_date_updated":"2024-06-10T10:44:26Z","doi":"10.1186/s12888-024-05849-2","publisher":"Springer Nature","_id":"17122","quality_controlled":"1","abstract":[{"text":"Background: Motor alterations and lowered physical activity are common in affective disorders. Previous research has indicated a link between depressive symptoms and declining muscle strength primarily focusing on the elderly but not younger individuals. Thus, we aimed to evaluate the relationship between mood and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy. The study was carried out as a prospective observational study at a German psychiatric university hospital between September 2021 and March 2022.\r\nMethods: Employing a standardized strength circuit consisting of computerized strength training devices, we measured the maximal muscle strength (Fmax) using three repetitions maximum across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3) over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood lipid profiling in a clinical setting. For analysis of psychopharmacotherapy, medication was split into activating (AM) and inhibiting (IM) medication and dosages were normalized by the respective WHO defined daily dose.\r\nResults: While we observed a significant decrease of the MADRS score and increase of the relative total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001), we did not reveal a significant bivariate correlation between disease severity (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with longer disease history displayed reduced rTFmax (p = .048). IM was significantly associated with decreased rTFmax (p = .032). Regression models provide a more substantial effect of gender, age, and IM on muscle strength than the depressive episode itself (p < .001).\r\nConclusions: The results of the study indicate that disease severity and muscle strength are not associated in young to middle-aged inpatients with affective disorders using a strength circuit as observational measurement. Future research will be needed to differentiate the effect of medication, gender, and age on muscle strength and to develop interventions for prevention of muscle weakness, especially in younger patients with chronic affective illnesses.","lang":"eng"}],"day":"29","fulldoi":"https://doi.org/10.1186/s12888-024-05849-2","has_accepted_license":"1","volume":24,"pmid":1,"date_published":"2024-05-29T00:00:00Z","title":"The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study","intvolume":"        24","acknowledgement":"This work was supported by the project ‘Fellows Ride’ of the Thomas Lurz und Dieter Schneider Stiftung and by the ‘Würzburger Bündnis gegen Depression’ (to S.K.-S).\r\nOpen Access funding enabled and organized by Projekt DEAL.","article_processing_charge":"Yes (via OA deal)","publication_status":"published","author":[{"first_name":"Hannah","full_name":"Ramming, Hannah","last_name":"Ramming"},{"full_name":"Theuerkauf, Linda","last_name":"Theuerkauf","first_name":"Linda"},{"first_name":"Olaf","last_name":"Hoos","full_name":"Hoos, Olaf"},{"last_name":"Lichter","full_name":"Lichter, Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","orcid":"0000-0002-1485-0351","first_name":"Katharina"},{"first_name":"Sarah","last_name":"Kittel-Schneider","full_name":"Kittel-Schneider, Sarah"}],"language":[{"iso":"eng"}],"publication":"BMC Psychiatry","article_number":"401","status":"public","department":[{"_id":"PeJo"}],"external_id":{"pmid":["38811916"]},"month":"05","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1471-244X"]},"type":"journal_article","year":"2024","oa":1,"citation":{"short":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, S. Kittel-Schneider, BMC Psychiatry 24 (2024).","ama":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. 2024;24. doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>","apa":"Ramming, H., Theuerkauf, L., Hoos, O., Lichter, K., &#38; Kittel-Schneider, S. (2024). The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>","mla":"Ramming, Hannah, et al. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>, vol. 24, 401, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>.","ista":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. 2024. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. BMC Psychiatry. 24, 401.","ieee":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, and S. Kittel-Schneider, “The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study,” <i>BMC Psychiatry</i>, vol. 24. Springer Nature, 2024.","chicago":"Ramming, Hannah, Linda Theuerkauf, Olaf Hoos, Katharina Lichter, and Sarah Kittel-Schneider. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>."},"date_created":"2024-06-09T22:01:01Z","file":[{"relation":"main_file","date_updated":"2024-06-10T10:44:26Z","file_id":"17131","file_name":"2024_BMCPsychiatry_Ramming.pdf","checksum":"5df60d3c9388955c5b682ea34748d59d","creator":"dernst","date_created":"2024-06-10T10:44:26Z","success":1,"content_type":"application/pdf","file_size":2320147,"access_level":"open_access"}],"ddc":["570"],"date_updated":"2025-04-23T07:51:51Z","article_type":"original"},{"article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","acknowledgement":"We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02.","title":"Information content and optimization of self-organized developmental systems","intvolume":"       121","publication_status":"published","author":[{"first_name":"David","last_name":"Brückner","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"volume":121,"pmid":1,"date_published":"2024-06-04T00:00:00Z","status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_number":"e2322326121","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://github.com/dbrueckner/SelforgInformation","relation":"software"},{"url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/","description":"News on the ISTA website","relation":"press_release"}]},"_id":"17123","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"National Academy of Sciences","doi":"10.1073/pnas.2322326121","file_date_updated":"2024-06-10T10:27:37Z","OA_place":"publisher","issue":"23","fulldoi":"https://doi.org/10.1073/pnas.2322326121","has_accepted_license":"1","quality_controlled":"1","day":"04","abstract":[{"lang":"eng","text":"A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes."}],"date_created":"2024-06-09T22:01:02Z","file":[{"checksum":"59797a75db7beb3721ed7a4d14c241f9","creator":"dernst","success":1,"date_created":"2024-06-10T10:27:37Z","access_level":"open_access","content_type":"application/pdf","file_size":12329234,"relation":"main_file","date_updated":"2024-06-10T10:27:37Z","file_id":"17130","file_name":"2024_PNAS_Brueckner.pdf"}],"citation":{"chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>.","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23. National Academy of Sciences, 2024.","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121.","apa":"Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>","mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>.","short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(23). doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>"},"oa":1,"date_updated":"2025-09-08T07:51:01Z","isi":1,"article_type":"original","ddc":["570"],"oa_version":"Published Version","scopus_import":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"external_id":{"isi":["001244835000006"],"pmid":["38819997"]},"month":"06","year":"2024","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"APC_amount":"2570,79 EUR","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"type":"journal_article","corr_author":"1"},{"isi":1,"article_type":"review","date_updated":"2025-09-08T07:52:37Z","date_created":"2024-06-09T22:01:02Z","citation":{"chicago":"Bassani, Carlos L., Greg Van Anders, Uri Banin, Dmitry Baranov, Qian Chen, Marjolein Dijkstra, Michael S. Dimitriyev, et al. “Nanocrystal Assemblies: Current Advances and Open Problems.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.3c10201\">https://doi.org/10.1021/acsnano.3c10201</a>.","ieee":"C. L. Bassani <i>et al.</i>, “Nanocrystal assemblies: Current advances and open problems,” <i>ACS Nano</i>, vol. 18, no. 23. American Chemical Society, pp. 14791–14840, 2024.","ista":"Bassani CL, Van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. 2024. Nanocrystal assemblies: Current advances and open problems. ACS Nano. 18(23), 14791–14840.","mla":"Bassani, Carlos L., et al. “Nanocrystal Assemblies: Current Advances and Open Problems.” <i>ACS Nano</i>, vol. 18, no. 23, American Chemical Society, 2024, pp. 14791–840, doi:<a href=\"https://doi.org/10.1021/acsnano.3c10201\">10.1021/acsnano.3c10201</a>.","apa":"Bassani, C. L., Van Anders, G., Banin, U., Baranov, D., Chen, Q., Dijkstra, M., … Travesset, A. (2024). Nanocrystal assemblies: Current advances and open problems. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c10201\">https://doi.org/10.1021/acsnano.3c10201</a>","short":"C.L. Bassani, G. Van Anders, U. Banin, D. Baranov, Q. Chen, M. Dijkstra, M.S. Dimitriyev, E. Efrati, J. Faraudo, O. Gang, N. Gaston, R. Golestanian, G.I. Guerrero-Garcia, M. Gruenwald, A. Haji-Akbari, M. Ibáñez, M. Karg, T. Kraus, B. Lee, R.C. Van Lehn, R.J. Macfarlane, B.M. Mognetti, A. Nikoubashman, S. Osat, O.V. Prezhdo, G.M. Rotskoff, L. Saiz, A.C. Shi, S. Skrabalak, I.I. Smalyukh, M. Tagliazucchi, D.V. Talapin, A.V. Tkachenko, S. Tretiak, D. Vaknin, A. Widmer-Cooper, G.C.L. Wong, X. Ye, S. Zhou, E. Rabani, M. Engel, A. Travesset, ACS Nano 18 (2024) 14791–14840.","ama":"Bassani CL, Van Anders G, Banin U, et al. Nanocrystal assemblies: Current advances and open problems. <i>ACS Nano</i>. 2024;18(23):14791-14840. doi:<a href=\"https://doi.org/10.1021/acsnano.3c10201\">10.1021/acsnano.3c10201</a>"},"year":"2024","type":"journal_article","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","scopus_import":"1","month":"05","external_id":{"pmid":["38814908"],"isi":["001236199900001"]},"department":[{"_id":"MaIb"}],"status":"public","page":"14791-14840","publication":"ACS Nano","language":[{"iso":"eng"}],"publication_status":"published","author":[{"last_name":"Bassani","full_name":"Bassani, Carlos L.","first_name":"Carlos L."},{"last_name":"Van Anders","full_name":"Van Anders, Greg","first_name":"Greg"},{"full_name":"Banin, Uri","last_name":"Banin","first_name":"Uri"},{"first_name":"Dmitry","full_name":"Baranov, Dmitry","last_name":"Baranov"},{"full_name":"Chen, Qian","last_name":"Chen","first_name":"Qian"},{"first_name":"Marjolein","full_name":"Dijkstra, Marjolein","last_name":"Dijkstra"},{"first_name":"Michael S.","full_name":"Dimitriyev, Michael S.","last_name":"Dimitriyev"},{"first_name":"Efi","last_name":"Efrati","full_name":"Efrati, Efi"},{"first_name":"Jordi","last_name":"Faraudo","full_name":"Faraudo, Jordi"},{"last_name":"Gang","full_name":"Gang, Oleg","first_name":"Oleg"},{"first_name":"Nicola","full_name":"Gaston, Nicola","last_name":"Gaston"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"last_name":"Guerrero-Garcia","full_name":"Guerrero-Garcia, G. Ivan","first_name":"G. Ivan"},{"full_name":"Gruenwald, Michael","last_name":"Gruenwald","first_name":"Michael"},{"last_name":"Haji-Akbari","full_name":"Haji-Akbari, Amir","first_name":"Amir"},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Matthias","last_name":"Karg","full_name":"Karg, Matthias"},{"last_name":"Kraus","full_name":"Kraus, Tobias","first_name":"Tobias"},{"first_name":"Byeongdu","full_name":"Lee, Byeongdu","last_name":"Lee"},{"first_name":"Reid C.","full_name":"Van Lehn, Reid C.","last_name":"Van Lehn"},{"first_name":"Robert J.","full_name":"Macfarlane, Robert J.","last_name":"Macfarlane"},{"full_name":"Mognetti, Bortolo M.","last_name":"Mognetti","first_name":"Bortolo M."},{"full_name":"Nikoubashman, Arash","last_name":"Nikoubashman","first_name":"Arash"},{"first_name":"Saeed","full_name":"Osat, Saeed","last_name":"Osat"},{"last_name":"Prezhdo","full_name":"Prezhdo, Oleg V.","first_name":"Oleg V."},{"full_name":"Rotskoff, Grant M.","last_name":"Rotskoff","first_name":"Grant M."},{"first_name":"Leonor","full_name":"Saiz, Leonor","last_name":"Saiz"},{"first_name":"An Chang","full_name":"Shi, An Chang","last_name":"Shi"},{"last_name":"Skrabalak","full_name":"Skrabalak, Sara","first_name":"Sara"},{"last_name":"Smalyukh","full_name":"Smalyukh, Ivan I.","first_name":"Ivan I."},{"full_name":"Tagliazucchi, Mario","last_name":"Tagliazucchi","first_name":"Mario"},{"first_name":"Dmitri V.","last_name":"Talapin","full_name":"Talapin, Dmitri V."},{"first_name":"Alexei V.","full_name":"Tkachenko, Alexei V.","last_name":"Tkachenko"},{"first_name":"Sergei","full_name":"Tretiak, Sergei","last_name":"Tretiak"},{"last_name":"Vaknin","full_name":"Vaknin, David","first_name":"David"},{"first_name":"Asaph","last_name":"Widmer-Cooper","full_name":"Widmer-Cooper, Asaph"},{"first_name":"Gerard C.L.","full_name":"Wong, Gerard C.L.","last_name":"Wong"},{"first_name":"Xingchen","full_name":"Ye, Xingchen","last_name":"Ye"},{"first_name":"Shan","full_name":"Zhou, Shan","last_name":"Zhou"},{"first_name":"Eran","last_name":"Rabani","full_name":"Rabani, Eran"},{"last_name":"Engel","full_name":"Engel, Michael","first_name":"Michael"},{"first_name":"Alex","last_name":"Travesset","full_name":"Travesset, Alex"}],"OA_type":"closed access","article_processing_charge":"No","acknowledgement":"This research was supported in part by the National Science Foundation under Grant No. NSF PHY-1748958 to the Kavli Institute for Theoretical Physics. The biophysics part of this paper was supported in part by the Gordon and Betty Moore Foundation Grant No. 2919.02. CLB acknowledges the sponsorship of the Alexander von Humboldt Foundation through the Humboldt Research Fellowship for postdoctoral researchers, and the support of the Emerging Talents Initiative (ETI) and the EAM Starting Grant (EAM-SG23-1) of the Competence Center Engineering of Advanced Materials of the Friedrich-Alexander-Universität Erlangen-Nürnberg. CLB and ME acknowledge the support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Project-ID 416229255-SFB 1411. The research of AT was supported by the U.S. Department of Energy (U.S. DOE), Office of Basic Energy Sciences, Division of Materials Sciences and Engineering. Iowa State University operates Ames National Laboratory for the U.S. DOE under Contract DE-AC02-07CH11358.","intvolume":"        18","title":"Nanocrystal assemblies: Current advances and open problems","volume":18,"date_published":"2024-05-30T00:00:00Z","pmid":1,"issue":"23","fulldoi":"https://doi.org/10.1021/acsnano.3c10201","day":"30","abstract":[{"lang":"eng","text":"We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies."}],"quality_controlled":"1","_id":"17125","publisher":"American Chemical Society","doi":"10.1021/acsnano.3c10201"},{"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031587221"],"issn":["0302-9743"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","year":"2024","external_id":{"isi":["001278247600009"]},"month":"05","main_file_link":[{"url":"https://eprint.iacr.org/2023/719.pdf","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","alternative_title":["LNCS"],"date_updated":"2025-09-08T07:48:18Z","isi":1,"oa":1,"citation":{"ieee":"E. Tairi and A. Ünal, “Lower bounds for lattice-based compact functional encryption,” in <i>Advances in Cryptology – EUROCRYPT 2024</i>, Zurich, Switzerland, 2024, vol. 14652, pp. 249–279.","chicago":"Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional Encryption.” In <i>Advances in Cryptology – EUROCRYPT 2024</i>, 14652:249–79. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">https://doi.org/10.1007/978-3-031-58723-8_9</a>.","ama":"Tairi E, Ünal A. Lower bounds for lattice-based compact functional encryption. In: <i>Advances in Cryptology – EUROCRYPT 2024</i>. Vol 14652. Springer Nature; 2024:249-279. doi:<a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">10.1007/978-3-031-58723-8_9</a>","short":"E. Tairi, A. Ünal, in:, Advances in Cryptology – EUROCRYPT 2024, Springer Nature, 2024, pp. 249–279.","ista":"Tairi E, Ünal A. 2024. Lower bounds for lattice-based compact functional encryption. Advances in Cryptology – EUROCRYPT 2024. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 14652, 249–279.","apa":"Tairi, E., &#38; Ünal, A. (2024). Lower bounds for lattice-based compact functional encryption. In <i>Advances in Cryptology – EUROCRYPT 2024</i> (Vol. 14652, pp. 249–279). Zurich, Switzerland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">https://doi.org/10.1007/978-3-031-58723-8_9</a>","mla":"Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional Encryption.” <i>Advances in Cryptology – EUROCRYPT 2024</i>, vol. 14652, Springer Nature, 2024, pp. 249–79, doi:<a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">10.1007/978-3-031-58723-8_9</a>."},"date_created":"2024-06-09T22:01:03Z","quality_controlled":"1","abstract":[{"text":"Functional encryption (FE) is a primitive where the holder of a master secret key can control which functions a user can evaluate on encrypted data. It is a powerful primitive that even implies indistinguishability obfuscation (iO), given sufficiently compact ciphertexts (Ananth-Jain, CRYPTO’15 and Bitansky-Vaikuntanathan, FOCS’15). However, despite being extensively studied, there are FE schemes, such as function-hiding inner-product FE (Bishop-Jain-Kowalczyk, AC’15, Abdalla-Catalano-Fiore-Gay-Ursu, CRYPTO’18) and compact quadratic FE (Baltico-Catalano-Fiore-Gay, Lin, CRYPTO’17), that can be only realized using pairings. This raises the question if there are some mathematical barriers that hinder us from realizing these FE schemes from other assumptions.\r\n\r\nIn this paper, we study the difficulty of constructing lattice-based compact FE. We generalize the impossibility results of Ünal (EC’20) for lattice-based function-hiding FE, and extend it to the case of compact FE. Concretely, we prove lower bounds for lattice-based compact FE schemes which meet some (natural) algebraic restrictions at encryption and decryption, and have ciphertexts of linear size and secret keys of minimal degree. We see our results as important indications of why it is hard to construct lattice-based FE schemes for new functionalities, and which mathematical barriers have to be overcome.","lang":"eng"}],"day":"08","conference":{"location":"Zurich, Switzerland","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","start_date":"2024-05-26","end_date":"2024-05-30"},"fulldoi":"https://doi.org/10.1007/978-3-031-58723-8_9","doi":"10.1007/978-3-031-58723-8_9","publisher":"Springer Nature","_id":"17126","language":[{"iso":"eng"}],"publication":"Advances in Cryptology – EUROCRYPT 2024","status":"public","page":"249-279","department":[{"_id":"KrPi"}],"date_published":"2024-05-08T00:00:00Z","volume":14652,"intvolume":"     14652","title":"Lower bounds for lattice-based compact functional encryption","acknowledgement":"We want to thank the anonymous reviewers of TCC and Eurocrypt for their very helpful comments and suggestions. This work has received funding from the Austrian Science Fund (FWF) and netidee SCIENCE via grant P31621-N38 (PROFET).","article_processing_charge":"No","publication_status":"published","author":[{"first_name":"Erkan","full_name":"Tairi, Erkan","last_name":"Tairi"},{"first_name":"Akin","id":"f6b56fb6-dc63-11ee-9dbf-f6780863a85a","last_name":"Ünal","full_name":"Ünal, Akin","orcid":"0000-0002-8929-0221"}]},{"language":[{"iso":"eng"}],"status":"public","page":"1339-1345","publication":"Nature Physics","department":[{"_id":"BjHo"}],"date_published":"2024-08-01T00:00:00Z","volume":20,"article_processing_charge":"No","acknowledgement":"We gratefully acknowledge the assistance of J. M. Lopez with DNSs at an early stage of this work. This work was partially supported by two grants from the Simons Foundation (grant nos. 662985 (N.G.) and 662960 (B.H.)) and by Ministry of Science and Technology, Taiwan (grant nos. MOST 109-2112-M-001-017-MY3 and MOST 111-2112-M-001-027-MY3 (H.-Y.S.)). Part of this work was performed using computing resources of CRIANN (Normandy, France).","intvolume":"        20","title":"Directed percolation and puff jamming near the transition to pipe turbulence","author":[{"id":"4787FE80-F248-11E8-B48F-1D18A9856A87","last_name":"Lemoult","full_name":"Lemoult, Grégoire M","first_name":"Grégoire M"},{"id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","last_name":"Vasudevan","full_name":"Vasudevan, Mukund","first_name":"Mukund"},{"first_name":"Hong Yan","full_name":"Shih, Hong Yan","last_name":"Shih"},{"full_name":"Linga, Gaute","last_name":"Linga","first_name":"Gaute"},{"first_name":"Joachim","last_name":"Mathiesen","full_name":"Mathiesen, Joachim"},{"last_name":"Goldenfeld","full_name":"Goldenfeld, Nigel","first_name":"Nigel"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"publication_status":"published","quality_controlled":"1","day":"01","abstract":[{"text":"The onset of turbulence in pipe flow has defied detailed understanding ever since the first observations of the spatially heterogeneous nature of the transition. Recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed-percolation non-equilibrium phase transition, but whether these findings are generic and also apply to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behaviour virtually impossible. Here we find a technical solution to that limitation and show that the universality class of the transition is directed percolation, from which a jammed phase of puffs emerges above the critical point. Our method is to experimentally characterize all pairwise interactions between localized patches of turbulence puffs and use these interactions as input for renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. The strong interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed-percolation scaling applies beyond simple closed shear flows and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases.","lang":"eng"}],"fulldoi":"https://doi.org/10.1038/s41567-024-02513-0","publisher":"Springer Nature","doi":"10.1038/s41567-024-02513-0","_id":"17128","date_updated":"2025-09-08T07:50:20Z","article_type":"original","isi":1,"citation":{"ista":"Lemoult GM, Vasudevan M, Shih HY, Linga G, Mathiesen J, Goldenfeld N, Hof B. 2024. Directed percolation and puff jamming near the transition to pipe turbulence. Nature Physics. 20, 1339–1345.","mla":"Lemoult, Grégoire M., et al. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1339–45, doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>.","apa":"Lemoult, G. M., Vasudevan, M., Shih, H. Y., Linga, G., Mathiesen, J., Goldenfeld, N., &#38; Hof, B. (2024). Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>","ama":"Lemoult GM, Vasudevan M, Shih HY, et al. Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. 2024;20:1339-1345. doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>","short":"G.M. Lemoult, M. Vasudevan, H.Y. Shih, G. Linga, J. Mathiesen, N. Goldenfeld, B. Hof, Nature Physics 20 (2024) 1339–1345.","chicago":"Lemoult, Grégoire M, Mukund Vasudevan, Hong Yan Shih, Gaute Linga, Joachim Mathiesen, Nigel Goldenfeld, and Björn Hof. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>.","ieee":"G. M. Lemoult <i>et al.</i>, “Directed percolation and puff jamming near the transition to pipe turbulence,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1339–1345, 2024."},"date_created":"2024-06-09T22:01:03Z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","corr_author":"1","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960"}],"year":"2024","external_id":{"isi":["001232300600001"]},"month":"08","oa_version":"None","scopus_import":"1"},{"ddc":["530"],"supervisor":[{"orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"date_updated":"2026-04-15T06:43:02Z","oa":1,"citation":{"short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>."},"file":[{"checksum":"258c353d47fa37ea63ea43b1e10a34a0","creator":"fhassani","date_created":"2024-06-12T07:53:19Z","file_size":28370759,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_updated":"2024-06-20T11:52:22Z","file_id":"17137","file_name":"Thesis_main_final.pdf"},{"relation":"source_file","file_id":"17138","date_updated":"2024-06-12T07:54:27Z","file_name":"Thesis_main.tex","checksum":"deffa5d0db88093f74812fa71520d5e1","creator":"fhassani","date_created":"2024-06-12T07:54:27Z","file_size":445735,"content_type":"text/x-tex","access_level":"closed"}],"date_created":"2024-06-11T18:20:05Z","corr_author":"1","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"year":"2024","month":"06","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13227"},{"status":"public","relation":"part_of_dissertation","id":"9928"},{"status":"public","id":"8755","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"status":"public","page":"161","date_published":"2024-06-11T00:00:00Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"author":[{"first_name":"Farid","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","last_name":"Hassani"}],"publication_status":"published","title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","article_processing_charge":"No","abstract":[{"text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing.","lang":"eng"}],"day":"11","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/at:ista:17133","OA_place":"publisher","doi":"10.15479/at:ista:17133","file_date_updated":"2024-06-20T11:52:22Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","_id":"17133","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","keyword":["Quantum information","Qubits","Superconducting devices"]},{"article_processing_charge":"No","acknowledgement":"I am grateful to Matthew Kwan for setting the problem, providing useful literature,\r\nfruitful discussions, text review, mentorship, general encouragement and support.","title":"Majority dynamics and internal partitions of random regular graphs: Experimental results","date_created":"2024-06-12T07:01:52Z","publication_status":"submitted","author":[{"last_name":"Arkhipov","full_name":"Arkhipov, Pavel","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","first_name":"Pavel"}],"arxiv":1,"citation":{"chicago":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>.","ieee":"P. Arkhipov, “Majority dynamics and internal partitions of random regular graphs: Experimental results,” <i>arXiv</i>. .","apa":"Arkhipov, P. (n.d.). Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>","mla":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, 2406.07026, doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>.","ista":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. arXiv, 2406.07026.","ama":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>","short":"P. Arkhipov, ArXiv (n.d.)."},"date_published":"2024-06-11T00:00:00Z","oa":1,"status":"public","date_updated":"2024-06-17T10:45:32Z","article_number":"2406.07026","publication":"arXiv","department":[{"_id":"GradSch"}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.07026","open_access":"1"}],"oa_version":"Preprint","_id":"17136","external_id":{"arxiv":["2406.07026"]},"doi":"10.48550/arXiv.2406.07026","month":"06","year":"2024","fulldoi":"https://doi.org/10.48550/arXiv.2406.07026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","abstract":[{"lang":"eng","text":"This paper focuses on Majority Dynamics in sparse graphs, in particular, as a\r\ntool to study internal cuts. It is known that, in Majority Dynamics on a finite\r\ngraph, each vertex eventually either comes to a fixed state, or oscillates with\r\nperiod two. The empirical evidence acquired by simulations suggests that for\r\nrandom odd-regular graphs, approximately half of the vertices end up\r\noscillating with high probability. We notice a local symmetry between\r\noscillating and non-oscillating vertices, that potentially can explain why the\r\nfraction of the oscillating vertices is concentrated around $\\frac{1}{2}$. In\r\nour simulations, we observe that the parts of random odd-regular graph under\r\nMajority Dynamics with high probability do not contain $\\lceil \\frac{d}{2}\r\n\\rceil$-cores at any timestep, and thus, one cannot use Majority Dynamics to\r\nprove that internal cuts exist in odd-regular graphs almost surely. However, we\r\nsuggest a modification of Majority Dynamics, that yields parts with desired\r\ncores with high probability."}],"type":"preprint"},{"_id":"17139","file_date_updated":"2024-06-17T09:36:51Z","doi":"10.25365/phaidra.463","publisher":"EuroCC Austria","conference":{"end_date":"2024-06-13","name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2024-06-10","location":"Grundlsee, Austria"},"has_accepted_license":"1","fulldoi":"https://doi.org/10.25365/phaidra.463","quality_controlled":"1","day":"13","title":"How much memory per CPU core is requested?","article_processing_charge":"No","author":[{"first_name":"Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"first_name":"Waleed","full_name":"Khalid, Waleed","last_name":"Khalid","id":"097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1"},{"full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano"},{"full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan"}],"publication_status":"published","date_published":"2024-06-13T00:00:00Z","publication":"ASHPC24 - Austrian-Slovenian HPC Meeting 2024","page":"46","status":"public","department":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"06","year":"2024","publication_identifier":{"isbn":["9783200096455"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference_abstract","file":[{"creator":"dernst","checksum":"f7d3dded6df2dcdb4818904cf2e1c183","access_level":"open_access","file_size":206746,"content_type":"application/pdf","success":1,"date_created":"2024-06-17T09:36:51Z","relation":"main_file","file_name":"2024_ASHPC_Schloegl.pdf","file_id":"17153","date_updated":"2024-06-17T09:36:51Z"}],"date_created":"2024-06-14T09:06:36Z","oa":1,"citation":{"chicago":"Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer. “How Much Memory per CPU Core Is Requested?” In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, 46. EuroCC Austria, 2024. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>.","ieee":"A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per CPU core is requested?,” in <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, Grundlsee, Austria, 2024, p. 46.","apa":"Schlögl, A., Khalid, W., Elefante, S., &#38; Stadlbauer, S. (2024). How much memory per CPU core is requested? In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i> (p. 46). Grundlsee, Austria: EuroCC Austria. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>","mla":"Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, EuroCC Austria, 2024, p. 46, doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>.","ista":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian HPC Meeting, 46.","short":"A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46.","ama":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core is requested? In: <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>. EuroCC Austria; 2024:46. doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>"},"date_updated":"2024-06-17T09:40:37Z","ddc":["000"]},{"external_id":{"isi":["001270051200001"],"pmid":["38794966"]},"month":"09","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa_version":"Published Version","publication_identifier":{"issn":["0022-0957"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","year":"2024","oa":1,"citation":{"ama":"Zhang Z, Chen H, Peng S, Han H. Slow and rapid auxin responses in Arabidopsis. <i>Journal of Experimental Botany</i>. 2024;75(18). doi:<a href=\"https://doi.org/10.1093/jxb/erae246\">10.1093/jxb/erae246</a>","short":"Z. Zhang, H. Chen, S. Peng, H. Han, Journal of Experimental Botany 75 (2024).","ista":"Zhang Z, Chen H, Peng S, Han H. 2024. Slow and rapid auxin responses in Arabidopsis. Journal of Experimental Botany. 75(18), erae246.","mla":"Zhang, Zilin, et al. “Slow and Rapid Auxin Responses in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 75, no. 18, erae246, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/jxb/erae246\">10.1093/jxb/erae246</a>.","apa":"Zhang, Z., Chen, H., Peng, S., &#38; Han, H. (2024). Slow and rapid auxin responses in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erae246\">https://doi.org/10.1093/jxb/erae246</a>","ieee":"Z. Zhang, H. Chen, S. Peng, and H. Han, “Slow and rapid auxin responses in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 75, no. 18. Oxford University Press, 2024.","chicago":"Zhang, Zilin, Huihuang Chen, Shuaiying Peng, and Huibin Han. “Slow and Rapid Auxin Responses in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jxb/erae246\">https://doi.org/10.1093/jxb/erae246</a>."},"file":[{"file_size":763097,"content_type":"application/pdf","access_level":"open_access","date_created":"2025-01-02T10:26:22Z","success":1,"creator":"dernst","checksum":"91b9435ed0f6640809c7588df19abf2f","file_name":"2024_JourExperimentalBotany_Zhang.pdf","file_id":"18720","date_updated":"2025-01-02T10:26:22Z","relation":"main_file"}],"date_created":"2024-06-15T19:50:15Z","ddc":["580"],"date_updated":"2025-09-08T07:57:50Z","article_type":"original","isi":1,"file_date_updated":"2025-01-02T10:26:22Z","doi":"10.1093/jxb/erae246","publisher":"Oxford University Press","OA_place":"publisher","_id":"17141","quality_controlled":"1","abstract":[{"text":"The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted to (de)active transcriptional regulation, thus controlling auxin-associated developmental processes. However, the theme of a rapid auxin response has emerged since the 2018 Auxins and Cytokinin in Plant Development conference. To date, a few signaling components have been identified to mediate both slow and rapid auxin responses, which unveils the complexity of auxin signaling.","lang":"eng"}],"day":"27","fulldoi":"https://doi.org/10.1093/jxb/erae246","has_accepted_license":"1","issue":"18","volume":75,"date_published":"2024-09-27T00:00:00Z","pmid":1,"title":"Slow and rapid auxin responses in Arabidopsis","intvolume":"        75","acknowledgement":"We thank other lab members for their critical comments on this manuscript. We also thank the editor and reviewers for their constructive comments to improve our manuscript. We apologize to authors whose important work we could not include due to space limitations.\r\nThis work is supported by funding from Jiangxi Agricultural University (9232308314) and the Science and Technology Department of Jiangxi Province (20223BCJ25037) to HBH, and the Science and Technology Department of Jiangxi Province (20202ACB215002) to SYP.","OA_type":"hybrid","article_processing_charge":"No","publication_status":"published","author":[{"first_name":"Zilin","full_name":"Zhang, Zilin","last_name":"Zhang"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"first_name":"Shuaiying","last_name":"Peng","full_name":"Peng, Shuaiying"},{"first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"}],"language":[{"iso":"eng"}],"publication":"Journal of Experimental Botany","article_number":"erae246","status":"public","department":[{"_id":"GradSch"},{"_id":"JiFr"}]},{"status":"public","publication":"PLoS Biology","article_number":"e3002668","department":[{"_id":"RySh"},{"_id":"GaNo"},{"_id":"MaJö"}],"ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"15385","relation":"research_data"}],"link":[{"url":"https://doi.org/10.5281/zenodo.11130587","relation":"software"}]},"acknowledgement":"This work was supported by a European Research Council Starting Grant 756502 (MJ). ","article_processing_charge":"Yes","OA_type":"gold","intvolume":"        22","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","publication_status":"published","author":[{"first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","full_name":"Burnett, Laura","last_name":"Burnett","orcid":"0000-0002-8937-410X"},{"full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","first_name":"Peter"},{"first_name":"Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Masson, Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","orcid":"0000-0002-2634-6283","last_name":"Masson","first_name":"Tomas"},{"full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga","first_name":"Tomas A"},{"last_name":"Contreras","full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"volume":22,"date_published":"2024-06-10T00:00:00Z","pmid":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1371/journal.pbio.3002668","quality_controlled":"1","day":"10","abstract":[{"lang":"eng","text":"Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments—a nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment and define a nondevelopmental source of such deficits in ASD."}],"_id":"17142","publisher":"Public Library of Science","doi":"10.1371/journal.pbio.3002668","file_date_updated":"2025-01-09T10:39:41Z","OA_place":"publisher","date_updated":"2025-09-08T07:57:11Z","article_type":"original","isi":1,"ddc":["570"],"date_created":"2024-06-16T22:01:05Z","file":[{"relation":"main_file","file_id":"18805","date_updated":"2025-01-09T10:39:41Z","file_name":"2024_PloS_Burnett.pdf","checksum":"496e1aa4fd5b92b7e4087ecc2c964133","creator":"dernst","date_created":"2025-01-09T10:39:41Z","success":1,"content_type":"application/pdf","file_size":4016568,"access_level":"open_access"}],"citation":{"chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>.","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice,” <i>PLoS Biology</i>, vol. 22. Public Library of Science, 2024.","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. 22, e3002668.","mla":"Burnett, Laura, et al. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>, vol. 22, e3002668, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, PLoS Biology 22 (2024).","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. 2024;22. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>"},"oa":1,"year":"2024","project":[{"call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"APC_amount":"6081,83 EUR","corr_author":"1","type":"journal_article","DOAJ_listed":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","external_id":{"pmid":["38857283"],"isi":["001246176800003"]},"month":"06"},{"publisher":"American Mathematical Society","doi":"10.1090/tran/9156","_id":"17143","quality_controlled":"1","day":"01","abstract":[{"text":"This paper deals with local criteria for the convergence to a global minimiser for gradient flow trajectories and their discretisations. To obtain quantitative estimates on the speed of convergence, we consider variations on the classical Kurdyka–Łojasiewicz inequality for a large class of parameter functions. Our assumptions are given in terms of the initial data, without any reference to an equilibrium point. The main results are convergence statements for gradient flow curves and proximal point sequences to a global minimiser, together with sharp quantitative estimates on the speed of convergence. These convergence results apply in the general setting of lower semicontinuous functionals on complete metric spaces, generalising recent results for smooth functionals on Rn. While the non-smooth setting covers very general spaces, it is also useful for (non)-smooth functionals on Rn.\r\n.","lang":"eng"}],"fulldoi":"https://doi.org/10.1090/tran/9156","issue":"6","volume":377,"date_published":"2024-06-01T00:00:00Z","article_processing_charge":"No","acknowledgement":"The authors gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 716117). This research was funded in part by the Austrian Science Fund (FWF) project 10.55776/ESP208. This research was funded in part by the Austrian Science Fund (FWF) project 10.55776/F65","intvolume":"       377","title":"Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces","publication_status":"published","author":[{"first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo"},{"first_name":"Jan","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","orcid":"0000-0002-0845-1338"},{"first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","full_name":"Pedrotti, Francesco"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"17336","relation":"dissertation_contains"}]},"status":"public","page":"3779-3804","publication":"Transactions of the American Mathematical Society","department":[{"_id":"JaMa"}],"ec_funded":1,"external_id":{"arxiv":["2304.05239"],"isi":["001203273300001"]},"month":"06","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.05239","open_access":"1"}],"oa_version":"Preprint","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"type":"journal_article","year":"2024","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208"}],"citation":{"ieee":"L. Dello Schiavo, J. Maas, and F. Pedrotti, “Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces,” <i>Transactions of the American Mathematical Society</i>, vol. 377, no. 6. American Mathematical Society, pp. 3779–3804, 2024.","chicago":"Dello Schiavo, Lorenzo, Jan Maas, and Francesco Pedrotti. “Local Conditions for Global Convergence of Gradient Flows and Proximal Point Sequences in Metric Spaces.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2024. <a href=\"https://doi.org/10.1090/tran/9156\">https://doi.org/10.1090/tran/9156</a>.","short":"L. Dello Schiavo, J. Maas, F. Pedrotti, Transactions of the American Mathematical Society 377 (2024) 3779–3804.","ama":"Dello Schiavo L, Maas J, Pedrotti F. Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces. <i>Transactions of the American Mathematical Society</i>. 2024;377(6):3779-3804. doi:<a href=\"https://doi.org/10.1090/tran/9156\">10.1090/tran/9156</a>","mla":"Dello Schiavo, Lorenzo, et al. “Local Conditions for Global Convergence of Gradient Flows and Proximal Point Sequences in Metric Spaces.” <i>Transactions of the American Mathematical Society</i>, vol. 377, no. 6, American Mathematical Society, 2024, pp. 3779–804, doi:<a href=\"https://doi.org/10.1090/tran/9156\">10.1090/tran/9156</a>.","apa":"Dello Schiavo, L., Maas, J., &#38; Pedrotti, F. (2024). Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/9156\">https://doi.org/10.1090/tran/9156</a>","ista":"Dello Schiavo L, Maas J, Pedrotti F. 2024. Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces. Transactions of the American Mathematical Society. 377(6), 3779–3804."},"oa":1,"date_created":"2024-06-16T22:01:06Z","arxiv":1,"date_updated":"2026-04-07T13:00:02Z","article_type":"original","isi":1}]