[{"ec_funded":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"},{"_id":"bd622a5c-d553-11ed-ba76-bae280ba8aff","name":"Graphical Games","grant_number":"894907"}],"department":[{"_id":"KrCh"}],"year":"2024","main_file_link":[{"open_access":"1","url":"https://schmiste.github.io/noms24.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-27T15:06:45Z","oa":1,"external_id":{"isi":["001270140300143"]},"language":[{"iso":"eng"}],"corr_author":"1","OA_place":"other","acknowledgement":"Research was supported by the Austrian Science Fund (FWF), project I 5025-N (DELTA), 2020-2024. Esra Ceylan’s research was supported by FFG, FEMtech Praktika für Studentinnen. Jakub Svoboda and Krishnendu Chatterjee were supported by the European Research Council (ERC) CoG 863818 (ForM-SMArt).","scopus_import":"1","doi":"10.1109/noms59830.2024.10575579","publisher":"IEEE","day":"01","OA_type":"green","publication_status":"published","quality_controlled":"1","publication":"NOMS 2024-2024 IEEE Network Operations and Management Symposium","title":"Congestion-free rerouting of network flows: Hardness and an FPT algorithm","conference":{"end_date":"2024-05-10","name":"NOMS: Network Operations and Management Symposiu ","location":"Seoul, Republic of Korea","start_date":"2024-05-06"},"author":[{"last_name":"Ceylan","full_name":"Ceylan, Esra","id":"cb1ca1d8-dcc0-11ef-baa5-9f1b3ef75933","first_name":"Esra"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub"}],"date_published":"2024-05-01T00:00:00Z","date_updated":"2025-11-05T07:34:27Z","month":"05","abstract":[{"lang":"eng","text":"Given the increasingly stringent requirements on the performance and efficiency of communication networks, over the last years, great efforts have been made to render networks more flexible and programmable. In particular, modern networks support a flexible rerouting of flows, e.g., depending on the dynamically changing traffic or network conditions. However, the underlying algorithmic problems are still not well-understood today.In this paper, we revisit the k-Network Flow Update problem that asks for a schedule to reroute k unsplittable flows from their current paths to the given new paths, in a congestion-free manner in a capacitated network. We show that the problem is already NP-hard for three acyclic flows on simple directed graphs. Our main contribution is an efficient algorithm for sparse networks; specifically the algorithm is fixed parameter tractable in the number of flows and the treewidth of a graph that is the union of all flows. Our results also settle the open complexity question in the literature."}],"oa_version":"Submitted Version","isi":1,"publication_identifier":{"isbn":["9798350327946"],"eissn":["2374-9709"]},"type":"conference","citation":{"mla":"Ceylan, Esra, et al. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” NOMS 2024-2024 IEEE Network Operations and Management Symposium, IEEE, 2024, doi:10.1109/noms59830.2024.10575579.","chicago":"Ceylan, Esra, Krishnendu Chatterjee, Stefan Schmid, and Jakub Svoboda. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” In NOMS 2024-2024 IEEE Network Operations and Management Symposium. IEEE, 2024. https://doi.org/10.1109/noms59830.2024.10575579.","ieee":"E. Ceylan, K. Chatterjee, S. Schmid, and J. Svoboda, “Congestion-free rerouting of network flows: Hardness and an FPT algorithm,” in NOMS 2024-2024 IEEE Network Operations and Management Symposium, Seoul, Republic of Korea, 2024.","ista":"Ceylan E, Chatterjee K, Schmid S, Svoboda J. 2024. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. NOMS 2024-2024 IEEE Network Operations and Management Symposium. NOMS: Network Operations and Management Symposiu .","short":"E. Ceylan, K. Chatterjee, S. Schmid, J. Svoboda, in:, NOMS 2024-2024 IEEE Network Operations and Management Symposium, IEEE, 2024.","apa":"Ceylan, E., Chatterjee, K., Schmid, S., & Svoboda, J. (2024). Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In NOMS 2024-2024 IEEE Network Operations and Management Symposium. Seoul, Republic of Korea: IEEE. https://doi.org/10.1109/noms59830.2024.10575579","ama":"Ceylan E, Chatterjee K, Schmid S, Svoboda J. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In: NOMS 2024-2024 IEEE Network Operations and Management Symposium. IEEE; 2024. doi:10.1109/noms59830.2024.10575579"},"article_processing_charge":"No","_id":"18925","status":"public"},{"title":"BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness","date_published":"2024-01-01T00:00:00Z","author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Hensel","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian"},{"last_name":"Laux","full_name":"Laux, Tim","first_name":"Tim"}],"page":"111-148","publication_status":"published","quality_controlled":"1","publication":"Indiana University Mathematics Journal","type":"journal_article","publication_identifier":{"issn":["0022-2518"]},"article_processing_charge":"No","citation":{"ama":"Hensel S, Laux T. BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics Journal. 2024;73(1):111-148. doi:10.1512/iumj.2024.73.9701","apa":"Hensel, S., & Laux, T. (2024). BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics Journal. Indiana University Mathematics Journal. https://doi.org/10.1512/iumj.2024.73.9701","short":"S. Hensel, T. Laux, Indiana University Mathematics Journal 73 (2024) 111–148.","ista":"Hensel S, Laux T. 2024. BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics Journal. 73(1), 111–148.","ieee":"S. Hensel and T. Laux, “BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness,” Indiana University Mathematics Journal, vol. 73, no. 1. Indiana University Mathematics Journal, pp. 111–148, 2024.","chicago":"Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana University Mathematics Journal. Indiana University Mathematics Journal, 2024. https://doi.org/10.1512/iumj.2024.73.9701.","mla":"Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana University Mathematics Journal, vol. 73, no. 1, Indiana University Mathematics Journal, 2024, pp. 111–48, doi:10.1512/iumj.2024.73.9701."},"status":"public","_id":"18926","article_type":"original","month":"01","abstract":[{"text":"We study weak solutions to mean curvature flow satisfying Young’s angle condition for general contact angles α ∈ (0, π). First, we construct BV solutions by using the Allen-Cahn approximation with boundary contact energy as proposed by Owen and Sternberg. Second, we prove the weak-strong uniqueness and stability for this solution concept. The main ingredient for both results is a relative energy, which can also be interpreted as a tilt excess. ","lang":"eng"}],"volume":73,"date_updated":"2025-01-27T15:23:57Z","issue":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-27T15:20:19Z","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["2112.11150"]},"OA_place":"repository","corr_author":"1","department":[{"_id":"JuFi"}],"intvolume":" 73","year":"2024","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2112.11150"}],"arxiv":1,"doi":"10.1512/iumj.2024.73.9701","publisher":"Indiana University Mathematics Journal","day":"01","OA_type":"green","scopus_import":"1"},{"day":"24","OA_type":"gold","alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","arxiv":1,"doi":"10.4230/LIPIcs.ITCS.2024.62","scopus_import":"1","acknowledgement":"Henzinger, Monika: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z 422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020-2024.\r\nSaha, Barna: This project is partially supported by NSF grants 1652303, 1909046, 2112533, and HDR TRIPODS Phase II grant 2217058.\r\nWe would like to thank Andrea Lincoln for many helpful discussions and insightful comments.","ddc":["000"],"OA_place":"publisher","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["2307.16771"],"isi":["001300389400062"]},"oa":1,"file_date_updated":"2025-01-27T15:33:24Z","date_created":"2025-01-27T15:33:42Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MoHe"}],"year":"2024","intvolume":" 287","project":[{"name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms","grant_number":"Z00422"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"ec_funded":1,"_id":"18928","status":"public","article_processing_charge":"Yes","citation":{"ama":"Henzinger M, Saha B, Seybold MP, Ye C. On the complexity of algorithms with predictions for dynamic graph problems. In: 15th Innovations in Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:62:1-62:25. doi:10.4230/LIPIcs.ITCS.2024.62","apa":"Henzinger, M., Saha, B., Seybold, M. P., & Ye, C. (2024). On the complexity of algorithms with predictions for dynamic graph problems. In 15th Innovations in Theoretical Computer Science Conference (Vol. 287, p. 62:1-62:25). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.62","short":"M. Henzinger, B. Saha, M.P. Seybold, C. Ye, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 62:1-62:25.","ista":"Henzinger M, Saha B, Seybold MP, Ye C. 2024. On the complexity of algorithms with predictions for dynamic graph problems. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 287, 62:1-62:25.","chicago":"Henzinger, Monika, Barna Saha, Martin P. Seybold, and Christopher Ye. “On the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” In 15th Innovations in Theoretical Computer Science Conference, 287:62:1-62:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.62.","ieee":"M. Henzinger, B. Saha, M. P. Seybold, and C. Ye, “On the complexity of algorithms with predictions for dynamic graph problems,” in 15th Innovations in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287, p. 62:1-62:25.","mla":"Henzinger, Monika, et al. “On the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” 15th Innovations in Theoretical Computer Science Conference, vol. 287, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 62:1-62:25, doi:10.4230/LIPIcs.ITCS.2024.62."},"type":"conference","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959773096"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","month":"01","abstract":[{"lang":"eng","text":"Algorithms with predictions is a new research direction that leverages machine learned predictions for algorithm design. So far a plethora of recent works have incorporated predictions to improve on worst-case bounds for online problems. In this paper, we initiate the study of complexity of dynamic data structures with predictions, including dynamic graph algorithms. Unlike online algorithms, the goal in dynamic data structures is to maintain the solution efficiently with every update.\r\nWe investigate three natural models of prediction: (1) δ-accurate predictions where each predicted request matches the true request with probability δ, (2) list-accurate predictions where a true request comes from a list of possible requests, and (3) bounded delay predictions where the true requests are a permutation of the predicted requests. We give general reductions among the prediction models, showing that bounded delay is the strongest prediction model, followed by list-accurate, and δ-accurate.\r\nFurther, we identify two broad problem classes based on lower bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show that locally correctable dynamic problems have strong conditional lower bounds for list-accurate predictions that are equivalent to the non-prediction setting, unless list-accurate predictions are perfect. Moreover, we show that locally reducible dynamic problems have time complexity that degrades gracefully with the quality of bounded delay predictions. We categorize problems with known OMv lower bounds accordingly and give several upper bounds in the delay model that show that our lower bounds are almost tight.\r\nWe note that concurrent work by v.d.Brand et al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic graph algorithms with predictions, but their work is mostly focused on showing upper bounds."}],"volume":287,"date_updated":"2025-09-09T12:11:33Z","date_published":"2024-01-24T00:00:00Z","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"first_name":"Barna","last_name":"Saha","full_name":"Saha, Barna"},{"last_name":"Seybold","full_name":"Seybold, Martin P.","first_name":"Martin P."},{"full_name":"Ye, Christopher","last_name":"Ye","first_name":"Christopher"}],"conference":{"end_date":"2024-02-02","name":"ITCS: Innovations in Theoretical Computer Science","location":"Berkeley, CA, United States","start_date":"2024-01-30"},"title":"On the complexity of algorithms with predictions for dynamic graph problems","publication":"15th Innovations in Theoretical Computer Science Conference","file":[{"date_updated":"2025-01-27T15:33:24Z","creator":"dernst","checksum":"15085a5b3697a408b92a4a7a27293927","relation":"main_file","success":1,"file_name":"2024_LIPICs_HenzingerMo.pdf","file_id":"18929","content_type":"application/pdf","access_level":"open_access","date_created":"2025-01-27T15:33:24Z","file_size":1084372}],"quality_controlled":"1","page":"62:1-62:25","publication_status":"published"},{"doi":"10.1091/mbc.e23-07-0289","publisher":"American Society for Cell Biology","OA_type":"hybrid","day":"01","acknowledgement":"We thank Professor José Paulo Leal, Department of Computer Science − Faculdade de Ciências da Universidade do Porto, for his invaluable help during the Implementation of NAGPKin. This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.","ddc":["570"],"scopus_import":"1","date_created":"2025-01-29T07:58:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-01-29T08:12:11Z","oa":1,"external_id":{"pmid":["38117593"]},"language":[{"iso":"eng"}],"OA_place":"publisher","department":[{"_id":"FlSc"}],"year":"2024","intvolume":" 35","publication_identifier":{"issn":["1059-1524"],"eissn":["1939-4586"]},"type":"journal_article","citation":{"chicago":"Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” Molecular Biology of the Cell. American Society for Cell Biology, 2024. https://doi.org/10.1091/mbc.e23-07-0289.","ieee":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation,” Molecular Biology of the Cell, vol. 35, no. 3. American Society for Cell Biology, 2024.","mla":"Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” Molecular Biology of the Cell, vol. 35, no. 3, mr1, American Society for Cell Biology, 2024, doi:10.1091/mbc.e23-07-0289.","short":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024).","ista":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 35(3), mr1.","apa":"Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., & Martins, P. M. (2024). NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e23-07-0289","ama":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 2024;35(3). doi:10.1091/mbc.e23-07-0289"},"article_processing_charge":"Yes (in subscription journal)","_id":"18934","status":"public","article_type":"original","issue":"3","date_updated":"2025-01-29T08:16:20Z","month":"03","abstract":[{"text":"The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt .","lang":"eng"}],"volume":35,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"title":"NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation","author":[{"first_name":"Zsuzsa","full_name":"Sárkány, Zsuzsa","last_name":"Sárkány"},{"id":"8125cbe2-9661-11ed-a754-afe96018f37d","first_name":"Francisco","last_name":"Figueiredo","full_name":"Figueiredo, Francisco"},{"first_name":"Sandra","last_name":"Macedo-Ribeiro","full_name":"Macedo-Ribeiro, Sandra"},{"first_name":"Pedro M.","last_name":"Martins","full_name":"Martins, Pedro M."}],"article_number":"mr1","date_published":"2024-03-01T00:00:00Z","publication_status":"published","pmid":1,"quality_controlled":"1","publication":"Molecular Biology of the Cell","file":[{"file_size":1699180,"date_created":"2025-01-29T08:12:11Z","file_name":"2024_MolecularBioCell_Sarkany.pdf","file_id":"18935","content_type":"application/pdf","access_level":"open_access","checksum":"d7deb6390f294da69321cfbe352ed611","success":1,"creator":"dernst","relation":"main_file","date_updated":"2025-01-29T08:12:11Z"}]},{"publication_status":"published","publication":"Physica B: Condensed Matter","quality_controlled":"1","title":"Tunable magnetoelectronic properties in Bi3+ substituted YCrO3","article_number":"416018","date_published":"2024-07-15T00:00:00Z","author":[{"first_name":"Sujata Kumari","full_name":"Ray, Sujata Kumari","last_name":"Ray"},{"first_name":"Anupama","full_name":"Pati, Anupama","last_name":"Pati"},{"last_name":"Sahoo","full_name":"Sahoo, Payala","first_name":"Payala"},{"first_name":"A.K.","full_name":"Sahoo, A.K.","last_name":"Sahoo"},{"id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","first_name":"Saurabh","last_name":"Singh","orcid":"0000-0003-2209-5269","full_name":"Singh, Saurabh"},{"full_name":"Takeuchi, Tsunehiro","last_name":"Takeuchi","first_name":"Tsunehiro"},{"first_name":"S.","full_name":"Dash, S.","last_name":"Dash"}],"month":"07","abstract":[{"text":"A detailed structural, magnetic as well as dielectric dynamics study is carried out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize in orthorhombic structure with Pnma symmetry and the grains are mostly stretched with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal negative magnetization in zero field is correlated to the competition among AFM and WFM phases. Maximum magnetization decreases while the coercivity first increases and then decreases with Bi is correlated to the competing effect between the local deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with improved permittivity might be associated with the 6s2 lone pair electron of Bi3+. Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11 eV), is explained in the framework of structural model and charge carrier hopping between Cr3+ and Cr4+ ions.","lang":"eng"}],"volume":685,"date_updated":"2025-01-29T08:37:14Z","article_type":"original","oa_version":"None","article_processing_charge":"No","citation":{"ama":"Ray SK, Pati A, Sahoo P, et al. Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter. 2024;685. doi:10.1016/j.physb.2024.416018","apa":"Ray, S. K., Pati, A., Sahoo, P., Sahoo, A. K., Singh, S., Takeuchi, T., & Dash, S. (2024). Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2024.416018","ista":"Ray SK, Pati A, Sahoo P, Sahoo AK, Singh S, Takeuchi T, Dash S. 2024. Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter. 685, 416018.","short":"S.K. Ray, A. Pati, P. Sahoo, A.K. Sahoo, S. Singh, T. Takeuchi, S. Dash, Physica B: Condensed Matter 685 (2024).","mla":"Ray, Sujata Kumari, et al. “Tunable Magnetoelectronic Properties in Bi3+ Substituted YCrO3.” Physica B: Condensed Matter, vol. 685, 416018, Elsevier, 2024, doi:10.1016/j.physb.2024.416018.","ieee":"S. K. Ray et al., “Tunable magnetoelectronic properties in Bi3+ substituted YCrO3,” Physica B: Condensed Matter, vol. 685. Elsevier, 2024.","chicago":"Ray, Sujata Kumari, Anupama Pati, Payala Sahoo, A.K. Sahoo, Saurabh Singh, Tsunehiro Takeuchi, and S. Dash. “Tunable Magnetoelectronic Properties in Bi3+ Substituted YCrO3.” Physica B: Condensed Matter. Elsevier, 2024. https://doi.org/10.1016/j.physb.2024.416018."},"type":"journal_article","publication_identifier":{"issn":["0921-4526"]},"status":"public","_id":"18937","year":"2024","intvolume":" 685","department":[{"_id":"MaIb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T08:33:04Z","language":[{"iso":"eng"}],"scopus_import":"1","acknowledgement":"The authors would like to acknowledge MHRD, Government of India for financial support. The author is also thankful to RRCAT, Indore for providing XPS beamline-14 of Indus II to conduct experimental work.","publisher":"Elsevier","doi":"10.1016/j.physb.2024.416018","day":"15","OA_type":"closed access"},{"pmid":1,"quality_controlled":"1","file":[{"success":1,"relation":"main_file","creator":"dernst","checksum":"5bd62c7cb4287e3706a1d45d6ef61fd1","date_updated":"2025-01-29T08:43:16Z","date_created":"2025-01-29T08:43:16Z","file_size":720902,"access_level":"open_access","content_type":"application/pdf","file_name":"2024_PNAS_Springstein.pdf","file_id":"18939"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_status":"published","author":[{"id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","first_name":"Benjamin L","last_name":"Springstein","orcid":"0000-0002-3461-5391","full_name":"Springstein, Benjamin L"},{"first_name":"Joao A.","full_name":"Paulo, Joao A.","last_name":"Paulo"},{"last_name":"Park","full_name":"Park, Hankum","first_name":"Hankum"},{"first_name":"Kemardo","full_name":"Henry, Kemardo","last_name":"Henry"},{"first_name":"Eleanor","full_name":"Fleming, Eleanor","last_name":"Fleming"},{"full_name":"Feder, Zoë","last_name":"Feder","first_name":"Zoë"},{"full_name":"Harper, J. Wade","last_name":"Harper","first_name":"J. Wade"},{"first_name":"Ann","last_name":"Hochschild","full_name":"Hochschild, Ann"}],"article_number":"e2317453121","date_published":"2024-02-06T00:00:00Z","title":"Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics","oa_version":"Published Version","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","date_updated":"2025-05-14T11:02:52Z","issue":"6","month":"02","abstract":[{"text":"The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.","lang":"eng"}],"volume":121,"_id":"18938","status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"type":"journal_article","citation":{"ieee":"B. L. Springstein et al., “Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 6. National Academy of Sciences, 2024.","chicago":"Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2317453121.","mla":"Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 6, e2317453121, National Academy of Sciences, 2024, doi:10.1073/pnas.2317453121.","short":"B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W. Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW, Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 121(6), e2317453121.","apa":"Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder, Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2317453121","ama":"Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(6). doi:10.1073/pnas.2317453121"},"article_processing_charge":"No","intvolume":" 121","year":"2024","department":[{"_id":"MaLo"}],"external_id":{"pmid":["38289956"]},"language":[{"iso":"eng"}],"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T08:39:27Z","file_date_updated":"2025-01-29T08:43:16Z","oa":1,"ddc":["570"],"acknowledgement":"We thank S. L. Dove for valuable discussion and comments on the manuscript and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H., AG011085 to J.W.H., and GM132129 to J.A.P.","scopus_import":"1","OA_type":"hybrid","day":"06","doi":"10.1073/pnas.2317453121","publisher":"National Academy of Sciences"},{"department":[{"_id":"CaHe"}],"intvolume":" 13","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T08:48:34Z","oa":1,"file_date_updated":"2025-01-29T08:50:18Z","language":[{"iso":"eng"}],"OA_place":"publisher","ddc":["570"],"acknowledgement":"This work was funded by the Austrian Science Foundation (FWF) grants P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger, Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure 6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5, David Mörsdorf for critically reading the manuscript and help with data visualization, and the Core Facility for Cell Imaging and Ultrastructure Research of the University of Vienna for access to the confocal microscope.","scopus_import":"1","doi":"10.7554/elife.80803","publisher":"eLife Sciences Publications","day":"07","OA_type":"gold","DOAJ_listed":"1","publication_status":"published","quality_controlled":"1","file":[{"relation":"main_file","creator":"dernst","success":1,"checksum":"24548a184215d3f4547bba535ccfd7b1","date_updated":"2025-01-29T08:50:18Z","date_created":"2025-01-29T08:50:18Z","file_size":11855972,"file_name":"2024_eLife_Knabl.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"18941"}],"publication":"eLife","title":"Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator","date_published":"2024-02-07T00:00:00Z","author":[{"last_name":"Knabl","full_name":"Knabl, Paul","first_name":"Paul"},{"first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer"},{"first_name":"Autumn P","full_name":"Pomreinke, Autumn P","last_name":"Pomreinke"},{"first_name":"Bob","last_name":"Zimmermann","full_name":"Zimmermann, Bob"},{"first_name":"Katherine W","full_name":"Rogers, Katherine W","last_name":"Rogers"},{"first_name":"Daniel","full_name":"Čapek, Daniel","last_name":"Čapek"},{"first_name":"Patrick","last_name":"Müller","full_name":"Müller, Patrick"},{"first_name":"Grigory","last_name":"Genikhovich","full_name":"Genikhovich, Grigory"}],"article_type":"original","volume":13,"month":"02","abstract":[{"text":"BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.","lang":"eng"}],"date_updated":"2025-01-29T08:56:21Z","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"journal_article","publication_identifier":{"issn":["2050-084X"]},"article_processing_charge":"Yes","citation":{"ama":"Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 2024;13. doi:10.7554/elife.80803","apa":"Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek, D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.80803","ista":"Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13.","short":"P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek, P. Müller, G. Genikhovich, ELife 13 (2024).","mla":"Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.80803.","ieee":"P. Knabl et al., “Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator,” eLife, vol. 13. eLife Sciences Publications, 2024.","chicago":"Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.80803."},"status":"public","_id":"18940"},{"publication":"Marine Ecology Progress Series","quality_controlled":"1","page":"23-42","publication_status":"published","date_published":"2024-07-25T00:00:00Z","author":[{"id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise","orcid":"0000-0003-0371-9339","last_name":"Fouqueau","full_name":"Fouqueau, Louise"},{"full_name":"Reynes, L","last_name":"Reynes","first_name":"L"},{"first_name":"F","last_name":"Tempera","full_name":"Tempera, F"},{"first_name":"T","last_name":"Bajjouk","full_name":"Bajjouk, T"},{"full_name":"Blanfuné, A","last_name":"Blanfuné","first_name":"A"},{"first_name":"C","last_name":"Chevalier","full_name":"Chevalier, C"},{"full_name":"Laurans, M","last_name":"Laurans","first_name":"M"},{"last_name":"Mauger","full_name":"Mauger, S","first_name":"S"},{"full_name":"Sourisseau, M","last_name":"Sourisseau","first_name":"M"},{"first_name":"J","full_name":"Assis, J","last_name":"Assis"},{"first_name":"L","last_name":"Lévêque","full_name":"Lévêque, L"},{"full_name":"Valero, M","last_name":"Valero","first_name":"M"}],"title":"Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes","oa_version":"Submitted Version","abstract":[{"text":"Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria digitata located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.","lang":"eng"}],"month":"07","volume":740,"date_updated":"2025-01-29T09:12:34Z","article_type":"original","_id":"18944","status":"public","article_processing_charge":"No","citation":{"ama":"Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. 2024;740:23-42. doi:10.3354/meps14640","apa":"Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier, C., … Valero, M. (2024). Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. Inter-Research Science Center. https://doi.org/10.3354/meps14640","short":"L. Fouqueau, L. Reynes, F. Tempera, T. Bajjouk, A. Blanfuné, C. Chevalier, M. Laurans, S. Mauger, M. Sourisseau, J. Assis, L. Lévêque, M. Valero, Marine Ecology Progress Series 740 (2024) 23–42.","ista":"Fouqueau L, Reynes L, Tempera F, Bajjouk T, Blanfuné A, Chevalier C, Laurans M, Mauger S, Sourisseau M, Assis J, Lévêque L, Valero M. 2024. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. 740, 23–42.","chicago":"Fouqueau, Louise, L Reynes, F Tempera, T Bajjouk, A Blanfuné, C Chevalier, M Laurans, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” Marine Ecology Progress Series. Inter-Research Science Center, 2024. https://doi.org/10.3354/meps14640.","ieee":"L. Fouqueau et al., “Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes,” Marine Ecology Progress Series, vol. 740. Inter-Research Science Center, pp. 23–42, 2024.","mla":"Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” Marine Ecology Progress Series, vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:10.3354/meps14640."},"type":"journal_article","publication_identifier":{"issn":["0171-8630"],"eissn":["1616-1599"]},"main_file_link":[{"url":"https://inria.hal.science/hal-04624490/","open_access":"1"}],"department":[{"_id":"NiBa"}],"intvolume":" 740","year":"2024","OA_place":"repository","corr_author":"1","language":[{"iso":"eng"}],"oa":1,"date_created":"2025-01-29T09:09:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","OA_type":"green","day":"25","publisher":"Inter-Research Science Center","doi":"10.3354/meps14640"},{"acknowledgement":"R.M.C. and K.B.M. are grateful for support by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) (grants 2013/50724–5 and 2014/50897–0), Embrapii (Empresa Brasileira de Pesquisa e Inovação Industrial), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) (grant 465651/2014–3) and Aché Laboratórios Farmacêuticos. R.M.C. and O.G. are also grateful for support by the Structural Genomics Consortium, a registered charity (1097737) that receives funds from AbbVie, Bayer AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genentech, Genome Canada through the Ontario Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN Grant 875510), Janssen, Merck KGaA, Merck & Co., Pfizer, Takeda, and Wellcome. B.L. and M.H. are grateful for support from the Swedish Research Council, Swedish Cancer Society, Karolinska Institutet and The Mark Foundation for Cancer Research. R.A.M.S. (2016/25320–6 and 2018/23322–7), A.S.S. (2019/14275–8), S.N.S.V (2018/09475–5), V.M.A. (2022/00743–2) and M.R.C. (2021/04853–4) were recipients of fellowships from the Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP. C.V.R. (88887.146077/2017–00), J.E.T. (88887.373547/2019–00) and P.Z.R (88887.136432/2017–00) were the recipient of fellowships from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES.\r\nWe thank all members of CQMED-UNICAMP for their help and support. We thank the staff of the Life Sciences Core Facility (LaCTAD) at UNICAMP for the Genomics and Mass Spectrometry analysis. We thank the NMR facility at UNICAMP Chemistry Institute for its assistance. We thank the staff at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P41 GM103403). The Pilatus 6M detector on the 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source; a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. We thank Diamond Light Source for access to beamline I24. The authors thank Tammy Havener (SGC-UNC), Abid Hussain Sayyid (KI), and Yiqiu Yang (KI) for valuable discussions and technical support.","scopus_import":"1","doi":"10.1021/acs.jmedchem.3c02250","publisher":"American Chemical Society","OA_type":"closed access","day":"23","year":"2024","department":[{"_id":"CaBe"}],"intvolume":" 67","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T09:14:19Z","language":[{"iso":"eng"}],"external_id":{"pmid":["38780468"]},"article_type":"original","month":"05","volume":67,"abstract":[{"lang":"eng","text":"Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division."}],"issue":"11","date_updated":"2025-01-29T09:19:15Z","oa_version":"None","type":"journal_article","publication_identifier":{"issn":["0022-2623"],"eissn":["1520-4804"]},"article_processing_charge":"No","citation":{"chicago":"Souza Gama, Fernando H. de, Luiz A. Dutra, Michael Hawgood, Caio Vinícius dos Reis, Ricardo A. M. Serafim, Marcos A. Ferreira, Bruno V. M. Teodoro, et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry. American Chemical Society, 2024. https://doi.org/10.1021/acs.jmedchem.3c02250.","ieee":"F. H. de Souza Gama et al., “Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε,” Journal of Medicinal Chemistry, vol. 67, no. 11. American Chemical Society, pp. 8609–8629, 2024.","mla":"de Souza Gama, Fernando H., et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry, vol. 67, no. 11, American Chemical Society, 2024, pp. 8609–29, doi:10.1021/acs.jmedchem.3c02250.","short":"F.H. de Souza Gama, L.A. Dutra, M. Hawgood, C.V. dos Reis, R.A.M. Serafim, M.A. Ferreira, B.V.M. Teodoro, J.E. Takarada, A.S. Santiago, D.-I. Balourdas, A.-S. Nilsson, B. Urien, V.M. Almeida, C. Gileadi, P.Z. Ramos, A.P. Testa Salmazo, S.N.S. Vasconcelos, M.R. Cunha, S. Mueller, S. Knapp, K.B. Massirer, J.M. Elkins, O. Gileadi, A. Mascarello, B.B.L.G. Lemmens, C.R.W. Guimarães, H. Azevedo, R.M. Couñago, Journal of Medicinal Chemistry 67 (2024) 8609–8629.","ista":"de Souza Gama FH, Dutra LA, Hawgood M, dos Reis CV, Serafim RAM, Ferreira MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas D-I, Nilsson A-S, Urien B, Almeida VM, Gileadi C, Ramos PZ, Testa Salmazo AP, Vasconcelos SNS, Cunha MR, Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG, Guimarães CRW, Azevedo H, Couñago RM. 2024. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 67(11), 8609–8629.","apa":"de Souza Gama, F. H., Dutra, L. A., Hawgood, M., dos Reis, C. V., Serafim, R. A. M., Ferreira, M. A., … Couñago, R. M. (2024). Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. American Chemical Society. https://doi.org/10.1021/acs.jmedchem.3c02250","ama":"de Souza Gama FH, Dutra LA, Hawgood M, et al. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 2024;67(11):8609-8629. doi:10.1021/acs.jmedchem.3c02250"},"status":"public","_id":"18945","publication_status":"published","page":"8609-8629","quality_controlled":"1","pmid":1,"publication":"Journal of Medicinal Chemistry","title":"Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε","date_published":"2024-05-23T00:00:00Z","author":[{"first_name":"Fernando H.","full_name":"de Souza Gama, Fernando H.","last_name":"de Souza Gama"},{"first_name":"Luiz A.","full_name":"Dutra, Luiz A.","last_name":"Dutra"},{"first_name":"Michael","full_name":"Hawgood, Michael","last_name":"Hawgood"},{"first_name":"Caio Vinícius","full_name":"dos Reis, Caio Vinícius","last_name":"dos Reis"},{"full_name":"Serafim, Ricardo A. M.","last_name":"Serafim","first_name":"Ricardo A. M."},{"last_name":"Ferreira","full_name":"Ferreira, Marcos A.","first_name":"Marcos A."},{"last_name":"Teodoro","full_name":"Teodoro, Bruno V. M.","first_name":"Bruno V. M."},{"first_name":"Jéssica Emi","full_name":"Takarada, Jéssica Emi","last_name":"Takarada"},{"first_name":"André S.","last_name":"Santiago","full_name":"Santiago, André S."},{"full_name":"Balourdas, Dimitrios-Ilias","last_name":"Balourdas","first_name":"Dimitrios-Ilias"},{"full_name":"Nilsson, Ann-Sofie","last_name":"Nilsson","first_name":"Ann-Sofie"},{"last_name":"Urien","full_name":"Urien, Bruno","first_name":"Bruno"},{"first_name":"Vitor M.","full_name":"Almeida, Vitor M.","last_name":"Almeida"},{"full_name":"Gileadi, Carina","last_name":"Gileadi","first_name":"Carina"},{"first_name":"Priscila Z.","full_name":"Ramos, Priscila Z.","last_name":"Ramos"},{"last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P"},{"full_name":"Vasconcelos, Stanley N. S.","last_name":"Vasconcelos","first_name":"Stanley N. S."},{"last_name":"Cunha","full_name":"Cunha, Micael R.","first_name":"Micael R."},{"first_name":"Susanne","full_name":"Mueller, Susanne","last_name":"Mueller"},{"first_name":"Stefan","last_name":"Knapp","full_name":"Knapp, Stefan"},{"last_name":"Massirer","full_name":"Massirer, Katlin B.","first_name":"Katlin B."},{"first_name":"Jonathan M.","full_name":"Elkins, Jonathan M.","last_name":"Elkins"},{"first_name":"Opher","last_name":"Gileadi","full_name":"Gileadi, Opher"},{"first_name":"Alessandra","last_name":"Mascarello","full_name":"Mascarello, Alessandra"},{"first_name":"Bennie B. L. G.","full_name":"Lemmens, Bennie B. L. G.","last_name":"Lemmens"},{"first_name":"Cristiano R. W.","last_name":"Guimarães","full_name":"Guimarães, Cristiano R. W."},{"last_name":"Azevedo","full_name":"Azevedo, Hatylas","first_name":"Hatylas"},{"first_name":"Rafael M.","full_name":"Couñago, Rafael M.","last_name":"Couñago"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12910"}],"department":[{"_id":"RoSe"}],"year":"2024","intvolume":" 215","external_id":{"arxiv":["2304.12910"]},"language":[{"iso":"eng"}],"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T10:30:08Z","oa":1,"acknowledgement":"It is our pleasure to thank Marco Falconi, Nataša Pavlović, Peter Pickl, Robert Seiringer and Avy Soffer for the collaboration on the works [11, 13, 14, 21, 33, 39]. L.B. was supported by the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111). N.L. acknowledges support from the Swiss National Science Foundation through the NCCR SwissMap and funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101024712. S.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project number 512258249.","scopus_import":"1","alternative_title":["Fundamental Theories of Physics"],"day":"04","OA_type":"green","series_title":"FTPH","doi":"10.1007/978-3-031-45434-9_22","arxiv":1,"editor":[{"last_name":"Bassi","full_name":"Bassi, Angelo","first_name":"Angelo"},{"last_name":"Goldstein","full_name":"Goldstein, Sheldon","first_name":"Sheldon"},{"last_name":"Tumulka","full_name":"Tumulka, Roderich","first_name":"Roderich"},{"first_name":"Nino","last_name":"Zanghi","full_name":"Zanghi, Nino"}],"publisher":"Springer Nature","quality_controlled":"1","publication":"Physics and the Nature of Reality","page":"307-321","publication_status":"published","place":"Cham","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","last_name":"Bossmann","orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea"},{"last_name":"Leopold","full_name":"Leopold, Nikolai","first_name":"Nikolai"},{"first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas"},{"last_name":"Petrat","full_name":"Petrat, Sören","first_name":"Sören"}],"date_published":"2024-02-04T00:00:00Z","title":"Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications","oa_version":"Preprint","date_updated":"2025-01-29T10:35:10Z","abstract":[{"text":"We consider a gas of N bosons with interactions in the mean-field scaling regime. We review a recent proof of the asymptotic expansion of its spectrum and eigenstates and two applications of this result, namely the derivation of an Edgeworth expansion for fluctuations of one-body operators and the computation of the binding energy of an inhomogeneous Bose gas to any order. Finally, we collect related results for the dynamics of the weakly interacting Bose gas and for the regularized Nelson model.","lang":"eng"}],"month":"02","volume":215,"_id":"18948","status":"public","publication_identifier":{"isbn":["9783031454332"],"eisbn":["9783031454349"],"eissn":["2365-6425"],"issn":["0168-1222"]},"type":"book_chapter","citation":{"ama":"Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In: Bassi A, Goldstein S, Tumulka R, Zanghi N, eds. Physics and the Nature of Reality. Vol 215. FTPH. Cham: Springer Nature; 2024:307-321. doi:10.1007/978-3-031-45434-9_22","apa":"Bossmann, L., Leopold, N., Mitrouskas, D. J., & Petrat, S. (2024). Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In A. Bassi, S. Goldstein, R. Tumulka, & N. Zanghi (Eds.), Physics and the Nature of Reality (Vol. 215, pp. 307–321). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-45434-9_22","ista":"Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. 2024.Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In: Physics and the Nature of Reality. Fundamental Theories of Physics, vol. 215, 307–321.","short":"L. Bossmann, N. Leopold, D.J. Mitrouskas, S. Petrat, in:, A. Bassi, S. Goldstein, R. Tumulka, N. Zanghi (Eds.), Physics and the Nature of Reality, Springer Nature, Cham, 2024, pp. 307–321.","mla":"Bossmann, Lea, et al. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” Physics and the Nature of Reality, edited by Angelo Bassi et al., vol. 215, Springer Nature, 2024, pp. 307–21, doi:10.1007/978-3-031-45434-9_22.","chicago":"Bossmann, Lea, Nikolai Leopold, David Johannes Mitrouskas, and Sören Petrat. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” In Physics and the Nature of Reality, edited by Angelo Bassi, Sheldon Goldstein, Roderich Tumulka, and Nino Zanghi, 215:307–21. FTPH. Cham: Springer Nature, 2024. https://doi.org/10.1007/978-3-031-45434-9_22.","ieee":"L. Bossmann, N. Leopold, D. J. Mitrouskas, and S. Petrat, “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications,” in Physics and the Nature of Reality, vol. 215, A. Bassi, S. Goldstein, R. Tumulka, and N. Zanghi, Eds. Cham: Springer Nature, 2024, pp. 307–321."},"article_processing_charge":"No"},{"type":"journal_article","publication_identifier":{"issn":["2752-938X"]},"article_processing_charge":"Yes","citation":{"apa":"Stankowski, S., Cutter, A. D., Satokangas, I., Lerch, B. A., Rolland, J., Smadja, C. M., … Kulmuni, J. (2024). Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzae001","ama":"Stankowski S, Cutter AD, Satokangas I, et al. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. 2024;3(1). doi:10.1093/evolinnean/kzae001","mla":"Stankowski, Sean, et al. “Toward the Integration of Speciation Research.” Evolutionary Journal of the Linnean Society, vol. 3, no. 1, kzae001, Oxford University Press, 2024, doi:10.1093/evolinnean/kzae001.","chicago":"Stankowski, Sean, Asher D Cutter, Ina Satokangas, Brian A Lerch, Jonathan Rolland, Carole M Smadja, J Carolina Segami Marzal, et al. “Toward the Integration of Speciation Research.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2024. https://doi.org/10.1093/evolinnean/kzae001.","ieee":"S. Stankowski et al., “Toward the integration of speciation research,” Evolutionary Journal of the Linnean Society, vol. 3, no. 1. Oxford University Press, 2024.","ista":"Stankowski S, Cutter AD, Satokangas I, Lerch BA, Rolland J, Smadja CM, Segami Marzal JC, Cooney CR, Feulner PGD, Domingos FMCB, North HL, Yamaguchi R, Butlin RK, Wolf JBW, Coughlan J, Heidbreder P, Hernández-Gutiérrez R, Barnard-Kubow KB, Peede D, Rancilhac L, Salvador RB, Thompson KA, Stacy EA, Moyle LC, Garlovsky MD, Maulana A, Kantelinen A, Cacho NI, Schneemann H, Domínguez M, Dopman EB, Lohse K, Rometsch SJ, Comeault AA, Merrill RM, Scordato ESC, Singhal S, Pärssinen V, Lackey ACR, Kumar S, Meier JI, Barton NH, Fraisse C, Ravinet M, Kulmuni J. 2024. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. 3(1), kzae001.","short":"S. Stankowski, A.D. Cutter, I. Satokangas, B.A. Lerch, J. Rolland, C.M. Smadja, J.C. Segami Marzal, C.R. Cooney, P.G.D. Feulner, F.M.C.B. Domingos, H.L. North, R. Yamaguchi, R.K. Butlin, J.B.W. Wolf, J. Coughlan, P. Heidbreder, R. Hernández-Gutiérrez, K.B. Barnard-Kubow, D. Peede, L. Rancilhac, R.B. Salvador, K.A. Thompson, E.A. Stacy, L.C. Moyle, M.D. Garlovsky, A. Maulana, A. Kantelinen, N.I. Cacho, H. Schneemann, M. Domínguez, E.B. Dopman, K. Lohse, S.J. Rometsch, A.A. Comeault, R.M. Merrill, E.S.C. Scordato, S. Singhal, V. Pärssinen, A.C.R. Lackey, S. Kumar, J.I. Meier, N.H. Barton, C. Fraisse, M. Ravinet, J. Kulmuni, Evolutionary Journal of the Linnean Society 3 (2024)."},"_id":"18949","status":"public","article_type":"original","volume":3,"abstract":[{"text":"Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.","lang":"eng"}],"month":"02","issue":"1","date_updated":"2025-01-29T10:55:54Z","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"title":"Toward the integration of speciation research","date_published":"2024-02-16T00:00:00Z","article_number":"kzae001","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Cutter, Asher D","last_name":"Cutter","first_name":"Asher D"},{"last_name":"Satokangas","full_name":"Satokangas, Ina","first_name":"Ina"},{"first_name":"Brian A","full_name":"Lerch, Brian A","last_name":"Lerch"},{"last_name":"Rolland","full_name":"Rolland, Jonathan","first_name":"Jonathan"},{"full_name":"Smadja, Carole M","last_name":"Smadja","first_name":"Carole M"},{"first_name":"J Carolina","last_name":"Segami Marzal","full_name":"Segami Marzal, J Carolina"},{"last_name":"Cooney","full_name":"Cooney, Christopher R","first_name":"Christopher R"},{"full_name":"Feulner, Philine G D","last_name":"Feulner","first_name":"Philine G D"},{"first_name":"Fabricius Maia Chaves Bicalho","full_name":"Domingos, Fabricius Maia Chaves Bicalho","last_name":"Domingos"},{"last_name":"North","full_name":"North, Henry L","first_name":"Henry L"},{"first_name":"Ryo","full_name":"Yamaguchi, Ryo","last_name":"Yamaguchi"},{"first_name":"Roger K","full_name":"Butlin, Roger K","last_name":"Butlin"},{"first_name":"Jochen B W","full_name":"Wolf, Jochen B W","last_name":"Wolf"},{"first_name":"Jenn","full_name":"Coughlan, Jenn","last_name":"Coughlan"},{"full_name":"Heidbreder, Patrick","last_name":"Heidbreder","first_name":"Patrick"},{"last_name":"Hernández-Gutiérrez","full_name":"Hernández-Gutiérrez, Rebeca","first_name":"Rebeca"},{"first_name":"Karen B","full_name":"Barnard-Kubow, Karen B","last_name":"Barnard-Kubow"},{"last_name":"Peede","full_name":"Peede, David","first_name":"David"},{"last_name":"Rancilhac","full_name":"Rancilhac, Loïs","first_name":"Loïs"},{"full_name":"Salvador, Rodrigo Brincalepe","last_name":"Salvador","first_name":"Rodrigo Brincalepe"},{"full_name":"Thompson, Ken A","last_name":"Thompson","first_name":"Ken A"},{"first_name":"Elizabeth A","full_name":"Stacy, Elizabeth A","last_name":"Stacy"},{"first_name":"Leonie C","full_name":"Moyle, Leonie C","last_name":"Moyle"},{"first_name":"Martin D","last_name":"Garlovsky","full_name":"Garlovsky, Martin D"},{"first_name":"Arif","last_name":"Maulana","full_name":"Maulana, Arif"},{"first_name":"Annina","last_name":"Kantelinen","full_name":"Kantelinen, Annina"},{"first_name":"N Ivalú","full_name":"Cacho, N Ivalú","last_name":"Cacho"},{"first_name":"Hilde","full_name":"Schneemann, Hilde","last_name":"Schneemann"},{"first_name":"Marisol","full_name":"Domínguez, Marisol","last_name":"Domínguez"},{"last_name":"Dopman","full_name":"Dopman, Erik B","first_name":"Erik B"},{"first_name":"Konrad","full_name":"Lohse, Konrad","last_name":"Lohse"},{"full_name":"Rometsch, Sina J","last_name":"Rometsch","first_name":"Sina J"},{"first_name":"Aaron A","full_name":"Comeault, Aaron A","last_name":"Comeault"},{"full_name":"Merrill, Richard M","last_name":"Merrill","first_name":"Richard M"},{"first_name":"Elizabeth S C","full_name":"Scordato, Elizabeth S C","last_name":"Scordato"},{"full_name":"Singhal, Sonal","last_name":"Singhal","first_name":"Sonal"},{"full_name":"Pärssinen, Varpu","last_name":"Pärssinen","first_name":"Varpu"},{"full_name":"Lackey, Alycia C R","last_name":"Lackey","first_name":"Alycia C R"},{"last_name":"Kumar","full_name":"Kumar, Sanghamitra","first_name":"Sanghamitra"},{"first_name":"Joana I","full_name":"Meier, Joana I","last_name":"Meier"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"first_name":"Jonna","full_name":"Kulmuni, Jonna","last_name":"Kulmuni"}],"publication_status":"published","quality_controlled":"1","publication":"Evolutionary Journal of the Linnean 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We are also grateful to everyone who applied to attend the workshop.\r\nFunding for the workshop was provided by the European Society for Evolutionary Biology through the Special Topic Network (STN) funding scheme.","scopus_import":"1","date_created":"2025-01-29T10:38:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2025-01-29T10:52:40Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","intvolume":" 3","year":"2024","department":[{"_id":"NiBa"}]},{"OA_type":"green","day":"01","arxiv":1,"doi":"10.1137/1.9781611977936.16","publisher":"Society for Industrial and Applied Mathematics","acknowledgement":"This work is a part of projects CUTACOMBS (Ma. Pilipczuk), BOBR (Mi. Pilipczuk), and VAMOS (K. S. Thejaswini) that have received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant agreements No 714704, 948057, and 101020093, respectively. Ma. Pilipczuk is also partially supported by Polish National Science Centre SONATA BIS-12 grant number 2022/46/E/ST6/00143.","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["2310.20433"]},"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T11:55:50Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.20433","open_access":"1"}],"ec_funded":1,"year":"2024","department":[{"_id":"ToHe"}],"project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"_id":"18955","status":"public","type":"conference","publication_identifier":{"isbn":["9781611977936"]},"article_processing_charge":"No","citation":{"apa":"Casares, A., Pilipczuk, M., Pilipczuk, M., Souza, U. S., & Thejaswini, K. S. (2024). Simple and tight complexity lower bounds for solving Rabin games. In 2024 Symposium on Simplicity in Algorithms (pp. 160–167). Alexandria, VA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977936.16","ama":"Casares A, Pilipczuk M, Pilipczuk M, Souza US, Thejaswini KS. Simple and tight complexity lower bounds for solving Rabin games. In: 2024 Symposium on Simplicity in Algorithms. Society for Industrial and Applied Mathematics; 2024:160-167. doi:10.1137/1.9781611977936.16","chicago":"Casares, Antonio, Marcin Pilipczuk, Michał Pilipczuk, Uéverton S. Souza, and K. S. Thejaswini. “Simple and Tight Complexity Lower Bounds for Solving Rabin Games.” In 2024 Symposium on Simplicity in Algorithms, 160–67. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977936.16.","ieee":"A. Casares, M. Pilipczuk, M. Pilipczuk, U. S. Souza, and K. S. Thejaswini, “Simple and tight complexity lower bounds for solving Rabin games,” in 2024 Symposium on Simplicity in Algorithms, Alexandria, VA, United States, 2024, pp. 160–167.","mla":"Casares, Antonio, et al. “Simple and Tight Complexity Lower Bounds for Solving Rabin Games.” 2024 Symposium on Simplicity in Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 160–67, doi:10.1137/1.9781611977936.16.","short":"A. Casares, M. Pilipczuk, M. Pilipczuk, U.S. Souza, K.S. Thejaswini, in:, 2024 Symposium on Simplicity in Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 160–167.","ista":"Casares A, Pilipczuk M, Pilipczuk M, Souza US, Thejaswini KS. 2024. Simple and tight complexity lower bounds for solving Rabin games. 2024 Symposium on Simplicity in Algorithms. SOSA: Symposium on Simplicity in Algorithms, 160–167."},"oa_version":"Preprint","abstract":[{"text":"We give a simple proof that assuming the Exponential Time Hypothesis (ETH), determining the winner of a Rabin game cannot be done in time 2o(k log k) · nO(1), where k is the number of pairs of vertex subsets involved in the winning condition and n is the vertex count of the game graph. While this result follows from the lower bounds provided by Calude et al [SIAM J. Comp. 2022], our reduction is considerably simpler and arguably provides more insight into the complexity of the problem. In fact, the analogous lower bounds discussed by Calude et al, for solving Muller games and multidimensional parity games, follow as simple corollaries of our approach. Our reduction also highlights the usefulness of a certain pivot problem — Permutation SAT — which may be of independent interest.","lang":"eng"}],"month":"01","date_updated":"2025-04-14T07:55:54Z","date_published":"2024-01-01T00:00:00Z","author":[{"first_name":"Antonio","full_name":"Casares, Antonio","last_name":"Casares"},{"full_name":"Pilipczuk, Marcin","last_name":"Pilipczuk","first_name":"Marcin"},{"first_name":"Michał","last_name":"Pilipczuk","full_name":"Pilipczuk, Michał"},{"last_name":"Souza","full_name":"Souza, Uéverton S.","first_name":"Uéverton S."},{"last_name":"Thejaswini","full_name":"Thejaswini, K. S.","id":"3807fb92-fdc1-11ee-bb4a-b4d8a431c753","first_name":"K. S."}],"title":"Simple and tight complexity lower bounds for solving Rabin games","conference":{"name":"SOSA: Symposium on Simplicity in Algorithms","end_date":"2024-01-10","start_date":"2024-01-08","location":"Alexandria, VA, United States"},"quality_controlled":"1","publication":"2024 Symposium on Simplicity in Algorithms","publication_status":"published","page":"160-167"},{"department":[{"_id":"FrLo"}],"year":"2024","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.06439"}],"date_created":"2025-01-29T12:22:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["2303.06439"],"isi":["001442947000143"]},"OA_place":"repository","corr_author":"1","arxiv":1,"doi":"10.1109/icip51287.2024.10647499","publisher":"IEEE","day":"01","OA_type":"green","publication_status":"published","page":"977-983","quality_controlled":"1","publication":"2024 IEEE International Conference on Image Processing","title":"Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image","conference":{"name":"ICIP: International Conference on Image Processing","end_date":"2024-10-30","start_date":"2024-10-27","location":"Abu Dhabi, United Arab Emirates"},"date_published":"2024-11-01T00:00:00Z","author":[{"last_name":"Demirel","full_name":"Demirel, Berker","id":"8b4bc47f-3200-11ee-973b-8f0e7be21a9f","first_name":"Berker"},{"last_name":"Ozkan","full_name":"Ozkan, Huseyin","first_name":"Huseyin"}],"related_material":{"link":[{"url":"https://github.com/berkerdemirel/decompl","relation":"software"}]},"month":"11","abstract":[{"lang":"eng","text":"Group Activity Recognition (GAR) aims to detect the activity performed by multiple actors in a scene. Prior works model the spatio-temporal features based on the RGB, optical flow or keypoint data types. On the contrary, our hypothesis is that by only using the RGB data without temporality, the performance can be maintained with a negligible loss in accuracy. To that end, we propose a novel GAR technique for volleyball videos, DECOMPL, which consists of two complementary branches. In the visual branch, it extracts the features using attention pooling. In the coordinate branch, it considers the configuration of the players and extracts the spatial information from the box coordinates. Moreover, we analyzed the Volleyball dataset that the recent literature is mostly based on, and systematically reannotated it to emphasize the group concept. Experimental results demonstrated the effectiveness of the proposed model DECOMPL, which delivered the best/second best GAR performance with the reannotations/original annotations among the comparable state-of-the-art methods. Code and new annotations are available at GitHub: https://github.com/berkerdemirel/decompl"}],"date_updated":"2025-09-09T12:13:12Z","oa_version":"Preprint","isi":1,"type":"conference","publication_identifier":{"eisbn":["9798350349399"],"eissn":["2381-8549"]},"article_processing_charge":"No","citation":{"ieee":"B. Demirel and H. Ozkan, “Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image,” in 2024 IEEE International Conference on Image Processing, Abu Dhabi, United Arab Emirates, 2024, pp. 977–983.","chicago":"Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning with Attention Pooling for Group Activity Recognition from a Single Volleyball Image.” In 2024 IEEE International Conference on Image Processing, 977–83. IEEE, 2024. https://doi.org/10.1109/icip51287.2024.10647499.","mla":"Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning with Attention Pooling for Group Activity Recognition from a Single Volleyball Image.” 2024 IEEE International Conference on Image Processing, IEEE, 2024, pp. 977–83, doi:10.1109/icip51287.2024.10647499.","short":"B. Demirel, H. Ozkan, in:, 2024 IEEE International Conference on Image Processing, IEEE, 2024, pp. 977–983.","ista":"Demirel B, Ozkan H. 2024. Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. 2024 IEEE International Conference on Image Processing. ICIP: International Conference on Image Processing, 977–983.","apa":"Demirel, B., & Ozkan, H. (2024). Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. In 2024 IEEE International Conference on Image Processing (pp. 977–983). Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/icip51287.2024.10647499","ama":"Demirel B, Ozkan H. Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. In: 2024 IEEE International Conference on Image Processing. IEEE; 2024:977-983. doi:10.1109/icip51287.2024.10647499"},"_id":"18956","status":"public"},{"author":[{"last_name":"Blackshear","full_name":"Blackshear, Sam","first_name":"Sam"},{"last_name":"Chursin","full_name":"Chursin, Andrey","first_name":"Andrey"},{"last_name":"Danezis","full_name":"Danezis, George","first_name":"George"},{"first_name":"Anastasios","full_name":"Kichidis, Anastasios","last_name":"Kichidis"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"last_name":"Li","full_name":"Li, Xun","first_name":"Xun"},{"full_name":"Logan, Mark","last_name":"Logan","first_name":"Mark"},{"first_name":"Ashok","full_name":"Menon, Ashok","last_name":"Menon"},{"last_name":"Nowacki","full_name":"Nowacki, Todd","first_name":"Todd"},{"last_name":"Sonnino","full_name":"Sonnino, Alberto","first_name":"Alberto"},{"first_name":"Brandon","full_name":"Williams, Brandon","last_name":"Williams"},{"first_name":"Lu","full_name":"Zhang, Lu","last_name":"Zhang"}],"date_published":"2024-12-09T00:00:00Z","title":"Sui Lutris: A blockchain combining broadcast and consensus","conference":{"location":"Salt Lake City, UT, United States","start_date":"2024-10-14","name":"CCS: Conference on Computer and Communications Security","end_date":"2024-10-18"},"quality_controlled":"1","publication":"Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security","page":"2606-2620","publication_status":"published","status":"public","_id":"18957","publication_identifier":{"isbn":["9798400706363"]},"type":"conference","citation":{"mla":"Blackshear, Sam, et al. “Sui Lutris: A Blockchain Combining Broadcast and Consensus.” Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, ACM, 2024, pp. 2606–20, doi:10.1145/3658644.3670286.","ieee":"S. Blackshear et al., “Sui Lutris: A blockchain combining broadcast and consensus,” in Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, Salt Lake City, UT, United States, 2024, pp. 2606–2620.","chicago":"Blackshear, Sam, Andrey Chursin, George Danezis, Anastasios Kichidis, Eleftherios Kokoris Kogias, Xun Li, Mark Logan, et al. “Sui Lutris: A Blockchain Combining Broadcast and Consensus.” In Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, 2606–20. ACM, 2024. https://doi.org/10.1145/3658644.3670286.","ista":"Blackshear S, Chursin A, Danezis G, Kichidis A, Kokoris Kogias E, Li X, Logan M, Menon A, Nowacki T, Sonnino A, Williams B, Zhang L. 2024. Sui Lutris: A blockchain combining broadcast and consensus. Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 2606–2620.","short":"S. Blackshear, A. Chursin, G. Danezis, A. Kichidis, E. Kokoris Kogias, X. Li, M. Logan, A. Menon, T. Nowacki, A. Sonnino, B. Williams, L. Zhang, in:, Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security, ACM, 2024, pp. 2606–2620.","apa":"Blackshear, S., Chursin, A., Danezis, G., Kichidis, A., Kokoris Kogias, E., Li, X., … Zhang, L. (2024). Sui Lutris: A blockchain combining broadcast and consensus. In Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security (pp. 2606–2620). Salt Lake City, UT, United States: ACM. https://doi.org/10.1145/3658644.3670286","ama":"Blackshear S, Chursin A, Danezis G, et al. Sui Lutris: A blockchain combining broadcast and consensus. In: Proceedings of the 2024 on ACM SIGSAC Conference on Computer and Communications Security. ACM; 2024:2606-2620. doi:10.1145/3658644.3670286"},"article_processing_charge":"No","isi":1,"oa_version":"Preprint","date_updated":"2025-09-09T12:13:55Z","abstract":[{"text":"Sui Lutris is the first smart-contract platform to sustainably achieve sub-second finality. It achieves this significant decrease by employing consensusless agreement not only for simple payments but for a large variety of transactions. Unlike prior work, Sui Lutris neither compromises expressiveness nor throughput and can run perpetually without restarts. Sui Lutris achieves this by safely integrating consensuless agreement with a high-throughput consensus protocol that is invoked out of the critical finality path but ensures that when a transaction is at risk of inconsistent concurrent accesses, its settlement is delayed until the total ordering is resolved. Building such a hybrid architecture is especially delicate during reconfiguration events, where the system needs to preserve the safety of the consensusless path without compromising the long-term liveness of potentially misconfigured clients. We thus develop a novel reconfiguration protocol, the first to provably show the safe and efficient reconfiguration of a consensusless blockchain. Sui Lutris is currently running in production and underpins the Sui smart-contract platform. Combined with the use of Objects instead of accounts it enables the safe execution of smart contracts that expose objects as a first-class resource. In our experiments Sui Lutris achieves latency lower than 0.5 seconds for throughput up to 5,000 certificates per second (150k ops/s with transaction blocks), compared to the state-of-the-art real-world consensus latencies of 3 seconds. Furthermore, it gracefully handles validators crash-recovery and does not suffer visible performance degradation during reconfiguration.","lang":"eng"}],"month":"12","external_id":{"arxiv":["2310.18042"],"isi":["001436367300178"]},"language":[{"iso":"eng"}],"OA_place":"repository","date_created":"2025-01-29T12:42:21Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.18042","open_access":"1"}],"year":"2024","department":[{"_id":"ElKo"}],"OA_type":"hybrid","day":"09","doi":"10.1145/3658644.3670286","arxiv":1,"publisher":"ACM","acknowledgement":"This work is funded by MystenLabs. We thank the Mysten Labs Engineering teams for valuable feedback broadly, and specifically Dmitry Perelman and Todd Fiala for managing the implementation effort. A number of folks contributed to specific aspects of the implementation of Sui Lutris (amongst many other contributions to the overall blockchain): Francois Garillot, Laura Makdah, Mingwei Tian, Andrew Schran, Sadhan Sood and William Smith implemented and optimized aspects of both Sui Lutris and Narwhal / Bullshark consensus; Alonso de Gortari oversaw the cryptoeconomics of the blockchain, and Emma Zhong, Ade Adepoju, Tim Zakia and Dario Russi designed and implemented staking and gas mechanisms. Adam Welc designed several Move tools and provided great feedback on the manuscript. We also extend our thanks to Patrick Kuo, Ge Gao, Chris Li, and Arun Koshy for their work on the Sui Lutris SDK, clients, and RPC layer; Kostas Chalkias, Jonas Lindstrøm, and Joy Wang built cryptographic components."},{"date_published":"2024-04-18T00:00:00Z","author":[{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Warzel, Simone","last_name":"Warzel","first_name":"Simone"}],"language":[{"iso":"eng"}],"title":"Many-body quantum systems","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T13:09:28Z","publication":"Oberwolfach Reports","quality_controlled":"1","department":[{"_id":"RoSe"}],"year":"2024","intvolume":" 20","page":"2247-2302","publication_status":"published","_id":"18958","day":"18","status":"public","publisher":"EMS Press","article_processing_charge":"No","citation":{"short":"C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 20 (2024) 2247–2302.","ista":"Hainzl C, Schlein B, Seiringer R, Warzel S. 2024. Many-body quantum systems. Oberwolfach Reports. 20(3), 2247–2302.","ieee":"C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,” Oberwolfach Reports, vol. 20, no. 3. EMS Press, pp. 2247–2302, 2024.","chicago":"Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel. “Many-Body Quantum Systems.” Oberwolfach Reports. EMS Press, 2024. https://doi.org/10.4171/owr/2023/39.","mla":"Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports, vol. 20, no. 3, EMS Press, 2024, pp. 2247–302, doi:10.4171/owr/2023/39.","ama":"Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach Reports. 2024;20(3):2247-2302. doi:10.4171/owr/2023/39","apa":"Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2024). Many-body quantum systems. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2023/39"},"type":"journal_article","publication_identifier":{"eissn":["1660-8941"],"issn":["1660-8933"]},"doi":"10.4171/owr/2023/39","acknowledgement":"The MFO and the workshop organizers would like to thank the National Science Foundation for supporting the participation of junior researchers in the workshop by the grant DMS-2230648, “US Junior Oberwolfach Fellows”.","oa_version":"None","volume":20,"abstract":[{"lang":"eng","text":"This workshop brought together experts on the analysis of quantum many-body problems and quantum statistical mechanics, with the goal of discussing the state-of-the-art of the field, recent developments as well as challenges for the future. The main topics of discussion concerned the equilibrium and dynamical behavior of (bosonic or fermionic) quantum gases, quantum spin systems, as well as quantum field theory models like the Nelson or Fröhlich model."}],"month":"04","issue":"3","date_updated":"2025-01-29T13:19:06Z","article_type":"original"},{"acknowledgement":"We thank Raluca-Georgia Diugan for her initial contributions and support afterward.\r\nThis research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/F85.","ddc":["000"],"doi":"10.56553/popets-2024-0134","publisher":"Privacy Enhancing Technologies Symposium Advisory Board","day":"01","OA_type":"gold","intvolume":" 2024","year":"2024","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"project":[{"_id":"34a34d57-11ca-11ed-8bc3-a2688a8724e1","name":"Security and Privacy by Design for Complex Systems","grant_number":"F8509"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-29T13:39:34Z","oa":1,"file_date_updated":"2025-01-29T13:44:47Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","article_type":"original","abstract":[{"text":"Automated contact tracing (ACT) emerged as a promising measure to curb the spread of Covid-19. Users enable ACT on their smartphones to automatically record contacts with other users. If a user tests positive for the disease, they report their diagnosis to alert their contacts.\r\nDesigning effective ACT protocols is challenging since they need to be efficient and secure while also ensuring users' privacy. As ACT protocols necessarily leak some information by design, defining privacy is difficult. For example, a user cannot deny having met another user. Ideally, however, the user can plausibly deny everything else, in particular, when they met. We call this privacy property contact-time deniability.\r\nWhile some early works discussed contact-time deniability informally, it has received little attention since then. We investigate deniability from a rigorous, theoretical point of view and arrive at the following impossibility result:\r\nA decentralized protocol with unidirectional communication cannot be contact-time deniable and replay-secure. This holds even if malicious users treat smartphones as black-boxes.\r\n Unidirectional protocols are usually very efficient and many proposals are unidirectional, e.g., the widely-deployed Google-Apple Exposure Notifications. So the impossibility result considerably constrains the design space of efficient, secure, and private ACT protocols. However, it can also be used as a guide; we discuss several possibilities to achieve contact-time deniability in practice.","lang":"eng"}],"volume":2024,"month":"07","date_updated":"2025-04-15T08:16:04Z","issue":"4","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"journal_article","publication_identifier":{"issn":["2299-0984"]},"article_processing_charge":"No","citation":{"ista":"Günther CU, Pietrzak KZ. 2024. Deniability in automated contact tracing: Impossibilities and possibilities. Proceedings on Privacy Enhancing Technologies. 2024(4), 636–648.","short":"C.U. Günther, K.Z. Pietrzak, Proceedings on Privacy Enhancing Technologies 2024 (2024) 636–648.","mla":"Günther, Christoph Ullrich, and Krzysztof Z. Pietrzak. “Deniability in Automated Contact Tracing: Impossibilities and Possibilities.” Proceedings on Privacy Enhancing Technologies, vol. 2024, no. 4, Privacy Enhancing Technologies Symposium Advisory Board, 2024, pp. 636–48, doi:10.56553/popets-2024-0134.","chicago":"Günther, Christoph Ullrich, and Krzysztof Z Pietrzak. “Deniability in Automated Contact Tracing: Impossibilities and Possibilities.” Proceedings on Privacy Enhancing Technologies. Privacy Enhancing Technologies Symposium Advisory Board, 2024. https://doi.org/10.56553/popets-2024-0134.","ieee":"C. U. Günther and K. Z. Pietrzak, “Deniability in automated contact tracing: Impossibilities and possibilities,” Proceedings on Privacy Enhancing Technologies, vol. 2024, no. 4. Privacy Enhancing Technologies Symposium Advisory Board, pp. 636–648, 2024.","ama":"Günther CU, Pietrzak KZ. Deniability in automated contact tracing: Impossibilities and possibilities. Proceedings on Privacy Enhancing Technologies. 2024;2024(4):636-648. doi:10.56553/popets-2024-0134","apa":"Günther, C. U., & Pietrzak, K. Z. (2024). Deniability in automated contact tracing: Impossibilities and possibilities. Proceedings on Privacy Enhancing Technologies. Bristol, UK/Virtual: Privacy Enhancing Technologies Symposium Advisory Board. https://doi.org/10.56553/popets-2024-0134"},"status":"public","_id":"18961","page":"636-648","publication_status":"published","quality_controlled":"1","file":[{"date_updated":"2025-01-29T13:44:47Z","success":1,"creator":"dernst","relation":"main_file","checksum":"348ed6adcf6ad2f925227bde1758cae6","file_id":"18962","file_name":"2024_ProcPrivacyEnhTech_Guenther.pdf","content_type":"application/pdf","access_level":"open_access","file_size":611567,"date_created":"2025-01-29T13:44:47Z"}],"publication":"Proceedings on Privacy Enhancing Technologies","title":"Deniability in automated contact tracing: Impossibilities and possibilities","conference":{"end_date":"2024-07-20","name":"PETs: Privacy Enhancing Technologies Symposium ","location":"Bristol, UK/Virtual","start_date":"2024-07-15"},"date_published":"2024-07-01T00:00:00Z","author":[{"full_name":"Günther, Christoph Ullrich","last_name":"Günther","first_name":"Christoph Ullrich","id":"ec98511c-eb8e-11eb-b029-edd25d7271a1"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}]},{"acknowledgement":"Yanwei Fu is the corresponding authour. Yanwei Fu is with School of Data Science, Fudan University, Shanghai Key Lab of Intelligent Information Processing, Fudan University, and Fudan ISTBI-ZJNU Algorithm Centre for Brain-inspired Intelligence, Zhejiang Normal University, Jinhua, China.","publisher":"IEEE","arxiv":1,"doi":"10.1109/cvpr52733.2024.02176","OA_type":"green","day":"15","department":[{"_id":"FrLo"}],"year":"2024","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.09196","open_access":"1"}],"oa":1,"date_created":"2025-01-29T14:27:39Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","language":[{"iso":"eng"}],"external_id":{"arxiv":["2406.09196"],"isi":["001342515506043"]},"abstract":[{"text":"Object-centric learning (OCL) extracts the representation of objects with slots, offering an exceptional blend of flexibility and interpretability for abstracting low-level perceptual features. A widely adopted method within OCL is slot attention, which utilizes attention mechanisms to iteratively refine slot representations. However, a major draw-back of most object-centric models, including slot attention, is their reliance on predefining the number of slots. This not only necessitates prior knowledge of the dataset but also overlooks the inherent variability in the number of objects present in each instance. To overcome this fundamental limitation, we present a novel complexity-aware object auto-encoder framework. Within this framework, we introduce an adaptive slot attention (AdaSlot) mecha-nism that dynamically determines the optimal number of slots based on the content of the data. This is achieved by proposing a discrete slot sampling module that is responsible for selecting an appropriate number of slots from a candidate list. Furthermore, we introduce a masked slot decoder that suppresses unselected slots during the decoding process. Our framework, tested extensively on object discovery tasks with various datasets, shows performance matching or exceeding top fixed-slot models. Moreover, our analysis substantiates that our method exhibits the capability to dynamically adapt the slot number according to each instance's complexity, offering the potential for further exploration in slot attention research. Project will be available at https://kfan21.github.io/AdaSlot/","lang":"eng"}],"month":"06","date_updated":"2025-09-09T12:15:17Z","related_material":{"link":[{"relation":"software","url":"https://kfan21.github.io/AdaSlot/"}]},"isi":1,"oa_version":"Preprint","article_processing_charge":"No","citation":{"ama":"Fan K, Bai Z, Xiao T, et al. Adaptive slot attention: Object discovery with dynamic slot number. In: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2024. doi:10.1109/cvpr52733.2024.02176","apa":"Fan, K., Bai, Z., Xiao, T., He, T., Horn, M., Fu, Y., … Zhang, Z. (2024). Adaptive slot attention: Object discovery with dynamic slot number. In 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition. Seattle, WA, United States: IEEE. https://doi.org/10.1109/cvpr52733.2024.02176","short":"K. Fan, Z. Bai, T. Xiao, T. He, M. Horn, Y. Fu, F. Locatello, Z. Zhang, in:, 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2024.","ista":"Fan K, Bai Z, Xiao T, He T, Horn M, Fu Y, Locatello F, Zhang Z. 2024. Adaptive slot attention: Object discovery with dynamic slot number. 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition.","chicago":"Fan, Ke, Zechen Bai, Tianjun Xiao, Tong He, Max Horn, Yanwei Fu, Francesco Locatello, and Zheng Zhang. “Adaptive Slot Attention: Object Discovery with Dynamic Slot Number.” In 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE, 2024. https://doi.org/10.1109/cvpr52733.2024.02176.","ieee":"K. Fan et al., “Adaptive slot attention: Object discovery with dynamic slot number,” in 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Seattle, WA, United States, 2024.","mla":"Fan, Ke, et al. “Adaptive Slot Attention: Object Discovery with Dynamic Slot Number.” 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2024, doi:10.1109/cvpr52733.2024.02176."},"type":"conference","publication_identifier":{"eisbn":["9798350353006"]},"_id":"18964","status":"public","publication_status":"published","publication":"2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition","quality_controlled":"1","conference":{"location":"Seattle, WA, United States","start_date":"2024-06-16","end_date":"2024-06-22","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"title":"Adaptive slot attention: Object discovery with dynamic slot number","date_published":"2024-06-15T00:00:00Z","author":[{"last_name":"Fan","full_name":"Fan, Ke","first_name":"Ke"},{"first_name":"Zechen","last_name":"Bai","full_name":"Bai, Zechen"},{"last_name":"Xiao","full_name":"Xiao, Tianjun","first_name":"Tianjun"},{"first_name":"Tong","last_name":"He","full_name":"He, Tong"},{"last_name":"Horn","full_name":"Horn, Max","first_name":"Max"},{"first_name":"Yanwei","full_name":"Fu, Yanwei","last_name":"Fu"},{"full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Zhang","full_name":"Zhang, Zheng","first_name":"Zheng"}]},{"ddc":["570"],"publisher":"Wiley","doi":"10.1002/alz.085971","day":"01","OA_type":"hybrid","intvolume":" 20","year":"2024","department":[{"_id":"LeSa"}],"file_date_updated":"2025-01-29T15:24:50Z","oa":1,"date_created":"2025-01-29T15:21:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","language":[{"iso":"eng"}],"date_updated":"2025-01-29T15:29:22Z","issue":"S6","volume":20,"month":"12","abstract":[{"lang":"eng","text":"Background: We identified small molecule tricyclic pyrone compound CP2 as a mild mitochondrial complex I (MCI) inhibitor that induces neuroprotection in multiple mouse models of AD. One of the major concerns while targeting mitochondria is the production of reactive oxygen species (ROS). CP2 consists of two diastereoisomers, D1 and D2, with distinct activity and toxicity profiles. This study was designed to understand how structure of D1 and D2 affects their binding to MCI and the consequential impact on ROS production.\r\n\r\nMethod: The X-ray crystallography and cryo-electron microscopy (cryo-EM) at global resolution of 3.25-3.27Å were employed to identify the molecular structure of D1 and D2 and the D1 binding to the isolated ovine MCI. The assessment of the MCI inhibition and the extent of ROS generation were done in isolated MCI and human neuroblastoma MC65 cells using flow cytometry, a Seahorse extracellular flux analyzer, and the kinetic studies.\r\n\r\nResult: In the closed conformation of MCI, D1 selectively binds to the deep Quinone-site (Qd) but not to the shallow Q-site (Qs), sharing the same binding pocket as rotenone. In the open MCI state, D1 exclusively binds to the Qs in contrast to rotenone, which binds Qd and Qs in both closed and open states. At the same concentrations, D1 inhibits respiration to a greater extent compared to D2 (5:1 ratio) and produces higher level of ROS.\r\n\r\nConclusion:Cryo-EM unambiguously identified binding of D1 to both the Qd and Qs sites, contingent upon the conformational state of MCI. In contrast to rotenone, D1 binds Qd only in the closed conformation during catalytic cycle, leading to mild inhibition. Superimposing X-ray crystallography data of D1 and D2 onto cryo-EM data suggests that the orientation of the methyl group in D2 induces a flatter conformation, resulting in lower binding affinity to MCI, which correlates with lower inhibition and toxicity compared to D1. At physiologically relevant concentrations, CP2 (D1:D2 = 1:1) demonstrates low MCI inhibition yielding negligible ROS levels. This observation provides new insight into the absence of toxicity associated with CP2 treatment in vivo, further highlighting feasibility for the development of safe and efficacious MCI inhibitors."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","has_accepted_license":"1","citation":{"apa":"Petrova, O., Trushin, S. A., Nguyen, T. K. O., Ostroot, M., Schellenberg, M., Johnson, G., … Sazanov, L. A. (2024). Structure‐activity relationship study of neuroprotective complex I inhibitor CP2. Alzheimer’s & Dementia (Vol. 20). Wiley. https://doi.org/10.1002/alz.085971","ama":"Petrova O, Trushin SA, Nguyen TKO, et al. Structure‐activity Relationship Study of Neuroprotective Complex I Inhibitor CP2. Vol 20. Wiley; 2024. doi:10.1002/alz.085971","ieee":"O. Petrova et al., Structure‐activity relationship study of neuroprotective complex I inhibitor CP2, vol. 20, no. S6. Wiley, 2024.","chicago":"Petrova, Olga, Sergey A Trushin, Thi Kim Oanh Nguyen, Mark Ostroot, Matthew Schellenberg, Graham Johnson, Eugenia Trushina, and Leonid A Sazanov. Structure‐activity Relationship Study of Neuroprotective Complex I Inhibitor CP2. Alzheimer’s & Dementia. Vol. 20. Wiley, 2024. https://doi.org/10.1002/alz.085971.","mla":"Petrova, Olga, et al. “Structure‐activity Relationship Study of Neuroprotective Complex I Inhibitor CP2.” Alzheimer’s & Dementia, vol. 20, no. S6, e085971, Wiley, 2024, doi:10.1002/alz.085971.","short":"O. Petrova, S.A. Trushin, T.K.O. Nguyen, M. Ostroot, M. Schellenberg, G. Johnson, E. Trushina, L.A. Sazanov, Structure‐activity Relationship Study of Neuroprotective Complex I Inhibitor CP2, Wiley, 2024.","ista":"Petrova O, Trushin SA, Nguyen TKO, Ostroot M, Schellenberg M, Johnson G, Trushina E, Sazanov LA. 2024. Structure‐activity relationship study of neuroprotective complex I inhibitor CP2, Wiley,p."},"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1552-5279"],"issn":["1552-5260"]},"type":"other_academic_publication","_id":"18967","status":"public","publication_status":"published","publication":"Alzheimer's & Dementia","file":[{"content_type":"application/pdf","file_id":"18968","access_level":"open_access","file_name":"2024_AlzheimerDementia_Petrova.pdf","date_created":"2025-01-29T15:24:50Z","file_size":70870,"date_updated":"2025-01-29T15:24:50Z","relation":"main_file","creator":"dernst","success":1,"checksum":"e914bd5f3a701659ab79d497a122811f"}],"quality_controlled":"1","title":"Structure‐activity relationship study of neuroprotective complex I inhibitor CP2","author":[{"id":"5D8C9660-5D49-11EA-8188-567B3DDC885E","first_name":"Olga","last_name":"Petrova","full_name":"Petrova, Olga"},{"first_name":"Sergey A","full_name":"Trushin, Sergey A","last_name":"Trushin"},{"first_name":"Thi Kim Oanh","last_name":"Nguyen","full_name":"Nguyen, Thi Kim Oanh"},{"last_name":"Ostroot","full_name":"Ostroot, Mark","first_name":"Mark"},{"full_name":"Schellenberg, Matthew","last_name":"Schellenberg","first_name":"Matthew"},{"first_name":"Graham","full_name":"Johnson, Graham","last_name":"Johnson"},{"first_name":"Eugenia","full_name":"Trushina, Eugenia","last_name":"Trushina"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"article_number":"e085971","date_published":"2024-12-01T00:00:00Z"},{"language":[{"iso":"eng"}],"OA_place":"publisher","date_created":"2025-01-29T15:34:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"url":"https://doi.org/10.4171/owr/2024/16","open_access":"1"}],"intvolume":" 21","year":"2024","department":[{"_id":"TaHa"}],"day":"05","OA_type":"hybrid","doi":"10.4171/owr/2024/16","publisher":"EMS Press","acknowledgement":"The MFO and the workshop organizers would like to thank the\r\nNational Science Foundation for supporting the participation of junior researchers\r\nby the grant DMS-2230648, “US Junior Oberwolfach Fellows”. Moreover, the\r\nMFO and the workshop organizers would like to thank the Oberwolfach Foundation for supporting the participation of junior researchers in the Arbeitsgemeinschaft.","ddc":["500"],"author":[{"last_name":"Hausel","orcid":"0000-0002-9582-2634","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamás"},{"first_name":"Davesh","last_name":"Maulik","full_name":"Maulik, Davesh"},{"first_name":"Anton","last_name":"Mellit","full_name":"Mellit, Anton"},{"full_name":"Schiffmann, Olivier","last_name":"Schiffmann","first_name":"Olivier"},{"last_name":"Shen","full_name":"Shen, Junliang","first_name":"Junliang"}],"date_published":"2024-05-05T00:00:00Z","title":"Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture","quality_controlled":"1","publication":"Oberwolfach Reports","page":"949-1004","publication_status":"published","status":"public","_id":"18970","publication_identifier":{"issn":["1660-8933"],"eissn":["1660-8941"]},"type":"journal_article","citation":{"short":"T. Hausel, D. Maulik, A. Mellit, O. Schiffmann, J. Shen, Oberwolfach Reports 21 (2024) 949–1004.","ista":"Hausel T, Maulik D, Mellit A, Schiffmann O, Shen J. 2024. Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture. Oberwolfach Reports. 21(2), 949–1004.","ieee":"T. Hausel, D. Maulik, A. Mellit, O. Schiffmann, and J. Shen, “Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture,” Oberwolfach Reports, vol. 21, no. 2. EMS Press, pp. 949–1004, 2024.","chicago":"Hausel, Tamás, Davesh Maulik, Anton Mellit, Olivier Schiffmann, and Junliang Shen. “Arbeitsgemeinschaft: Geometry and Representation Theory around the P=W Conjecture.” Oberwolfach Reports. EMS Press, 2024. https://doi.org/10.4171/owr/2024/16.","mla":"Hausel, Tamás, et al. “Arbeitsgemeinschaft: Geometry and Representation Theory around the P=W Conjecture.” Oberwolfach Reports, vol. 21, no. 2, EMS Press, 2024, pp. 949–1004, doi:10.4171/owr/2024/16.","ama":"Hausel T, Maulik D, Mellit A, Schiffmann O, Shen J. Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture. Oberwolfach Reports. 2024;21(2):949-1004. doi:10.4171/owr/2024/16","apa":"Hausel, T., Maulik, D., Mellit, A., Schiffmann, O., & Shen, J. (2024). Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2024/16"},"article_processing_charge":"No","oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png"},"article_type":"original","issue":"2","date_updated":"2025-01-29T15:39:55Z","month":"05","volume":21,"abstract":[{"lang":"eng","text":"Given a smooth projective curve C, nonabelian Hodge theory gives a diffeomorphism between two different moduli spaces associated to C. The first is the moduli space of Higgs bundles on C of rank n, which is equipped with the structure of an algebraic completely integrable Hamiltonian system. The second is the character variety of representations of the fundamental group of C into GL(n). In 2012, de Cataldo, Hausel, and Migliorini [1] proposed the P=W conjecture which identifies the perverse filtration on the cohomology of the Higgs moduli space with the weight filtration on the cohomology of the character variety. Recently, in 2022, two independent proofs of the P=W Conjecture appeared, in work of Maulik &Shen [2] and Hausel, Mellit, Minets &Schiffmann [6]. The aim of the Arbeitsgemeinschaft was to understand the P=W Conjecture and these two recent proofs."}]},{"related_material":{"link":[{"url":"https://github.com/rarefin/CoBalT","relation":"software"}]},"abstract":[{"text":"Models prone to spurious correlations in training data often produce brittle predictions and introduce unintended biases. Addressing this challenge typically involves methods relying on prior knowledge and group annotation to remove spurious correlations, which may not be readily available in many applications. In this paper, we establish a novel connection between unsupervised object-centric learning and mitigation of spurious correlations. Instead of directly inferring subgroups with varying correlations with labels, our approach focuses on discovering concepts: discrete ideas that are shared across input samples. Leveraging existing object-centric representation learning, we introduce CoBalT: a concept balancing technique that effectively mitigates spurious correlations without requiring human labeling of subgroups. Evaluation across the benchmark datasets for sub-population shifts demonstrate superior or competitive performance compared state-of-the-art baselines, without the need for group annotation. Code is available at https://github.com/rarefin/CoBalT","lang":"eng"}],"month":"07","volume":235,"date_updated":"2025-01-30T07:23:10Z","oa_version":"Preprint","type":"conference","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","citation":{"mla":"Arefin, Rifat, et al. “Unsupervised Concept Discovery Mitigates Spurious Correlations.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 1672–88.","ieee":"R. Arefin et al., “Unsupervised concept discovery mitigates spurious correlations,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 1672–1688.","chicago":"Arefin, Rifat, Yan Zhang, Aristide Baratin, Francesco Locatello, Irina Rish, Dianbo Liu, and Kenji Kawaguchi. “Unsupervised Concept Discovery Mitigates Spurious Correlations.” In Proceedings of the 41st International Conference on Machine Learning, 235:1672–88. ML Research Press, 2024.","ista":"Arefin R, Zhang Y, Baratin A, Locatello F, Rish I, Liu D, Kawaguchi K. 2024. Unsupervised concept discovery mitigates spurious correlations. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 1672–1688.","short":"R. Arefin, Y. Zhang, A. Baratin, F. Locatello, I. Rish, D. Liu, K. Kawaguchi, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 1672–1688.","apa":"Arefin, R., Zhang, Y., Baratin, A., Locatello, F., Rish, I., Liu, D., & Kawaguchi, K. (2024). Unsupervised concept discovery mitigates spurious correlations. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 1672–1688). Vienna, Austria: ML Research Press.","ama":"Arefin R, Zhang Y, Baratin A, et al. Unsupervised concept discovery mitigates spurious correlations. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:1672-1688."},"_id":"18971","status":"public","publication_status":"published","page":"1672-1688","quality_controlled":"1","publication":"Proceedings of the 41st International Conference on Machine Learning","title":"Unsupervised concept discovery mitigates spurious correlations","conference":{"start_date":"2024-07-21","location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning"},"date_published":"2024-07-30T00:00:00Z","author":[{"first_name":"Rifat","last_name":"Arefin","full_name":"Arefin, Rifat"},{"last_name":"Zhang","full_name":"Zhang, Yan","first_name":"Yan"},{"first_name":"Aristide","last_name":"Baratin","full_name":"Baratin, Aristide"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Rish, Irina","last_name":"Rish","first_name":"Irina"},{"full_name":"Liu, Dianbo","last_name":"Liu","first_name":"Dianbo"},{"first_name":"Kenji","full_name":"Kawaguchi, Kenji","last_name":"Kawaguchi"}],"acknowledgement":"We acknowledge the support of the Canada CIFAR AI Chair Program and IVADO. We thank Mila and Compute Canada for providing computational resources.\r\n","scopus_import":"1","arxiv":1,"publisher":"ML Research Press","OA_type":"green","day":"30","alternative_title":["PMLR"],"department":[{"_id":"FrLo"}],"year":"2024","intvolume":" 235","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2402.13368"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-30T07:21:57Z","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["2402.13368"]},"OA_place":"repository"}]