[{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","scopus_import":"1","page":"684-685","status":"public","doi":"10.1038/s41567-024-02401-7","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"quality_controlled":"1","article_processing_charge":"No","type":"journal_article","_id":"18919","title":"Through the slopes of a light-induced phase transition","department":[{"_id":"DeBa"}],"publisher":"Springer Nature","publication":"Nature Physics","citation":{"mla":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” <i>Nature Physics</i>, vol. 20, no. 5, Springer Nature, 2024, pp. 684–85, doi:<a href=\"https://doi.org/10.1038/s41567-024-02401-7\">10.1038/s41567-024-02401-7</a>.","apa":"Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02401-7\">https://doi.org/10.1038/s41567-024-02401-7</a>","ieee":"D. R. Baykusheva, “Through the slopes of a light-induced phase transition,” <i>Nature Physics</i>, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024.","ama":"Baykusheva DR. Through the slopes of a light-induced phase transition. <i>Nature Physics</i>. 2024;20(5):684-685. doi:<a href=\"https://doi.org/10.1038/s41567-024-02401-7\">10.1038/s41567-024-02401-7</a>","ista":"Baykusheva DR. 2024. Through the slopes of a light-induced phase transition. Nature Physics. 20(5), 684–685.","chicago":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02401-7\">https://doi.org/10.1038/s41567-024-02401-7</a>.","short":"D.R. Baykusheva, Nature Physics 20 (2024) 684–685."},"day":"01","OA_type":"closed access","date_updated":"2025-09-09T12:08:10Z","publication_status":"published","external_id":{"isi":["001162208200002"]},"corr_author":"1","author":[{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"}],"date_created":"2025-01-27T14:29:20Z","date_published":"2024-05-01T00:00:00Z","article_type":"letter_note","year":"2024","intvolume":"        20","language":[{"iso":"eng"}],"issue":"5","isi":1,"month":"05","abstract":[{"lang":"eng","text":"The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling."}],"volume":20},{"volume":10,"month":"04","abstract":[{"text":"The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.","lang":"eng"}],"intvolume":"        10","oa":1,"issue":"15","acknowledgement":"We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core Facility and Proteomics Core Facility of the Central European Institute of Technology (CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR); and (iii) Plant Sciences Core Facility for support with obtaining scientific data presented here. We acknowledge support from the project National Institute of Virology and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European Union - Next Generation EU. This work received funding from the Czech Science Foundation grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI” (no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship funded by Brno city municipality to M.H.","language":[{"iso":"eng"}],"date_created":"2025-01-27T14:32:34Z","date_published":"2024-04-01T00:00:00Z","file_date_updated":"2025-01-27T14:40:08Z","year":"2024","article_type":"original","author":[{"full_name":"Homola, Miroslav","last_name":"Homola","first_name":"Miroslav"},{"id":"3b7984c9-17ff-11ed-b6fe-f943c4a5b626","full_name":"Büttner, Renate Carina","last_name":"Büttner","first_name":"Renate Carina"},{"last_name":"Füzik","first_name":"Tibor","full_name":"Füzik, Tibor"},{"full_name":"Křepelka, Pavel","last_name":"Křepelka","first_name":"Pavel"},{"first_name":"Radka","last_name":"Holbová","full_name":"Holbová, Radka"},{"first_name":"Jiří","last_name":"Nováček","full_name":"Nováček, Jiří"},{"last_name":"Chaillet","first_name":"Marten L.","full_name":"Chaillet, Marten L."},{"first_name":"Jakub","last_name":"Žák","full_name":"Žák, Jakub"},{"first_name":"Danyil","last_name":"Grybchuk","full_name":"Grybchuk, Danyil"},{"first_name":"Friedrich","last_name":"Förster","full_name":"Förster, Friedrich"},{"first_name":"William H.","last_name":"Wilson","full_name":"Wilson, William H."},{"full_name":"Schroeder, Declan C.","last_name":"Schroeder","first_name":"Declan C."},{"full_name":"Plevka, Pavel","first_name":"Pavel","last_name":"Plevka"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","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)"},"article_number":"eadk1954 ","pmid":1,"external_id":{"pmid":["38598627"]},"DOAJ_listed":"1","OA_type":"gold","date_updated":"2025-05-14T09:29:04Z","day":"01","file":[{"file_size":40623405,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-27T14:40:08Z","date_updated":"2025-01-27T14:40:08Z","file_name":"2024_ScienceAdv_Homola.pdf","file_id":"18921","checksum":"291dd7ceccbe6bfd8e0a9157584f88e9","success":1}],"department":[{"_id":"EM-Fac"}],"publisher":"American Association for the Advancement of Science","has_accepted_license":"1","publication":"Science Advances","citation":{"mla":"Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>, vol. 10, no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>.","apa":"Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>","ieee":"M. Homola <i>et al.</i>, “Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi,” <i>Science Advances</i>, vol. 10, no. 15. American Association for the Advancement of Science, 2024.","ama":"Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. 2024;10(15). doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>","ista":"Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 10(15), eadk1954.","chicago":"Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>.","short":"M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L. Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka, Science Advances 10 (2024)."},"_id":"18920","title":"Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","OA_place":"publisher","ddc":["570"],"article_processing_charge":"Yes","type":"journal_article","status":"public","publication_identifier":{"eissn":["2375-2548"]},"doi":"10.1126/sciadv.adk1954","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","related_material":{"link":[{"relation":"software","url":" https://github.com/fuzikt/tomostarpy."}]}},{"title":"Computing the 3-edge-connected components of directed graphs in linear time","_id":"18922","publication":"65th Annual Symposium on Foundations of Computer Science","citation":{"chicago":"Georgiadis, Loukas, Giuseppe F. Italiano, and Evangelos Kosinas. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” In <i>65th Annual Symposium on Foundations of Computer Science</i>, 62–85. IEEE, 2024. <a href=\"https://doi.org/10.1109/focs61266.2024.00015\">https://doi.org/10.1109/focs61266.2024.00015</a>.","ista":"Georgiadis L, Italiano GF, Kosinas E. 2024. Computing the 3-edge-connected components of directed graphs in linear time. 65th Annual Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science, 62–85.","short":"L. Georgiadis, G.F. Italiano, E. Kosinas, in:, 65th Annual Symposium on Foundations of Computer Science, IEEE, 2024, pp. 62–85.","ieee":"L. Georgiadis, G. F. Italiano, and E. Kosinas, “Computing the 3-edge-connected components of directed graphs in linear time,” in <i>65th Annual Symposium on Foundations of Computer Science</i>, Chicago, IL, United States, 2024, pp. 62–85.","mla":"Georgiadis, Loukas, et al. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” <i>65th Annual Symposium on Foundations of Computer Science</i>, IEEE, 2024, pp. 62–85, doi:<a href=\"https://doi.org/10.1109/focs61266.2024.00015\">10.1109/focs61266.2024.00015</a>.","apa":"Georgiadis, L., Italiano, G. F., &#38; Kosinas, E. (2024). Computing the 3-edge-connected components of directed graphs in linear time. In <i>65th Annual Symposium on Foundations of Computer Science</i> (pp. 62–85). Chicago, IL, United States: IEEE. <a href=\"https://doi.org/10.1109/focs61266.2024.00015\">https://doi.org/10.1109/focs61266.2024.00015</a>","ama":"Georgiadis L, Italiano GF, Kosinas E. Computing the 3-edge-connected components of directed graphs in linear time. In: <i>65th Annual Symposium on Foundations of Computer Science</i>. IEEE; 2024:62-85. doi:<a href=\"https://doi.org/10.1109/focs61266.2024.00015\">10.1109/focs61266.2024.00015</a>"},"department":[{"_id":"MoHe"}],"publisher":"IEEE","day":"01","date_updated":"2025-09-09T12:08:47Z","OA_type":"closed access","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","scopus_import":"1","page":"62-85","conference":{"location":"Chicago, IL, United States","start_date":"2024-10-27","name":"FOCS: Foundations of Computer Science","end_date":"2024-10-30"},"publication_identifier":{"isbn":["9798331516741"]},"doi":"10.1109/focs61266.2024.00015","quality_controlled":"1","status":"public","type":"conference","article_processing_charge":"No","date_published":"2024-10-01T00:00:00Z","year":"2024","date_created":"2025-01-27T14:50:23Z","acknowledgement":"Giuseppe F. Italiano was partially supported by the Italian Ministry of\r\nUniversity and Reseach under PRIN Project n. 2022TS4Y3N - EXPAND: scalable algorithms for EXPloratory Analyses of heterogeneous and dynamic Networked Data.\r\n","isi":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Let G be a directed graph with m edges and n vertices. We present a deterministic linear-time algorithm for computing the 3-edge-connected components of G. This is a significant improvement over the previous best bound by Georgiadis et al. [SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel characterization of 2-edge cuts in directed graphs and on a new technique that exploits the concept of divergent spanning trees and 2-connectivity-light graphs, and requires a careful modification of the minset-poset technique of Gabow [TALG 2016]. As a side result, our new technique yields also an oracle for providing in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected. The oracle uses space O(n) and can be built in O(mlog n) time: given two query vertices, it determines in constant time whether they are 3-edge-connected, or provides a k-edge cut, with k≤ 2, that separates them."}],"month":"10","external_id":{"isi":["001419526400005"]},"corr_author":"1","publication_status":"published","author":[{"full_name":"Georgiadis, Loukas","first_name":"Loukas","last_name":"Georgiadis"},{"full_name":"Italiano, Giuseppe F.","last_name":"Italiano","first_name":"Giuseppe F."},{"first_name":"Evangelos","last_name":"Kosinas","full_name":"Kosinas, Evangelos","id":"4c7f9625-dbbc-11ee-9d86-bdcc2db5a949"}]},{"date_published":"2024-08-14T00:00:00Z","file_date_updated":"2025-01-27T15:03:09Z","year":"2024","article_type":"original","date_created":"2025-01-27T15:00:44Z","oa":1,"language":[{"iso":"eng"}],"acknowledgement":"The authors would like to thank Alexander Keesling, Maddie Cain, Nate Gemelke, and Phillip Weinberg for helpful discussions and Danylo Lykov who had early contributions to this work.\r\n10.13039/100000185-Defense Advanced Research Projects Agency Noisy Intermediate-Scale Quantum Devices (Grant Number: W911NF2010021), DARPA Small Business Technology Transfer program (Grant Number: 140D0422C0035).","intvolume":"         5","abstract":[{"text":"Combinatorial optimization is a challenging problem applicable in a wide range of fields from logistics to finance. Recently, quantum computing has been used to attempt to solve these problems using a range of algorithms, including parameterized quantum circuits, adiabatic protocols, and quantum annealing. These solutions typically have several challenges: 1) there is little to no performance gain over classical methods; 2) not all constraints and objectives may be efficiently encoded in the quantum ansatz; and 3) the solution domain of the objective function may not be the same as the bit strings of measurement outcomes. This work presents “nonnative hybrid algorithms”: a framework to overcome these challenges by integrating quantum and classical resources with a hybrid approach. By designing nonnative quantum variational anosatzes that inherit some but not all problem structure, measurement outcomes from the quantum computer can act as a resource to be used by classical routines to indirectly compute optimal solutions, partially overcoming the challenges of contemporary quantum optimization approaches. These methods are demonstrated using a publicly available neutral-atom quantum computer on two simple problems of Max k-Cut and maximum independent set. We find improvements in solution quality when comparing the hybrid algorithm to its “no quantum” version, a demonstration of a “comparative advantage.”","lang":"eng"}],"month":"08","volume":5,"publication_status":"published","tmp":{"image":"/images/cc_by.png","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)"},"author":[{"last_name":"Wurtz","first_name":"Jonathan","full_name":"Wurtz, Jonathan"},{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan"},{"full_name":"Wang, Sheng-Tao","last_name":"Wang","first_name":"Sheng-Tao"}],"OA_place":"publisher","title":"Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms","_id":"18923","publication":"IEEE Transactions on Quantum Engineering","has_accepted_license":"1","citation":{"short":"J. Wurtz, S. Sack, S.-T. Wang, IEEE Transactions on Quantum Engineering 5 (2024) 1–14.","chicago":"Wurtz, Jonathan, Stefan Sack, and Sheng-Tao Wang. “Solving Nonnative Combinatorial Optimization Problems Using Hybrid Quantum–Classical Algorithms.” <i>IEEE Transactions on Quantum Engineering</i>. Institute of Electrical and Electronics Engineers , 2024. <a href=\"https://doi.org/10.1109/tqe.2024.3443660\">https://doi.org/10.1109/tqe.2024.3443660</a>.","ista":"Wurtz J, Sack S, Wang S-T. 2024. Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms. IEEE Transactions on Quantum Engineering. 5, 1–14.","ama":"Wurtz J, Sack S, Wang S-T. Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms. <i>IEEE Transactions on Quantum Engineering</i>. 2024;5:1-14. doi:<a href=\"https://doi.org/10.1109/tqe.2024.3443660\">10.1109/tqe.2024.3443660</a>","ieee":"J. Wurtz, S. Sack, and S.-T. Wang, “Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms,” <i>IEEE Transactions on Quantum Engineering</i>, vol. 5. Institute of Electrical and Electronics Engineers , pp. 1–14, 2024.","apa":"Wurtz, J., Sack, S., &#38; Wang, S.-T. (2024). Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms. <i>IEEE Transactions on Quantum Engineering</i>. Institute of Electrical and Electronics Engineers . <a href=\"https://doi.org/10.1109/tqe.2024.3443660\">https://doi.org/10.1109/tqe.2024.3443660</a>","mla":"Wurtz, Jonathan, et al. “Solving Nonnative Combinatorial Optimization Problems Using Hybrid Quantum–Classical Algorithms.” <i>IEEE Transactions on Quantum Engineering</i>, vol. 5, Institute of Electrical and Electronics Engineers , 2024, pp. 1–14, doi:<a href=\"https://doi.org/10.1109/tqe.2024.3443660\">10.1109/tqe.2024.3443660</a>."},"file":[{"file_id":"18924","checksum":"19b84e35cba05bde72bfe7e0b54c3e6c","success":1,"date_updated":"2025-01-27T15:03:09Z","file_name":"2024_IEEEQuantumComputing_Wurtz.pdf","access_level":"open_access","date_created":"2025-01-27T15:03:09Z","relation":"main_file","file_size":1753095,"content_type":"application/pdf","creator":"dernst"}],"publisher":"Institute of Electrical and Electronics Engineers ","department":[{"_id":"MaSe"}],"day":"14","date_updated":"2025-01-27T15:06:15Z","OA_type":"hybrid","oa_version":"Published Version","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1-14","doi":"10.1109/tqe.2024.3443660","publication_identifier":{"issn":["2689-1808"]},"quality_controlled":"1","status":"public","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","ddc":["530"]},{"conference":{"end_date":"2024-05-10","name":"NOMS: Network Operations and Management Symposiu ","start_date":"2024-05-06","location":"Seoul, Republic of Korea"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","ec_funded":1,"status":"public","publication_identifier":{"isbn":["9798350327946"],"eissn":["2374-9709"]},"doi":"10.1109/noms59830.2024.10575579","quality_controlled":"1","article_processing_charge":"No","type":"conference","_id":"18925","title":"Congestion-free rerouting of network flows: Hardness and an FPT algorithm","OA_place":"other","main_file_link":[{"url":"https://schmiste.github.io/noms24.pdf","open_access":"1"}],"department":[{"_id":"KrCh"}],"publisher":"IEEE","publication":"NOMS 2024-2024 IEEE Network Operations and Management Symposium","citation":{"mla":"Ceylan, Esra, et al. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>, IEEE, 2024, doi:<a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">10.1109/noms59830.2024.10575579</a>.","apa":"Ceylan, E., Chatterjee, K., Schmid, S., &#38; Svoboda, J. (2024). Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. Seoul, Republic of Korea: IEEE. <a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">https://doi.org/10.1109/noms59830.2024.10575579</a>","ieee":"E. Ceylan, K. Chatterjee, S. Schmid, and J. Svoboda, “Congestion-free rerouting of network flows: Hardness and an FPT algorithm,” in <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>, Seoul, Republic of Korea, 2024.","ama":"Ceylan E, Chatterjee K, Schmid S, Svoboda J. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In: <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. IEEE; 2024. doi:<a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">10.1109/noms59830.2024.10575579</a>","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 .","chicago":"Ceylan, Esra, Krishnendu Chatterjee, Stefan Schmid, and Jakub Svoboda. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” In <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">https://doi.org/10.1109/noms59830.2024.10575579</a>.","short":"E. Ceylan, K. Chatterjee, S. Schmid, J. Svoboda, in:, NOMS 2024-2024 IEEE Network Operations and Management Symposium, IEEE, 2024."},"day":"01","OA_type":"green","date_updated":"2025-11-05T07:34:27Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"},{"grant_number":"894907","name":"Graphical Games","_id":"bd622a5c-d553-11ed-ba76-bae280ba8aff"}],"publication_status":"published","external_id":{"isi":["001270140300143"]},"corr_author":"1","author":[{"full_name":"Ceylan, Esra","id":"cb1ca1d8-dcc0-11ef-baa5-9f1b3ef75933","first_name":"Esra","last_name":"Ceylan"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"last_name":"Svoboda","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267"}],"date_created":"2025-01-27T15:06:45Z","date_published":"2024-05-01T00:00:00Z","year":"2024","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).","language":[{"iso":"eng"}],"isi":1,"oa":1,"month":"05","abstract":[{"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.","lang":"eng"}]},{"external_id":{"arxiv":["2112.11150"]},"corr_author":"1","publication_status":"published","author":[{"last_name":"Hensel","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian"},{"first_name":"Tim","last_name":"Laux","full_name":"Laux, Tim"}],"date_published":"2024-01-01T00:00:00Z","article_type":"original","year":"2024","date_created":"2025-01-27T15:20:19Z","issue":"1","language":[{"iso":"eng"}],"oa":1,"intvolume":"        73","abstract":[{"lang":"eng","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. "}],"month":"01","volume":73,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Preprint","page":"111-148","publication_identifier":{"issn":["0022-2518"]},"doi":"10.1512/iumj.2024.73.9701","quality_controlled":"1","status":"public","type":"journal_article","arxiv":1,"article_processing_charge":"No","OA_place":"repository","_id":"18926","title":"BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness","publication":"Indiana University Mathematics Journal","citation":{"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.","chicago":"Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” <i>Indiana University Mathematics Journal</i>. Indiana University Mathematics Journal, 2024. <a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">https://doi.org/10.1512/iumj.2024.73.9701</a>.","ama":"Hensel S, Laux T. BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. <i>Indiana University Mathematics Journal</i>. 2024;73(1):111-148. doi:<a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">10.1512/iumj.2024.73.9701</a>","apa":"Hensel, S., &#38; Laux, T. (2024). BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. <i>Indiana University Mathematics Journal</i>. Indiana University Mathematics Journal. <a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">https://doi.org/10.1512/iumj.2024.73.9701</a>","mla":"Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” <i>Indiana University Mathematics Journal</i>, vol. 73, no. 1, Indiana University Mathematics Journal, 2024, pp. 111–48, doi:<a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">10.1512/iumj.2024.73.9701</a>.","ieee":"S. Hensel and T. Laux, “BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness,” <i>Indiana University Mathematics Journal</i>, vol. 73, no. 1. Indiana University Mathematics Journal, pp. 111–148, 2024."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2112.11150","open_access":"1"}],"department":[{"_id":"JuFi"}],"publisher":"Indiana University Mathematics Journal","day":"01","date_updated":"2025-01-27T15:23:57Z","OA_type":"green"},{"file":[{"checksum":"15085a5b3697a408b92a4a7a27293927","file_id":"18929","success":1,"date_updated":"2025-01-27T15:33:24Z","file_name":"2024_LIPICs_HenzingerMo.pdf","access_level":"open_access","relation":"main_file","date_created":"2025-01-27T15:33:24Z","file_size":1084372,"content_type":"application/pdf","creator":"dernst"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"has_accepted_license":"1","publication":"15th Innovations in Theoretical Computer Science Conference","citation":{"apa":"Henzinger, M., Saha, B., Seybold, M. P., &#38; Ye, C. (2024). On the complexity of algorithms with predictions for dynamic graph problems. In <i>15th Innovations in Theoretical Computer Science Conference</i> (Vol. 287, p. 62:1-62:25). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">https://doi.org/10.4230/LIPIcs.ITCS.2024.62</a>","mla":"Henzinger, Monika, et al. “On the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” <i>15th Innovations in Theoretical Computer Science Conference</i>, vol. 287, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 62:1-62:25, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">10.4230/LIPIcs.ITCS.2024.62</a>.","ieee":"M. Henzinger, B. Saha, M. P. Seybold, and C. Ye, “On the complexity of algorithms with predictions for dynamic graph problems,” in <i>15th Innovations in Theoretical Computer Science Conference</i>, Berkeley, CA, United States, 2024, vol. 287, p. 62:1-62:25.","ama":"Henzinger M, Saha B, Seybold MP, Ye C. On the complexity of algorithms with predictions for dynamic graph problems. In: <i>15th Innovations in Theoretical Computer Science Conference</i>. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:62:1-62:25. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">10.4230/LIPIcs.ITCS.2024.62</a>","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 <i>15th Innovations in Theoretical Computer Science Conference</i>, 287:62:1-62:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">https://doi.org/10.4230/LIPIcs.ITCS.2024.62</a>.","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."},"_id":"18928","title":"On the complexity of algorithms with predictions for dynamic graph problems","OA_place":"publisher","OA_type":"gold","date_updated":"2025-09-09T12:11:33Z","day":"24","alternative_title":["LIPIcs"],"status":"public","ec_funded":1,"publication_identifier":{"isbn":["9783959773096"],"eissn":["1868-8969"]},"doi":"10.4230/LIPIcs.ITCS.2024.62","quality_controlled":"1","conference":{"location":"Berkeley, CA, United States","start_date":"2024-01-30","name":"ITCS: Innovations in Theoretical Computer Science","end_date":"2024-02-02"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","scopus_import":"1","page":"62:1-62:25","ddc":["000"],"arxiv":1,"article_processing_charge":"Yes","type":"conference","intvolume":"       287","oa":1,"language":[{"iso":"eng"}],"isi":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.","date_created":"2025-01-27T15:33:42Z","file_date_updated":"2025-01-27T15:33:24Z","date_published":"2024-01-24T00:00:00Z","year":"2024","volume":287,"month":"01","abstract":[{"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.","lang":"eng"}],"project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422","name":"Efficient algorithms"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H"},{"last_name":"Saha","first_name":"Barna","full_name":"Saha, Barna"},{"full_name":"Seybold, Martin P.","last_name":"Seybold","first_name":"Martin P."},{"full_name":"Ye, Christopher","last_name":"Ye","first_name":"Christopher"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","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)"},"external_id":{"isi":["001300389400062"],"arxiv":["2307.16771"]},"corr_author":"1"},{"day":"01","date_updated":"2025-12-04T14:46:28Z","OA_type":"hybrid","OA_place":"publisher","title":"Sumsets in the set of squares","_id":"18930","citation":{"mla":"Elsholtz, Christian, and Lena Wurzinger. “Sumsets in the Set of Squares.” <i>The Quarterly Journal of Mathematics</i>, vol. 75, no. 4, Oxford University Press, 2024, pp. 1243–54, doi:<a href=\"https://doi.org/10.1093/qmath/haae044\">10.1093/qmath/haae044</a>.","apa":"Elsholtz, C., &#38; Wurzinger, L. (2024). Sumsets in the set of squares. <i>The Quarterly Journal of Mathematics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/qmath/haae044\">https://doi.org/10.1093/qmath/haae044</a>","ieee":"C. Elsholtz and L. Wurzinger, “Sumsets in the set of squares,” <i>The Quarterly Journal of Mathematics</i>, vol. 75, no. 4. Oxford University Press, pp. 1243–1254, 2024.","ama":"Elsholtz C, Wurzinger L. Sumsets in the set of squares. <i>The Quarterly Journal of Mathematics</i>. 2024;75(4):1243-1254. doi:<a href=\"https://doi.org/10.1093/qmath/haae044\">10.1093/qmath/haae044</a>","ista":"Elsholtz C, Wurzinger L. 2024. Sumsets in the set of squares. The Quarterly Journal of Mathematics. 75(4), 1243–1254.","chicago":"Elsholtz, Christian, and Lena Wurzinger. “Sumsets in the Set of Squares.” <i>The Quarterly Journal of Mathematics</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/qmath/haae044\">https://doi.org/10.1093/qmath/haae044</a>.","short":"C. Elsholtz, L. Wurzinger, The Quarterly Journal of Mathematics 75 (2024) 1243–1254."},"has_accepted_license":"1","publication":"The Quarterly Journal of Mathematics","publisher":"Oxford University Press","department":[{"_id":"TiBr"}],"file":[{"file_size":424645,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-28T07:03:51Z","date_updated":"2025-01-28T07:03:51Z","file_name":"2024_QuarterlyJourMath_Elsholtz.pdf","file_id":"18931","checksum":"1a06e052761d3f1e873463d6f529dd82","success":1}],"type":"journal_article","article_processing_charge":"Yes (via OA deal)","ddc":["510"],"page":"1243-1254","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","doi":"10.1093/qmath/haae044","publication_identifier":{"issn":["0033-5606"],"eissn":["1464-3847"]},"status":"public","abstract":[{"lang":"eng","text":"We study sumsets 𝒜 + ℬ in the set of squares 𝒮 (and, more generally, in the set of kth powers 𝒮k, where k ≥2 is an integer). It is known by a result of Gyarmati that 𝒜 + ℬ ⊂ 𝒮k ∩[1,N] implies that min(|𝒜|,|ℬ|) =Ok(logN). Here, we study how the upper bound on |ℬ| decreases, when the size of |𝒜| increases (or vice versa). In particular, if |𝒜| ≥ Ck1m m(logN)1m , then |ℬ| = Ok(m2logN), for sufficiently large N, a positive integer m and an explicit constant C > 0. For example, with m ∼ loglogN this gives: If |𝒜| ≥ CkloglogN,then |ℬ| = Ok(logN(loglogN)2)."}],"month":"12","volume":75,"year":"2024","article_type":"original","file_date_updated":"2025-01-28T07:03:51Z","date_published":"2024-12-01T00:00:00Z","date_created":"2025-01-28T06:55:31Z","isi":1,"issue":"4","oa":1,"language":[{"iso":"eng"}],"acknowledgement":"This manuscript grew out of the second author’s MSc Thesis at Graz University of Technology [34]. C. Elsholtz is supported by a joint FWF-ANR project ArithRand, grant numbers FWF I 4945-N and ANR-20-CE91-0006. Both authors would like to thank Igor Shparlinski for drawing our attention to related character sum estimates. Furthermore, we would like to thank the referee for a careful reading of the paper.","intvolume":"        75","corr_author":"1","external_id":{"isi":["001304396600001"]},"tmp":{"image":"/images/cc_by.png","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)"},"publication_status":"published","author":[{"last_name":"Elsholtz","first_name":"Christian","full_name":"Elsholtz, Christian"},{"first_name":"Lena","last_name":"Wurzinger","full_name":"Wurzinger, Lena","orcid":"0009-0004-5360-0074","id":"50c57d72-32a8-11ee-aeea-d652094d2ccd"}],"PlanS_conform":"1"},{"external_id":{"pmid":["38117593"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"pmid":1,"article_number":"mr1","author":[{"full_name":"Sárkány, Zsuzsa","last_name":"Sárkány","first_name":"Zsuzsa"},{"full_name":"Figueiredo, Francisco","id":"8125cbe2-9661-11ed-a754-afe96018f37d","first_name":"Francisco","last_name":"Figueiredo"},{"first_name":"Sandra","last_name":"Macedo-Ribeiro","full_name":"Macedo-Ribeiro, Sandra"},{"first_name":"Pedro M.","last_name":"Martins","full_name":"Martins, Pedro M."}],"date_published":"2024-03-01T00:00:00Z","file_date_updated":"2025-01-29T08:12:11Z","year":"2024","article_type":"original","date_created":"2025-01-29T07:58:40Z","issue":"3","oa":1,"language":[{"iso":"eng"}],"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.","intvolume":"        35","abstract":[{"lang":"eng","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 ."}],"month":"03","volume":35,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","publication_identifier":{"issn":["1059-1524"],"eissn":["1939-4586"]},"doi":"10.1091/mbc.e23-07-0289","quality_controlled":"1","status":"public","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","ddc":["570"],"OA_place":"publisher","_id":"18934","title":"NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation","publication":"Molecular Biology of the Cell","has_accepted_license":"1","citation":{"ieee":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation,” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3. American Society for Cell Biology, 2024.","apa":"Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., &#38; Martins, P. M. (2024). NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>","mla":"Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3, mr1, American Society for Cell Biology, 2024, doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>.","ama":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. 2024;35(3). doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>","chicago":"Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2024. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>.","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.","short":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024)."},"file":[{"success":1,"file_id":"18935","checksum":"d7deb6390f294da69321cfbe352ed611","file_name":"2024_MolecularBioCell_Sarkany.pdf","date_updated":"2025-01-29T08:12:11Z","relation":"main_file","date_created":"2025-01-29T08:12:11Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1699180}],"department":[{"_id":"FlSc"}],"publisher":"American Society for Cell Biology","day":"01","date_updated":"2025-01-29T08:16:20Z","OA_type":"hybrid"},{"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.","language":[{"iso":"eng"}],"intvolume":"       685","date_published":"2024-07-15T00:00:00Z","year":"2024","article_type":"original","date_created":"2025-01-29T08:33:04Z","volume":685,"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"}],"month":"07","author":[{"last_name":"Ray","first_name":"Sujata Kumari","full_name":"Ray, Sujata Kumari"},{"full_name":"Pati, Anupama","first_name":"Anupama","last_name":"Pati"},{"first_name":"Payala","last_name":"Sahoo","full_name":"Sahoo, Payala"},{"full_name":"Sahoo, A.K.","first_name":"A.K.","last_name":"Sahoo"},{"orcid":"0000-0003-2209-5269","full_name":"Singh, Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","first_name":"Saurabh","last_name":"Singh"},{"last_name":"Takeuchi","first_name":"Tsunehiro","full_name":"Takeuchi, Tsunehiro"},{"first_name":"S.","last_name":"Dash","full_name":"Dash, S."}],"publication_status":"published","article_number":"416018","publication":"Physica B: Condensed Matter","citation":{"ieee":"S. K. Ray <i>et al.</i>, “Tunable magnetoelectronic properties in Bi3+ substituted YCrO3,” <i>Physica B: Condensed Matter</i>, vol. 685. Elsevier, 2024.","apa":"Ray, S. K., Pati, A., Sahoo, P., Sahoo, A. K., Singh, S., Takeuchi, T., &#38; Dash, S. (2024). Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. <i>Physica B: Condensed Matter</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physb.2024.416018\">https://doi.org/10.1016/j.physb.2024.416018</a>","mla":"Ray, Sujata Kumari, et al. “Tunable Magnetoelectronic Properties in Bi3+ Substituted YCrO3.” <i>Physica B: Condensed Matter</i>, vol. 685, 416018, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.physb.2024.416018\">10.1016/j.physb.2024.416018</a>.","ama":"Ray SK, Pati A, Sahoo P, et al. Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. <i>Physica B: Condensed Matter</i>. 2024;685. doi:<a href=\"https://doi.org/10.1016/j.physb.2024.416018\">10.1016/j.physb.2024.416018</a>","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.” <i>Physica B: Condensed Matter</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.physb.2024.416018\">https://doi.org/10.1016/j.physb.2024.416018</a>.","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)."},"department":[{"_id":"MaIb"}],"publisher":"Elsevier","title":"Tunable magnetoelectronic properties in Bi3+ substituted YCrO3","_id":"18937","date_updated":"2025-01-29T08:37:14Z","OA_type":"closed access","day":"15","doi":"10.1016/j.physb.2024.416018","publication_identifier":{"issn":["0921-4526"]},"quality_controlled":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":"1","type":"journal_article","article_processing_charge":"No"},{"date_created":"2025-01-29T08:39:27Z","year":"2024","article_type":"original","file_date_updated":"2025-01-29T08:43:16Z","date_published":"2024-02-06T00:00:00Z","intvolume":"       121","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.","issue":"6","oa":1,"language":[{"iso":"eng"}],"month":"02","abstract":[{"lang":"eng","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."}],"volume":121,"pmid":1,"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"e2317453121","publication_status":"published","external_id":{"pmid":["38289956"]},"author":[{"id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","full_name":"Springstein, Benjamin L","orcid":"0000-0002-3461-5391","last_name":"Springstein","first_name":"Benjamin L"},{"full_name":"Paulo, Joao A.","first_name":"Joao A.","last_name":"Paulo"},{"last_name":"Park","first_name":"Hankum","full_name":"Park, Hankum"},{"last_name":"Henry","first_name":"Kemardo","full_name":"Henry, Kemardo"},{"last_name":"Fleming","first_name":"Eleanor","full_name":"Fleming, Eleanor"},{"last_name":"Feder","first_name":"Zoë","full_name":"Feder, Zoë"},{"first_name":"J. Wade","last_name":"Harper","full_name":"Harper, J. Wade"},{"first_name":"Ann","last_name":"Hochschild","full_name":"Hochschild, Ann"}],"_id":"18938","title":"Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics","OA_place":"publisher","department":[{"_id":"MaLo"}],"publisher":"National Academy of Sciences","file":[{"content_type":"application/pdf","file_size":720902,"creator":"dernst","access_level":"open_access","date_created":"2025-01-29T08:43:16Z","relation":"main_file","date_updated":"2025-01-29T08:43:16Z","file_name":"2024_PNAS_Springstein.pdf","checksum":"5bd62c7cb4287e3706a1d45d6ef61fd1","file_id":"18939","success":1}],"citation":{"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.","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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>.","ama":"Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(6). doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>","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. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>","mla":"Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6, e2317453121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>.","ieee":"B. L. Springstein <i>et al.</i>, “Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6. National Academy of Sciences, 2024."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","day":"06","OA_type":"hybrid","date_updated":"2025-05-14T11:02:52Z","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","quality_controlled":"1","doi":"10.1073/pnas.2317453121","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_processing_charge":"No","type":"journal_article","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.","language":[{"iso":"eng"}],"oa":1,"intvolume":"        13","year":"2024","article_type":"original","file_date_updated":"2025-01-29T08:50:18Z","date_published":"2024-02-07T00:00:00Z","date_created":"2025-01-29T08:48:34Z","volume":13,"abstract":[{"lang":"eng","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 <jats:italic>Nematostella vectensis</jats:italic>, several of which were conserved in <jats:italic>Drosophila</jats:italic> and <jats:italic>Xenopus</jats:italic>. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in <jats:italic>Nematostella</jats:italic> 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 <jats:italic>zswim4-6</jats:italic>, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression."}],"month":"02","DOAJ_listed":"1","author":[{"full_name":"Knabl, Paul","first_name":"Paul","last_name":"Knabl"},{"last_name":"Schauer","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra"},{"full_name":"Pomreinke, Autumn P","last_name":"Pomreinke","first_name":"Autumn P"},{"first_name":"Bob","last_name":"Zimmermann","full_name":"Zimmermann, Bob"},{"last_name":"Rogers","first_name":"Katherine W","full_name":"Rogers, Katherine W"},{"full_name":"Čapek, Daniel","first_name":"Daniel","last_name":"Čapek"},{"full_name":"Müller, Patrick","first_name":"Patrick","last_name":"Müller"},{"first_name":"Grigory","last_name":"Genikhovich","full_name":"Genikhovich, Grigory"}],"tmp":{"image":"/images/cc_by.png","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)"},"publication_status":"published","citation":{"ieee":"P. Knabl <i>et al.</i>, “Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 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.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.80803\">10.7554/elife.80803</a>.","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. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.80803\">https://doi.org/10.7554/elife.80803</a>","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. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.80803\">10.7554/elife.80803</a>","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.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.80803\">https://doi.org/10.7554/elife.80803</a>.","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)."},"publication":"eLife","has_accepted_license":"1","department":[{"_id":"CaHe"}],"publisher":"eLife Sciences Publications","file":[{"creator":"dernst","content_type":"application/pdf","file_size":11855972,"relation":"main_file","date_created":"2025-01-29T08:50:18Z","access_level":"open_access","file_name":"2024_eLife_Knabl.pdf","date_updated":"2025-01-29T08:50:18Z","success":1,"file_id":"18941","checksum":"24548a184215d3f4547bba535ccfd7b1"}],"OA_place":"publisher","title":"Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator","_id":"18940","date_updated":"2025-01-29T08:56:21Z","OA_type":"gold","day":"07","quality_controlled":"1","doi":"10.7554/elife.80803","publication_identifier":{"issn":["2050-084X"]},"status":"public","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"type":"journal_article","article_processing_charge":"Yes"},{"type":"journal_article","article_processing_charge":"No","page":"23-42","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","quality_controlled":"1","publication_identifier":{"eissn":["1616-1599"],"issn":["0171-8630"]},"doi":"10.3354/meps14640","status":"public","day":"25","date_updated":"2025-01-29T09:12:34Z","OA_type":"green","OA_place":"repository","title":"Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes","_id":"18944","citation":{"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.” <i>Marine Ecology Progress Series</i>. Inter-Research Science Center, 2024. <a href=\"https://doi.org/10.3354/meps14640\">https://doi.org/10.3354/meps14640</a>.","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.","mla":"Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” <i>Marine Ecology Progress Series</i>, vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:<a href=\"https://doi.org/10.3354/meps14640\">10.3354/meps14640</a>.","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. <i>Marine Ecology Progress Series</i>. Inter-Research Science Center. <a href=\"https://doi.org/10.3354/meps14640\">https://doi.org/10.3354/meps14640</a>","ieee":"L. Fouqueau <i>et al.</i>, “Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes,” <i>Marine Ecology Progress Series</i>, vol. 740. Inter-Research Science Center, pp. 23–42, 2024.","ama":"Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. <i>Marine Ecology Progress Series</i>. 2024;740:23-42. doi:<a href=\"https://doi.org/10.3354/meps14640\">10.3354/meps14640</a>"},"publication":"Marine Ecology Progress Series","department":[{"_id":"NiBa"}],"publisher":"Inter-Research Science Center","main_file_link":[{"url":"https://inria.hal.science/hal-04624490/","open_access":"1"}],"corr_author":"1","publication_status":"published","author":[{"id":"1676e173-8143-11ed-8927-fe165216a93f","orcid":"0000-0003-0371-9339","full_name":"Fouqueau, Louise","last_name":"Fouqueau","first_name":"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","first_name":"A","last_name":"Blanfuné"},{"last_name":"Chevalier","first_name":"C","full_name":"Chevalier, C"},{"full_name":"Laurans, M","first_name":"M","last_name":"Laurans"},{"full_name":"Mauger, S","last_name":"Mauger","first_name":"S"},{"last_name":"Sourisseau","first_name":"M","full_name":"Sourisseau, M"},{"last_name":"Assis","first_name":"J","full_name":"Assis, J"},{"last_name":"Lévêque","first_name":"L","full_name":"Lévêque, L"},{"last_name":"Valero","first_name":"M","full_name":"Valero, M"}],"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 <jats:italic>Lam</jats:italic><jats:italic>inaria digitata</jats:italic> 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,"article_type":"original","year":"2024","date_published":"2024-07-25T00:00:00Z","date_created":"2025-01-29T09:09:10Z","oa":1,"language":[{"iso":"eng"}],"intvolume":"       740"},{"volume":67,"abstract":[{"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.","lang":"eng"}],"month":"05","language":[{"iso":"eng"}],"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.","issue":"11","intvolume":"        67","article_type":"original","year":"2024","date_published":"2024-05-23T00:00:00Z","date_created":"2025-01-29T09:14:19Z","author":[{"full_name":"de Souza Gama, Fernando H.","first_name":"Fernando H.","last_name":"de Souza Gama"},{"full_name":"Dutra, Luiz A.","first_name":"Luiz A.","last_name":"Dutra"},{"full_name":"Hawgood, Michael","last_name":"Hawgood","first_name":"Michael"},{"last_name":"dos Reis","first_name":"Caio Vinícius","full_name":"dos Reis, Caio Vinícius"},{"full_name":"Serafim, Ricardo A. M.","first_name":"Ricardo A. M.","last_name":"Serafim"},{"full_name":"Ferreira, Marcos A.","first_name":"Marcos A.","last_name":"Ferreira"},{"first_name":"Bruno V. M.","last_name":"Teodoro","full_name":"Teodoro, Bruno V. M."},{"first_name":"Jéssica Emi","last_name":"Takarada","full_name":"Takarada, Jéssica Emi"},{"last_name":"Santiago","first_name":"André S.","full_name":"Santiago, André S."},{"full_name":"Balourdas, Dimitrios-Ilias","last_name":"Balourdas","first_name":"Dimitrios-Ilias"},{"last_name":"Nilsson","first_name":"Ann-Sofie","full_name":"Nilsson, Ann-Sofie"},{"last_name":"Urien","first_name":"Bruno","full_name":"Urien, Bruno"},{"last_name":"Almeida","first_name":"Vitor M.","full_name":"Almeida, Vitor M."},{"full_name":"Gileadi, Carina","first_name":"Carina","last_name":"Gileadi"},{"last_name":"Ramos","first_name":"Priscila Z.","full_name":"Ramos, Priscila Z."},{"full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P","last_name":"Testa Salmazo"},{"last_name":"Vasconcelos","first_name":"Stanley N. S.","full_name":"Vasconcelos, Stanley N. S."},{"full_name":"Cunha, Micael R.","last_name":"Cunha","first_name":"Micael R."},{"full_name":"Mueller, Susanne","last_name":"Mueller","first_name":"Susanne"},{"first_name":"Stefan","last_name":"Knapp","full_name":"Knapp, Stefan"},{"last_name":"Massirer","first_name":"Katlin B.","full_name":"Massirer, Katlin B."},{"full_name":"Elkins, Jonathan M.","last_name":"Elkins","first_name":"Jonathan M."},{"first_name":"Opher","last_name":"Gileadi","full_name":"Gileadi, Opher"},{"full_name":"Mascarello, Alessandra","first_name":"Alessandra","last_name":"Mascarello"},{"last_name":"Lemmens","first_name":"Bennie B. L. G.","full_name":"Lemmens, Bennie B. L. G."},{"last_name":"Guimarães","first_name":"Cristiano R. W.","full_name":"Guimarães, Cristiano R. W."},{"full_name":"Azevedo, Hatylas","first_name":"Hatylas","last_name":"Azevedo"},{"last_name":"Couñago","first_name":"Rafael M.","full_name":"Couñago, Rafael M."}],"external_id":{"pmid":["38780468"]},"pmid":1,"publication_status":"published","date_updated":"2025-01-29T09:19:15Z","OA_type":"closed access","day":"23","citation":{"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. <i>Journal of Medicinal Chemistry</i>. 2024;67(11):8609-8629. doi:<a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">10.1021/acs.jmedchem.3c02250</a>","ieee":"F. H. de Souza Gama <i>et al.</i>, “Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε,” <i>Journal of Medicinal Chemistry</i>, 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.” <i>Journal of Medicinal Chemistry</i>, vol. 67, no. 11, American Chemical Society, 2024, pp. 8609–29, doi:<a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">10.1021/acs.jmedchem.3c02250</a>.","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. <i>Journal of Medicinal Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">https://doi.org/10.1021/acs.jmedchem.3c02250</a>","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.","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.” <i>Journal of Medicinal Chemistry</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">https://doi.org/10.1021/acs.jmedchem.3c02250</a>.","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."},"publication":"Journal of Medicinal Chemistry","publisher":"American Chemical Society","department":[{"_id":"CaBe"}],"_id":"18945","title":"Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε","type":"journal_article","article_processing_charge":"No","quality_controlled":"1","doi":"10.1021/acs.jmedchem.3c02250","publication_identifier":{"issn":["0022-2623"],"eissn":["1520-4804"]},"status":"public","page":"8609-8629","oa_version":"None","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"mla":"Bossmann, Lea, et al. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” <i>Physics and the Nature of Reality</i>, edited by Angelo Bassi et al., vol. 215, Springer Nature, 2024, pp. 307–21, doi:<a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">10.1007/978-3-031-45434-9_22</a>.","apa":"Bossmann, L., Leopold, N., Mitrouskas, D. J., &#38; 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, &#38; N. Zanghi (Eds.), <i>Physics and the Nature of Reality</i> (Vol. 215, pp. 307–321). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">https://doi.org/10.1007/978-3-031-45434-9_22</a>","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 <i>Physics and the Nature of Reality</i>, vol. 215, A. Bassi, S. Goldstein, R. Tumulka, and N. Zanghi, Eds. Cham: Springer Nature, 2024, pp. 307–321.","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. <i>Physics and the Nature of Reality</i>. Vol 215. FTPH. Cham: Springer Nature; 2024:307-321. doi:<a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">10.1007/978-3-031-45434-9_22</a>","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.","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 <i>Physics and the Nature of Reality</i>, edited by Angelo Bassi, Sheldon Goldstein, Roderich Tumulka, and Nino Zanghi, 215:307–21. FTPH. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">https://doi.org/10.1007/978-3-031-45434-9_22</a>.","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."},"place":"Cham","publication":"Physics and the Nature of Reality","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12910"}],"OA_place":"repository","title":"Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications","_id":"18948","date_updated":"2025-01-29T10:35:10Z","OA_type":"green","alternative_title":["Fundamental Theories of Physics"],"day":"04","quality_controlled":"1","publication_identifier":{"issn":["0168-1222"],"eisbn":["9783031454349"],"isbn":["9783031454332"],"eissn":["2365-6425"]},"doi":"10.1007/978-3-031-45434-9_22","status":"public","page":"307-321","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","arxiv":1,"article_processing_charge":"No","oa":1,"language":[{"iso":"eng"}],"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.","intvolume":"       215","year":"2024","date_published":"2024-02-04T00:00:00Z","editor":[{"last_name":"Bassi","first_name":"Angelo","full_name":"Bassi, Angelo"},{"full_name":"Goldstein, Sheldon","last_name":"Goldstein","first_name":"Sheldon"},{"first_name":"Roderich","last_name":"Tumulka","full_name":"Tumulka, Roderich"},{"full_name":"Zanghi, Nino","first_name":"Nino","last_name":"Zanghi"}],"date_created":"2025-01-29T10:30:08Z","volume":215,"series_title":"FTPH","abstract":[{"lang":"eng","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."}],"month":"02","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343","last_name":"Bossmann","first_name":"Lea"},{"last_name":"Leopold","first_name":"Nikolai","full_name":"Leopold, Nikolai"},{"last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes"},{"last_name":"Petrat","first_name":"Sören","full_name":"Petrat, Sören"}],"external_id":{"arxiv":["2304.12910"]},"publication_status":"published"},{"author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Cutter, Asher D","last_name":"Cutter","first_name":"Asher D"},{"full_name":"Satokangas, Ina","first_name":"Ina","last_name":"Satokangas"},{"last_name":"Lerch","first_name":"Brian A","full_name":"Lerch, Brian A"},{"last_name":"Rolland","first_name":"Jonathan","full_name":"Rolland, Jonathan"},{"last_name":"Smadja","first_name":"Carole M","full_name":"Smadja, Carole M"},{"last_name":"Segami Marzal","first_name":"J Carolina","full_name":"Segami Marzal, J Carolina"},{"first_name":"Christopher R","last_name":"Cooney","full_name":"Cooney, Christopher R"},{"full_name":"Feulner, Philine G D","last_name":"Feulner","first_name":"Philine G D"},{"full_name":"Domingos, Fabricius Maia Chaves Bicalho","last_name":"Domingos","first_name":"Fabricius Maia Chaves Bicalho"},{"last_name":"North","first_name":"Henry L","full_name":"North, Henry L"},{"full_name":"Yamaguchi, Ryo","last_name":"Yamaguchi","first_name":"Ryo"},{"full_name":"Butlin, Roger K","last_name":"Butlin","first_name":"Roger K"},{"last_name":"Wolf","first_name":"Jochen B W","full_name":"Wolf, Jochen B W"},{"first_name":"Jenn","last_name":"Coughlan","full_name":"Coughlan, Jenn"},{"first_name":"Patrick","last_name":"Heidbreder","full_name":"Heidbreder, Patrick"},{"full_name":"Hernández-Gutiérrez, Rebeca","last_name":"Hernández-Gutiérrez","first_name":"Rebeca"},{"full_name":"Barnard-Kubow, Karen B","first_name":"Karen B","last_name":"Barnard-Kubow"},{"full_name":"Peede, David","first_name":"David","last_name":"Peede"},{"last_name":"Rancilhac","first_name":"Loïs","full_name":"Rancilhac, Loïs"},{"full_name":"Salvador, Rodrigo Brincalepe","last_name":"Salvador","first_name":"Rodrigo Brincalepe"},{"full_name":"Thompson, Ken A","first_name":"Ken A","last_name":"Thompson"},{"full_name":"Stacy, Elizabeth A","last_name":"Stacy","first_name":"Elizabeth A"},{"first_name":"Leonie C","last_name":"Moyle","full_name":"Moyle, Leonie C"},{"first_name":"Martin D","last_name":"Garlovsky","full_name":"Garlovsky, Martin D"},{"full_name":"Maulana, Arif","last_name":"Maulana","first_name":"Arif"},{"full_name":"Kantelinen, Annina","last_name":"Kantelinen","first_name":"Annina"},{"full_name":"Cacho, N Ivalú","last_name":"Cacho","first_name":"N Ivalú"},{"last_name":"Schneemann","first_name":"Hilde","full_name":"Schneemann, Hilde"},{"last_name":"Domínguez","first_name":"Marisol","full_name":"Domínguez, Marisol"},{"last_name":"Dopman","first_name":"Erik B","full_name":"Dopman, Erik B"},{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"first_name":"Sina J","last_name":"Rometsch","full_name":"Rometsch, Sina J"},{"full_name":"Comeault, Aaron A","last_name":"Comeault","first_name":"Aaron A"},{"full_name":"Merrill, Richard M","first_name":"Richard M","last_name":"Merrill"},{"last_name":"Scordato","first_name":"Elizabeth S C","full_name":"Scordato, Elizabeth S C"},{"last_name":"Singhal","first_name":"Sonal","full_name":"Singhal, Sonal"},{"last_name":"Pärssinen","first_name":"Varpu","full_name":"Pärssinen, Varpu"},{"full_name":"Lackey, Alycia C R","first_name":"Alycia C R","last_name":"Lackey"},{"full_name":"Kumar, Sanghamitra","last_name":"Kumar","first_name":"Sanghamitra"},{"full_name":"Meier, Joana I","last_name":"Meier","first_name":"Joana I"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"last_name":"Kulmuni","first_name":"Jonna","full_name":"Kulmuni, Jonna"}],"corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_number":"kzae001","publication_status":"published","acknowledgement":"We thank the staff of the Tvärminne Zoological Station (University of Helsinki) for their hospitality during the workshop. 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.","oa":1,"issue":"1","language":[{"iso":"eng"}],"intvolume":"         3","year":"2024","article_type":"original","file_date_updated":"2025-01-29T10:52:40Z","date_published":"2024-02-16T00:00:00Z","date_created":"2025-01-29T10:38:17Z","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","quality_controlled":"1","doi":"10.1093/evolinnean/kzae001","publication_identifier":{"issn":["2752-938X"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","ddc":["570"],"type":"journal_article","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. <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolinnean/kzae001\">https://doi.org/10.1093/evolinnean/kzae001</a>","mla":"Stankowski, Sean, et al. “Toward the Integration of Speciation Research.” <i>Evolutionary Journal of the Linnean Society</i>, vol. 3, no. 1, kzae001, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/evolinnean/kzae001\">10.1093/evolinnean/kzae001</a>.","ieee":"S. Stankowski <i>et al.</i>, “Toward the integration of speciation research,” <i>Evolutionary Journal of the Linnean Society</i>, vol. 3, no. 1. Oxford University Press, 2024.","ama":"Stankowski S, Cutter AD, Satokangas I, et al. Toward the integration of speciation research. <i>Evolutionary Journal of the Linnean Society</i>. 2024;3(1). doi:<a href=\"https://doi.org/10.1093/evolinnean/kzae001\">10.1093/evolinnean/kzae001</a>","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.","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.” <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/evolinnean/kzae001\">https://doi.org/10.1093/evolinnean/kzae001</a>.","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)."},"publication":"Evolutionary Journal of the Linnean Society","has_accepted_license":"1","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","file":[{"access_level":"open_access","date_created":"2025-01-29T10:52:40Z","relation":"main_file","file_size":3935454,"content_type":"application/pdf","creator":"dernst","file_id":"18950","checksum":"db08120a92527acaef476bd93f2b87f9","success":1,"date_updated":"2025-01-29T10:52:40Z","file_name":"2024_EvolJourLinneanSoc_Stankowski.pdf"}],"OA_place":"publisher","_id":"18949","title":"Toward the integration of speciation research","date_updated":"2025-01-29T10:55:54Z","OA_type":"gold","day":"16"},{"department":[{"_id":"MaKw"}],"publisher":"EMS Press","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.10930","open_access":"1"}],"citation":{"ieee":"I. Hartarsky, L. Lichev, and F. L. Toninelli, “Local dimer dynamics in higher dimensions,” <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions</i>. EMS Press, 2024.","mla":"Hartarsky, Ivailo, et al. “Local Dimer Dynamics in Higher Dimensions.” <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions</i>, EMS Press, 2024, doi:<a href=\"https://doi.org/10.4171/aihpd/200\">10.4171/aihpd/200</a>.","apa":"Hartarsky, I., Lichev, L., &#38; Toninelli, F. L. (2024). Local dimer dynamics in higher dimensions. <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions</i>. EMS Press. <a href=\"https://doi.org/10.4171/aihpd/200\">https://doi.org/10.4171/aihpd/200</a>","ama":"Hartarsky I, Lichev L, Toninelli FL. Local dimer dynamics in higher dimensions. <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions</i>. 2024. doi:<a href=\"https://doi.org/10.4171/aihpd/200\">10.4171/aihpd/200</a>","chicago":"Hartarsky, Ivailo, Lyuben Lichev, and Fabio Lucio Toninelli. “Local Dimer Dynamics in Higher Dimensions.” <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions</i>. EMS Press, 2024. <a href=\"https://doi.org/10.4171/aihpd/200\">https://doi.org/10.4171/aihpd/200</a>.","ista":"Hartarsky I, Lichev L, Toninelli FL. 2024. Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions.","short":"I. Hartarsky, L. Lichev, F.L. Toninelli, Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions (2024)."},"publication":"Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions","title":"Local dimer dynamics in higher dimensions","_id":"18951","OA_place":"repository","OA_type":"gold","date_updated":"2025-07-08T08:39:55Z","day":"26","status":"public","quality_controlled":"1","publication_identifier":{"eissn":["2308-5835"],"issn":["2308-5827"]},"doi":"10.4171/aihpd/200","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Preprint","arxiv":1,"article_processing_charge":"Yes","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"date_created":"2025-01-29T10:57:09Z","article_type":"original","year":"2024","date_published":"2024-08-26T00:00:00Z","month":"08","abstract":[{"text":"We consider local dynamics of the dimer model (perfect matchings) on hypercubic boxes [n] \r\nd . These consist of successively switching the dimers along alternating cycles of prescribed (small) lengths. We study the connectivity properties of the dimer configuration space equipped with these transitions. Answering a question of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any configuration admits an alternating cycle of length at most 6. We further establish that any configuration on [n] d  features order n d−2  alternating cycles of length at most 4d−2. We also prove that the dynamics of dimer configurations on the unit hypercube of dimension d is ergodic when switching alternating cycles of length at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped boxes in the triangular lattice are ergodic for switching alternating cycles of lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also uses 8-cycles. None of our proofs make reference to height functions.","lang":"eng"}],"DOAJ_listed":"1","author":[{"first_name":"Ivailo","last_name":"Hartarsky","full_name":"Hartarsky, Ivailo"},{"full_name":"Lichev, Lyuben","id":"9aa8388e-d003-11ee-8458-c4c1d7447977","first_name":"Lyuben","last_name":"Lichev"},{"first_name":"Fabio Lucio","last_name":"Toninelli","full_name":"Toninelli, Fabio Lucio"}],"publication_status":"epub_ahead","external_id":{"arxiv":["2304.10930"]}},{"has_accepted_license":"1","publication":"Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials","citation":{"short":"L.M. Hunnisett, J. Nyman, N. Francia, N.S. Abraham, C.S. Adjiman, S. Aitipamula, T. Alkhidir, M. Almehairbi, A. Anelli, D.M. Anstine, J.E. Anthony, J.E. Arnold, F. Bahrami, M.A. Bellucci, R.M. Bhardwaj, I. Bier, J.A. Bis, A.D. Boese, D.H. Bowskill, J. Bramley, J.G. Brandenburg, D.E. Braun, P.W.V. Butler, J. Cadden, S. Carino, E.J. Chan, C. Chang, B. Cheng, S.M. Clarke, S.J. Coles, R.I. Cooper, R. Couch, R. Cuadrado, T. Darden, G.M. Day, H. Dietrich, Y. Ding, A. DiPasquale, B. Dhokale, B.P. van Eijck, M.R.J. Elsegood, D. Firaha, W. Fu, K. Fukuzawa, J. Glover, H. Goto, C. Greenwell, R. Guo, J. Harter, J. Helfferich, D.W.M. Hofmann, J. Hoja, J. Hone, R. Hong, G. Hutchison, Y. Ikabata, O. Isayev, O. Ishaque, V. Jain, Y. Jin, A. Jing, E.R. Johnson, I. Jones, K.V.J. Jose, E.A. Kabova, A. Keates, P.F. Kelly, D. Khakimov, S. Konstantinopoulos, L.N. Kuleshova, H. Li, X. Lin, A. List, C. Liu, Y.M. Liu, Z. Liu, Z.-P. Liu, J.W. Lubach, N. Marom, A.A. Maryewski, H. Matsui, A. Mattei, R.A. Mayo, J.W. Melkumov, S. Mohamed, Z. Momenzadeh Abardeh, H.S. Muddana, N. Nakayama, K.S. Nayal, M.A. Neumann, R. Nikhar, S. Obata, D. O’Connor, A.R. Oganov, K. Okuwaki, A. Otero-de-la-Roza, C.C. Pantelides, S. Parkin, C.J. Pickard, L. Pilia, T. Pivina, R. Podeszwa, A.J.A. Price, L.S. Price, S.L. Price, M.R. Probert, A. Pulido, G.R. Ramteke, A.U. Rehman, S.M. Reutzel-Edens, J. Rogal, M.J. Ross, A.F. Rumson, G. Sadiq, Z.M. Saeed, A. Salimi, M. Salvalaglio, L. Sanders de Almada, K. Sasikumar, S. Sekharan, C. Shang, K. Shankland, K. Shinohara, B. Shi, X. Shi, A.G. Skillman, H. Song, N. Strasser, J. van de Streek, I.J. Sugden, G. Sun, K. Szalewicz, B.I. Tan, L. Tan, F. Tarczynski, C.R. Taylor, A. Tkatchenko, R. Tom, M.E. Tuckerman, Y. Utsumi, L. Vogt-Maranto, J. Weatherston, L.J. Wilkinson, R.D. Willacy, L. Wojtas, G.R. Woollam, Z. Yang, E. Yonemochi, X. Yue, Q. Zeng, Y. Zhang, T. Zhou, Y. Zhou, R. Zubatyuk, J.C. Cole, Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 80 (2024) 517–547.","ista":"Hunnisett LM et al. 2024. The seventh blind test of crystal structure prediction: Structure generation methods. Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials. 80(6), 517–547.","chicago":"Hunnisett, Lily M., Jonas Nyman, Nicholas Francia, Nathan S. Abraham, Claire S. Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, et al. “The Seventh Blind Test of Crystal Structure Prediction: Structure Generation Methods.” <i>Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials</i>. International Union of Crystallography, 2024. <a href=\"https://doi.org/10.1107/s2052520624007492\">https://doi.org/10.1107/s2052520624007492</a>.","ama":"Hunnisett LM, Nyman J, Francia N, et al. The seventh blind test of crystal structure prediction: Structure generation methods. <i>Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials</i>. 2024;80(6):517-547. doi:<a href=\"https://doi.org/10.1107/s2052520624007492\">10.1107/s2052520624007492</a>","mla":"Hunnisett, Lily M., et al. “The Seventh Blind Test of Crystal Structure Prediction: Structure Generation Methods.” <i>Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials</i>, vol. 80, no. 6, International Union of Crystallography, 2024, pp. 517–47, doi:<a href=\"https://doi.org/10.1107/s2052520624007492\">10.1107/s2052520624007492</a>.","apa":"Hunnisett, L. M., Nyman, J., Francia, N., Abraham, N. S., Adjiman, C. S., Aitipamula, S., … Cole, J. C. (2024). The seventh blind test of crystal structure prediction: Structure generation methods. <i>Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials</i>. International Union of Crystallography. <a href=\"https://doi.org/10.1107/s2052520624007492\">https://doi.org/10.1107/s2052520624007492</a>","ieee":"L. M. Hunnisett <i>et al.</i>, “The seventh blind test of crystal structure prediction: Structure generation methods,” <i>Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials</i>, vol. 80, no. 6. International Union of Crystallography, pp. 517–547, 2024."},"file":[{"creator":"dernst","file_size":10061037,"content_type":"application/pdf","date_created":"2025-01-29T11:09:48Z","relation":"main_file","access_level":"open_access","file_name":"2024_ActaCrystallographicaB_Hunnisett.pdf","date_updated":"2025-01-29T11:09:48Z","success":1,"file_id":"18954","checksum":"33b8083e76564cc918182b0b0b2cc023"}],"publisher":"International Union of Crystallography","department":[{"_id":"BiCh"}],"OA_place":"publisher","title":"The seventh blind test of crystal structure prediction: Structure generation methods","_id":"18952","date_updated":"2025-09-09T12:12:31Z","OA_type":"hybrid","day":"01","doi":"10.1107/s2052520624007492","publication_identifier":{"issn":["2052-5206"]},"quality_controlled":"1","status":"public","oa_version":"Published Version","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"517-547","ddc":["540"],"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"The CCDC Blind Test Team. The CCDC organizers (L. M. Hunnisett, J. Nyman, N. Francia, I. Sugden, G. Sadiq, and J. C. Cole) gratefully acknowledge numerous CCDC colleagues for\r\ntheir helpful feedback and suggestions on the manuscript (P. McCabe, E. Pidcock, P. Martinez-Bulit, C. Kingsbury), providing useful python knowledge (A. Moldovan), providing and maintaining internal compute resources (K. Taylor, M. Burling, J. Swift, L. Wallis), monitoring and depositing structures in the CSD (S. Ward, K. Orzechowska, V. Menon), support in organization of the blind test meeting (E. Clarke),and improvements to the Crystal Packing Similarity tool (M.\r\nRead). Data analysis was performed using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/T022159/1), and DiRAC funding from the Science and Technology Facilities Council (www.dirac.ac.uk). N. Francia  thanks M. Salvalaglio for advice on the metadynamics simulations and the University College London for providing access to the Kathleen High Performance Computing Facility Kathleen@UCL) on which simulations were performed. N. Francia also thanks V. Kurlin and D. E. Widdowson for counselling on crystal structure similarity. I. Sugden and N. Francia participated in the blind test as members of Groups 1 and 24, respectively. They were involved in the analysis of the results.\r\nand in writing this paper only after all results were made\r\navailable to participants.","issue":"6","language":[{"iso":"eng"}],"isi":1,"oa":1,"intvolume":"        80","file_date_updated":"2025-01-29T11:09:48Z","date_published":"2024-12-01T00:00:00Z","article_type":"original","year":"2024","date_created":"2025-01-29T11:07:36Z","volume":80,"abstract":[{"text":"A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.","lang":"eng"}],"month":"12","author":[{"last_name":"Hunnisett","first_name":"Lily M.","full_name":"Hunnisett, Lily M."},{"full_name":"Nyman, Jonas","first_name":"Jonas","last_name":"Nyman"},{"full_name":"Francia, Nicholas","last_name":"Francia","first_name":"Nicholas"},{"full_name":"Abraham, Nathan S.","last_name":"Abraham","first_name":"Nathan S."},{"first_name":"Claire S.","last_name":"Adjiman","full_name":"Adjiman, Claire S."},{"last_name":"Aitipamula","first_name":"Srinivasulu","full_name":"Aitipamula, Srinivasulu"},{"first_name":"Tamador","last_name":"Alkhidir","full_name":"Alkhidir, Tamador"},{"last_name":"Almehairbi","first_name":"Mubarak","full_name":"Almehairbi, Mubarak"},{"last_name":"Anelli","first_name":"Andrea","full_name":"Anelli, Andrea"},{"last_name":"Anstine","first_name":"Dylan M.","full_name":"Anstine, Dylan M."},{"last_name":"Anthony","first_name":"John E.","full_name":"Anthony, John E."},{"full_name":"Arnold, Joseph E.","last_name":"Arnold","first_name":"Joseph E."},{"first_name":"Faezeh","last_name":"Bahrami","full_name":"Bahrami, Faezeh"},{"last_name":"Bellucci","first_name":"Michael A.","full_name":"Bellucci, Michael A."},{"last_name":"Bhardwaj","first_name":"Rajni M.","full_name":"Bhardwaj, Rajni M."},{"full_name":"Bier, Imanuel","first_name":"Imanuel","last_name":"Bier"},{"last_name":"Bis","first_name":"Joanna A.","full_name":"Bis, Joanna A."},{"full_name":"Boese, A. Daniel","last_name":"Boese","first_name":"A. Daniel"},{"full_name":"Bowskill, David H.","last_name":"Bowskill","first_name":"David H."},{"full_name":"Bramley, James","first_name":"James","last_name":"Bramley"},{"full_name":"Brandenburg, Jan Gerit","last_name":"Brandenburg","first_name":"Jan Gerit"},{"full_name":"Braun, Doris E.","first_name":"Doris E.","last_name":"Braun"},{"full_name":"Butler, Patrick W. V.","first_name":"Patrick W. V.","last_name":"Butler"},{"last_name":"Cadden","first_name":"Joseph","full_name":"Cadden, Joseph"},{"full_name":"Carino, Stephen","first_name":"Stephen","last_name":"Carino"},{"last_name":"Chan","first_name":"Eric J.","full_name":"Chan, Eric J."},{"first_name":"Chao","last_name":"Chang","full_name":"Chang, Chao"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing"},{"last_name":"Clarke","first_name":"Sarah M.","full_name":"Clarke, Sarah M."},{"full_name":"Coles, Simon J.","last_name":"Coles","first_name":"Simon J."},{"last_name":"Cooper","first_name":"Richard I.","full_name":"Cooper, Richard I."},{"last_name":"Couch","first_name":"Ricky","full_name":"Couch, Ricky"},{"last_name":"Cuadrado","first_name":"Ramon","full_name":"Cuadrado, Ramon"},{"full_name":"Darden, Tom","first_name":"Tom","last_name":"Darden"},{"first_name":"Graeme M.","last_name":"Day","full_name":"Day, Graeme M."},{"full_name":"Dietrich, Hanno","last_name":"Dietrich","first_name":"Hanno"},{"full_name":"Ding, Yiming","first_name":"Yiming","last_name":"Ding"},{"last_name":"DiPasquale","first_name":"Antonio","full_name":"DiPasquale, Antonio"},{"last_name":"Dhokale","first_name":"Bhausaheb","full_name":"Dhokale, Bhausaheb"},{"first_name":"Bouke P.","last_name":"van Eijck","full_name":"van Eijck, Bouke P."},{"full_name":"Elsegood, Mark R. J.","first_name":"Mark R. J.","last_name":"Elsegood"},{"full_name":"Firaha, Dzmitry","last_name":"Firaha","first_name":"Dzmitry"},{"first_name":"Wenbo","last_name":"Fu","full_name":"Fu, Wenbo"},{"full_name":"Fukuzawa, Kaori","first_name":"Kaori","last_name":"Fukuzawa"},{"full_name":"Glover, Joseph","first_name":"Joseph","last_name":"Glover"},{"first_name":"Hitoshi","last_name":"Goto","full_name":"Goto, Hitoshi"},{"full_name":"Greenwell, Chandler","first_name":"Chandler","last_name":"Greenwell"},{"full_name":"Guo, Rui","first_name":"Rui","last_name":"Guo"},{"first_name":"Jürgen","last_name":"Harter","full_name":"Harter, Jürgen"},{"last_name":"Helfferich","first_name":"Julian","full_name":"Helfferich, Julian"},{"full_name":"Hofmann, Detlef W. M.","last_name":"Hofmann","first_name":"Detlef W. M."},{"full_name":"Hoja, Johannes","first_name":"Johannes","last_name":"Hoja"},{"full_name":"Hone, John","last_name":"Hone","first_name":"John"},{"full_name":"Hong, Richard","first_name":"Richard","last_name":"Hong"},{"first_name":"Geoffrey","last_name":"Hutchison","full_name":"Hutchison, Geoffrey"},{"full_name":"Ikabata, Yasuhiro","last_name":"Ikabata","first_name":"Yasuhiro"},{"full_name":"Isayev, Olexandr","last_name":"Isayev","first_name":"Olexandr"},{"last_name":"Ishaque","first_name":"Ommair","full_name":"Ishaque, Ommair"},{"full_name":"Jain, Varsha","first_name":"Varsha","last_name":"Jain"},{"full_name":"Jin, Yingdi","last_name":"Jin","first_name":"Yingdi"},{"last_name":"Jing","first_name":"Aling","full_name":"Jing, Aling"},{"full_name":"Johnson, Erin R.","first_name":"Erin R.","last_name":"Johnson"},{"first_name":"Ian","last_name":"Jones","full_name":"Jones, Ian"},{"last_name":"Jose","first_name":"K. V. Jovan","full_name":"Jose, K. V. Jovan"},{"full_name":"Kabova, Elena A.","first_name":"Elena A.","last_name":"Kabova"},{"last_name":"Keates","first_name":"Adam","full_name":"Keates, Adam"},{"first_name":"Paul F.","last_name":"Kelly","full_name":"Kelly, Paul F."},{"last_name":"Khakimov","first_name":"Dmitry","full_name":"Khakimov, Dmitry"},{"first_name":"Stefanos","last_name":"Konstantinopoulos","full_name":"Konstantinopoulos, Stefanos"},{"full_name":"Kuleshova, Liudmila N.","last_name":"Kuleshova","first_name":"Liudmila N."},{"full_name":"Li, He","first_name":"He","last_name":"Li"},{"full_name":"Lin, Xiaolu","last_name":"Lin","first_name":"Xiaolu"},{"full_name":"List, Alexander","last_name":"List","first_name":"Alexander"},{"full_name":"Liu, Congcong","first_name":"Congcong","last_name":"Liu"},{"full_name":"Liu, Yifei Michelle","last_name":"Liu","first_name":"Yifei Michelle"},{"full_name":"Liu, Zenghui","first_name":"Zenghui","last_name":"Liu"},{"first_name":"Zhi-Pan","last_name":"Liu","full_name":"Liu, Zhi-Pan"},{"full_name":"Lubach, Joseph W.","first_name":"Joseph W.","last_name":"Lubach"},{"full_name":"Marom, Noa","first_name":"Noa","last_name":"Marom"},{"last_name":"Maryewski","first_name":"Alexander A.","full_name":"Maryewski, Alexander A."},{"first_name":"Hiroyuki","last_name":"Matsui","full_name":"Matsui, Hiroyuki"},{"first_name":"Alessandra","last_name":"Mattei","full_name":"Mattei, Alessandra"},{"full_name":"Mayo, R. Alex","first_name":"R. Alex","last_name":"Mayo"},{"full_name":"Melkumov, John W.","last_name":"Melkumov","first_name":"John W."},{"last_name":"Mohamed","first_name":"Sharmarke","full_name":"Mohamed, Sharmarke"},{"first_name":"Zahrasadat","last_name":"Momenzadeh Abardeh","full_name":"Momenzadeh Abardeh, Zahrasadat"},{"last_name":"Muddana","first_name":"Hari S.","full_name":"Muddana, Hari S."},{"last_name":"Nakayama","first_name":"Naofumi","full_name":"Nakayama, Naofumi"},{"full_name":"Nayal, Kamal Singh","first_name":"Kamal Singh","last_name":"Nayal"},{"first_name":"Marcus A.","last_name":"Neumann","full_name":"Neumann, Marcus A."},{"full_name":"Nikhar, Rahul","last_name":"Nikhar","first_name":"Rahul"},{"last_name":"Obata","first_name":"Shigeaki","full_name":"Obata, Shigeaki"},{"first_name":"Dana","last_name":"O'Connor","full_name":"O'Connor, Dana"},{"full_name":"Oganov, Artem R.","first_name":"Artem R.","last_name":"Oganov"},{"last_name":"Okuwaki","first_name":"Koji","full_name":"Okuwaki, Koji"},{"full_name":"Otero-de-la-Roza, Alberto","last_name":"Otero-de-la-Roza","first_name":"Alberto"},{"full_name":"Pantelides, Constantinos C.","first_name":"Constantinos C.","last_name":"Pantelides"},{"first_name":"Sean","last_name":"Parkin","full_name":"Parkin, Sean"},{"full_name":"Pickard, Chris J.","first_name":"Chris J.","last_name":"Pickard"},{"full_name":"Pilia, Luca","last_name":"Pilia","first_name":"Luca"},{"full_name":"Pivina, Tatyana","last_name":"Pivina","first_name":"Tatyana"},{"first_name":"Rafał","last_name":"Podeszwa","full_name":"Podeszwa, Rafał"},{"full_name":"Price, Alastair J. A.","last_name":"Price","first_name":"Alastair J. A."},{"full_name":"Price, Louise S.","last_name":"Price","first_name":"Louise S."},{"full_name":"Price, Sarah L.","first_name":"Sarah L.","last_name":"Price"},{"full_name":"Probert, Michael R.","first_name":"Michael R.","last_name":"Probert"},{"first_name":"Angeles","last_name":"Pulido","full_name":"Pulido, Angeles"},{"full_name":"Ramteke, Gunjan Rajendra","last_name":"Ramteke","first_name":"Gunjan Rajendra"},{"first_name":"Atta Ur","last_name":"Rehman","full_name":"Rehman, Atta Ur"},{"full_name":"Reutzel-Edens, Susan M.","first_name":"Susan M.","last_name":"Reutzel-Edens"},{"full_name":"Rogal, Jutta","last_name":"Rogal","first_name":"Jutta"},{"last_name":"Ross","first_name":"Marta J.","full_name":"Ross, Marta J."},{"first_name":"Adrian F.","last_name":"Rumson","full_name":"Rumson, Adrian F."},{"full_name":"Sadiq, Ghazala","last_name":"Sadiq","first_name":"Ghazala"},{"full_name":"Saeed, Zeinab M.","first_name":"Zeinab M.","last_name":"Saeed"},{"first_name":"Alireza","last_name":"Salimi","full_name":"Salimi, Alireza"},{"full_name":"Salvalaglio, Matteo","first_name":"Matteo","last_name":"Salvalaglio"},{"last_name":"Sanders de Almada","first_name":"Leticia","full_name":"Sanders de Almada, Leticia"},{"first_name":"Kiran","last_name":"Sasikumar","full_name":"Sasikumar, Kiran"},{"full_name":"Sekharan, Sivakumar","last_name":"Sekharan","first_name":"Sivakumar"},{"first_name":"Cheng","last_name":"Shang","full_name":"Shang, Cheng"},{"full_name":"Shankland, Kenneth","first_name":"Kenneth","last_name":"Shankland"},{"full_name":"Shinohara, Kotaro","first_name":"Kotaro","last_name":"Shinohara"},{"full_name":"Shi, Baimei","last_name":"Shi","first_name":"Baimei"},{"first_name":"Xuekun","last_name":"Shi","full_name":"Shi, Xuekun"},{"full_name":"Skillman, A. Geoffrey","last_name":"Skillman","first_name":"A. Geoffrey"},{"first_name":"Hongxing","last_name":"Song","full_name":"Song, Hongxing"},{"last_name":"Strasser","first_name":"Nina","full_name":"Strasser, Nina"},{"full_name":"van de Streek, Jacco","first_name":"Jacco","last_name":"van de Streek"},{"last_name":"Sugden","first_name":"Isaac J.","full_name":"Sugden, Isaac J."},{"full_name":"Sun, Guangxu","last_name":"Sun","first_name":"Guangxu"},{"full_name":"Szalewicz, Krzysztof","last_name":"Szalewicz","first_name":"Krzysztof"},{"full_name":"Tan, Benjamin I.","last_name":"Tan","first_name":"Benjamin I."},{"first_name":"Lu","last_name":"Tan","full_name":"Tan, Lu"},{"first_name":"Frank","last_name":"Tarczynski","full_name":"Tarczynski, Frank"},{"full_name":"Taylor, Christopher R.","last_name":"Taylor","first_name":"Christopher R."},{"last_name":"Tkatchenko","first_name":"Alexandre","full_name":"Tkatchenko, Alexandre"},{"last_name":"Tom","first_name":"Rithwik","full_name":"Tom, Rithwik"},{"full_name":"Tuckerman, Mark E.","last_name":"Tuckerman","first_name":"Mark E."},{"full_name":"Utsumi, Yohei","first_name":"Yohei","last_name":"Utsumi"},{"first_name":"Leslie","last_name":"Vogt-Maranto","full_name":"Vogt-Maranto, Leslie"},{"full_name":"Weatherston, Jake","last_name":"Weatherston","first_name":"Jake"},{"last_name":"Wilkinson","first_name":"Luke J.","full_name":"Wilkinson, Luke J."},{"last_name":"Willacy","first_name":"Robert D.","full_name":"Willacy, Robert D."},{"first_name":"Lukasz","last_name":"Wojtas","full_name":"Wojtas, Lukasz"},{"full_name":"Woollam, Grahame R.","first_name":"Grahame R.","last_name":"Woollam"},{"full_name":"Yang, Zhuocen","last_name":"Yang","first_name":"Zhuocen"},{"full_name":"Yonemochi, Etsuo","last_name":"Yonemochi","first_name":"Etsuo"},{"full_name":"Yue, Xin","last_name":"Yue","first_name":"Xin"},{"full_name":"Zeng, Qun","last_name":"Zeng","first_name":"Qun"},{"full_name":"Zhang, Yizu","first_name":"Yizu","last_name":"Zhang"},{"last_name":"Zhou","first_name":"Tian","full_name":"Zhou, Tian"},{"full_name":"Zhou, Yunfei","first_name":"Yunfei","last_name":"Zhou"},{"full_name":"Zubatyuk, Roman","first_name":"Roman","last_name":"Zubatyuk"},{"full_name":"Cole, Jason C.","last_name":"Cole","first_name":"Jason C."}],"external_id":{"pmid":["39405196"],"isi":["001388840500003"]},"publication_status":"published","tmp":{"image":"/images/cc_by.png","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)"},"pmid":1},{"author":[{"full_name":"Casares, Antonio","last_name":"Casares","first_name":"Antonio"},{"full_name":"Pilipczuk, Marcin","first_name":"Marcin","last_name":"Pilipczuk"},{"last_name":"Pilipczuk","first_name":"Michał","full_name":"Pilipczuk, Michał"},{"first_name":"Uéverton S.","last_name":"Souza","full_name":"Souza, Uéverton S."},{"last_name":"Thejaswini","first_name":"K. S.","id":"3807fb92-fdc1-11ee-bb4a-b4d8a431c753","full_name":"Thejaswini, K. S."}],"external_id":{"arxiv":["2310.20433"]},"publication_status":"published","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"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","language":[{"iso":"eng"}],"oa":1,"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.","date_published":"2024-01-01T00:00:00Z","year":"2024","date_created":"2025-01-29T11:55:50Z","type":"conference","arxiv":1,"article_processing_charge":"No","publication_identifier":{"isbn":["9781611977936"]},"doi":"10.1137/1.9781611977936.16","quality_controlled":"1","status":"public","ec_funded":1,"scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"160-167","conference":{"location":"Alexandria, VA, United States","name":"SOSA: Symposium on Simplicity in Algorithms","start_date":"2024-01-08","end_date":"2024-01-10"},"date_updated":"2025-04-14T07:55:54Z","OA_type":"green","day":"01","publication":"2024 Symposium on Simplicity in Algorithms","citation":{"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 <i>2024 Symposium on Simplicity in Algorithms</i>, 160–67. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/1.9781611977936.16\">https://doi.org/10.1137/1.9781611977936.16</a>.","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.","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.","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 <i>2024 Symposium on Simplicity in Algorithms</i>, Alexandria, VA, United States, 2024, pp. 160–167.","apa":"Casares, A., Pilipczuk, M., Pilipczuk, M., Souza, U. S., &#38; Thejaswini, K. S. (2024). Simple and tight complexity lower bounds for solving Rabin games. In <i>2024 Symposium on Simplicity in Algorithms</i> (pp. 160–167). Alexandria, VA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977936.16\">https://doi.org/10.1137/1.9781611977936.16</a>","mla":"Casares, Antonio, et al. “Simple and Tight Complexity Lower Bounds for Solving Rabin Games.” <i>2024 Symposium on Simplicity in Algorithms</i>, Society for Industrial and Applied Mathematics, 2024, pp. 160–67, doi:<a href=\"https://doi.org/10.1137/1.9781611977936.16\">10.1137/1.9781611977936.16</a>.","ama":"Casares A, Pilipczuk M, Pilipczuk M, Souza US, Thejaswini KS. Simple and tight complexity lower bounds for solving Rabin games. In: <i>2024 Symposium on Simplicity in Algorithms</i>. Society for Industrial and Applied Mathematics; 2024:160-167. doi:<a href=\"https://doi.org/10.1137/1.9781611977936.16\">10.1137/1.9781611977936.16</a>"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.20433","open_access":"1"}],"department":[{"_id":"ToHe"}],"publisher":"Society for Industrial and Applied Mathematics","OA_place":"repository","title":"Simple and tight complexity lower bounds for solving Rabin games","_id":"18955"},{"type":"conference","arxiv":1,"article_processing_charge":"No","page":"977-983","related_material":{"link":[{"url":"https://github.com/berkerdemirel/decompl","relation":"software"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","conference":{"end_date":"2024-10-30","name":"ICIP: International Conference on Image Processing","start_date":"2024-10-27","location":"Abu Dhabi, United Arab Emirates"},"quality_controlled":"1","publication_identifier":{"eissn":["2381-8549"],"eisbn":["9798350349399"]},"doi":"10.1109/icip51287.2024.10647499","status":"public","day":"01","date_updated":"2025-09-09T12:13:12Z","OA_type":"green","OA_place":"repository","_id":"18956","title":"Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image","citation":{"ama":"Demirel B, Ozkan H. Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. In: <i>2024 IEEE International Conference on Image Processing</i>. IEEE; 2024:977-983. doi:<a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">10.1109/icip51287.2024.10647499</a>","ieee":"B. Demirel and H. Ozkan, “Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image,” in <i>2024 IEEE International Conference on Image Processing</i>, Abu Dhabi, United Arab Emirates, 2024, pp. 977–983.","mla":"Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning with Attention Pooling for Group Activity Recognition from a Single Volleyball Image.” <i>2024 IEEE International Conference on Image Processing</i>, IEEE, 2024, pp. 977–83, doi:<a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">10.1109/icip51287.2024.10647499</a>.","apa":"Demirel, B., &#38; Ozkan, H. (2024). Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. In <i>2024 IEEE International Conference on Image Processing</i> (pp. 977–983). Abu Dhabi, United Arab Emirates: IEEE. <a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">https://doi.org/10.1109/icip51287.2024.10647499</a>","short":"B. Demirel, H. Ozkan, in:, 2024 IEEE International Conference on Image Processing, IEEE, 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 <i>2024 IEEE International Conference on Image Processing</i>, 977–83. IEEE, 2024. <a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">https://doi.org/10.1109/icip51287.2024.10647499</a>.","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."},"publication":"2024 IEEE International Conference on Image Processing","department":[{"_id":"FrLo"}],"publisher":"IEEE","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2303.06439","open_access":"1"}],"corr_author":"1","external_id":{"arxiv":["2303.06439"],"isi":["001442947000143"]},"publication_status":"published","author":[{"first_name":"Berker","last_name":"Demirel","full_name":"Demirel, Berker","id":"8b4bc47f-3200-11ee-973b-8f0e7be21a9f"},{"first_name":"Huseyin","last_name":"Ozkan","full_name":"Ozkan, Huseyin"}],"abstract":[{"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","lang":"eng"}],"month":"11","year":"2024","date_published":"2024-11-01T00:00:00Z","date_created":"2025-01-29T12:22:24Z","language":[{"iso":"eng"}],"oa":1,"isi":1}]