[{"citation":{"short":"M. Panoukidou, S. Weir, V. Sorichetti, Y.G. Fosado, M. Lenz, D. Michieletto, Physical Review Research 6 (2024).","ista":"Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. 2024. Runaway transition in irreversible polymer condensation with cyclization. Physical Review Research. 6(2), 023189.","chicago":"Panoukidou, Maria, Simon Weir, Valerio Sorichetti, Yair Gutierrez Fosado, Martin Lenz, and Davide Michieletto. “Runaway Transition in Irreversible Polymer Condensation with Cyclization.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">https://doi.org/10.1103/PhysRevResearch.6.023189</a>.","mla":"Panoukidou, Maria, et al. “Runaway Transition in Irreversible Polymer Condensation with Cyclization.” <i>Physical Review Research</i>, vol. 6, no. 2, 023189, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">10.1103/PhysRevResearch.6.023189</a>.","ama":"Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. Runaway transition in irreversible polymer condensation with cyclization. <i>Physical Review Research</i>. 2024;6(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">10.1103/PhysRevResearch.6.023189</a>","apa":"Panoukidou, M., Weir, S., Sorichetti, V., Fosado, Y. G., Lenz, M., &#38; Michieletto, D. (2024). Runaway transition in irreversible polymer condensation with cyclization. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">https://doi.org/10.1103/PhysRevResearch.6.023189</a>","ieee":"M. Panoukidou, S. Weir, V. Sorichetti, Y. G. Fosado, M. Lenz, and D. Michieletto, “Runaway transition in irreversible polymer condensation with cyclization,” <i>Physical Review Research</i>, vol. 6, no. 2. American Physical Society, 2024."},"abstract":[{"lang":"eng","text":"The process of polymer condensation, i.e., the formation of bonds between reactive end groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclization. Using a generalized Smoluchowski theory, molecular dynamics simulations and experiments with DNA and ATP-consuming T4 ligase, we find that this system displays a transition, from a ring-dominated regime with finite-length chains at infinite time to a linear-polymers-dominated one with chains that keep growing in time. Finally, we show that fluids prepared close to the transition may have widely different compositions and rheology at large condensation times."}],"type":"journal_article","quality_controlled":"1","volume":6,"department":[{"_id":"AnSa"}],"publisher":"American Physical Society","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2024-05-26T22:00:58Z","external_id":{"arxiv":["2210.14010"]},"_id":"17050","month":"05","scopus_import":"1","issue":"2","oa":1,"file":[{"access_level":"open_access","file_size":1409416,"creator":"dernst","success":1,"date_created":"2024-05-27T06:37:01Z","file_name":"2024_PhysicalReviewResearch_Panoukidou.pdf","relation":"main_file","content_type":"application/pdf","checksum":"63a962d49ef1e21a3367d265784df14b","file_id":"17055","date_updated":"2024-05-27T06:37:01Z"}],"day":"01","doi":"10.1103/PhysRevResearch.6.023189","date_published":"2024-05-01T00:00:00Z","intvolume":"         6","article_number":"023189","year":"2024","publication_identifier":{"eissn":["2643-1564"]},"article_type":"original","acknowledgement":"D.M. acknowledges the support of the Royal Society via a University Research Fellowship. This project has received support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No. 947918 to D.M. and No. 677532 to M.L.). The authors acknowledge insightful discussions with Daan Noordermeer and Antonio Valdes, who also kindly gifted us with the 1288 plasmid.","arxiv":1,"publication":"Physical Review Research","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"oa_version":"Published Version","DOAJ_listed":"1","title":"Runaway transition in irreversible polymer condensation with cyclization","author":[{"first_name":"Maria","full_name":"Panoukidou, Maria","last_name":"Panoukidou"},{"last_name":"Weir","full_name":"Weir, Simon","first_name":"Simon"},{"first_name":"Valerio","orcid":"0000-0002-9645-6576","last_name":"Sorichetti","full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b"},{"first_name":"Yair Gutierrez","last_name":"Fosado","full_name":"Fosado, Yair Gutierrez"},{"last_name":"Lenz","full_name":"Lenz, Martin","first_name":"Martin"},{"first_name":"Davide","last_name":"Michieletto","full_name":"Michieletto, Davide"}],"date_updated":"2025-05-14T09:32:40Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-05-27T06:37:01Z"},{"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-09-08T07:35:40Z","page":"315-344","author":[{"orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","full_name":"Auerbach, Benedikt","first_name":"Benedikt"},{"id":"ec98511c-eb8e-11eb-b029-edd25d7271a1","full_name":"Günther, Christoph Ullrich","last_name":"Günther","first_name":"Christoph Ullrich"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"}],"title":"Trapdoor memory-hard functions","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"F8509","_id":"34a34d57-11ca-11ed-8bc3-a2688a8724e1","name":"Security and Privacy by Design for Complex Systems"}],"publication":"43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques","isi":1,"year":"2024","publication_identifier":{"isbn":["9783031587337"],"eissn":["1611-3349"],"issn":["0302-9743"]},"acknowledgement":"We thank the Eurocrypt reviewers for their thorough review and for pointing out related works. This research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/F85.","intvolume":"     14653","date_published":"2024-05-01T00:00:00Z","doi":"10.1007/978-3-031-58734-4_11","day":"01","oa":1,"scopus_import":"1","month":"05","_id":"17051","alternative_title":["LNCS"],"external_id":{"isi":["001274940200011"]},"conference":{"start_date":"2024-05-26","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","location":"Zurich, Switzerland","end_date":"2024-05-30"},"date_created":"2024-05-26T22:00:58Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2024/312"}],"publisher":"Springer Nature","corr_author":"1","department":[{"_id":"KrPi"}],"volume":14653,"quality_controlled":"1","type":"conference","abstract":[{"lang":"eng","text":"Memory-hard functions (MHF) are functions whose evaluation provably requires\r\na lot of memory. While MHFs are an unkeyed primitive, it is natural to consider the\r\nnotion of trapdoor MHFs (TMHFs). A TMHF is like an MHF, but when sampling\r\nthe public parameters one also samples a trapdoor which allows evaluating the\r\nfunction much cheaper.\r\nBiryukov and Perrin (Asiacrypt’17) were the first to consider TMHFs and put\r\nforth a candidate TMHF construction called Diodon that is based on the Scrypt\r\nMHF (Percival, BSDCan’09). To allow for a trapdoor, Scrypt’s initial hash chain\r\nis replaced by a sequence of squares in a group of unknown order where the order of\r\nthe group is the trapdoor. For a length n sequence of squares and a group of order\r\nN, Diodon’s cumulative memory complexity (CMC) is O(n2log N) without the\r\ntrapdoor and O(n log(n) log(N)2) with knowledge of it.\r\nWhile Scrypt is proven to be optimally memory-hard in the random oracle\r\nmodel (Alwen et al., Eurocrypt’17), Diodon’s memory-hardness has not been\r\nproven so far. In this work, we fill this gap by rigorously analyzing a specific\r\ninstantiation of Diodon. We show that its CMC is lower bounded by Ω( n2log nlog N)\r\nwhich almost matches the upper bound. Our proof is based Alwen et al.’s lower\r\nbound on Scrypt’s CMC but requires non-trivial modifications due to the algebraic\r\nstructure of Diodon. Most importantly, our analysis involves a more elaborate\r\ncompression argument and a solvability criterion for certain systems of Diophantine\r\nequations."}],"citation":{"mla":"Auerbach, Benedikt, et al. “Trapdoor Memory-Hard Functions.” <i>43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>, vol. 14653, Springer Nature, 2024, pp. 315–44, doi:<a href=\"https://doi.org/10.1007/978-3-031-58734-4_11\">10.1007/978-3-031-58734-4_11</a>.","ista":"Auerbach B, Günther CU, Pietrzak KZ. 2024. Trapdoor memory-hard functions. 43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 14653, 315–344.","chicago":"Auerbach, Benedikt, Christoph Ullrich Günther, and Krzysztof Z Pietrzak. “Trapdoor Memory-Hard Functions.” In <i>43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>, 14653:315–44. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-58734-4_11\">https://doi.org/10.1007/978-3-031-58734-4_11</a>.","ama":"Auerbach B, Günther CU, Pietrzak KZ. Trapdoor memory-hard functions. In: <i>43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>. Vol 14653. Springer Nature; 2024:315-344. doi:<a href=\"https://doi.org/10.1007/978-3-031-58734-4_11\">10.1007/978-3-031-58734-4_11</a>","ieee":"B. Auerbach, C. U. Günther, and K. Z. Pietrzak, “Trapdoor memory-hard functions,” in <i>43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>, Zurich, Switzerland, 2024, vol. 14653, pp. 315–344.","apa":"Auerbach, B., Günther, C. U., &#38; Pietrzak, K. Z. (2024). Trapdoor memory-hard functions. In <i>43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques</i> (Vol. 14653, pp. 315–344). Zurich, Switzerland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-58734-4_11\">https://doi.org/10.1007/978-3-031-58734-4_11</a>","short":"B. Auerbach, C.U. Günther, K.Z. Pietrzak, in:, 43rd Annual International Conference on the Theory and Applications of Cryptographic Techniques, Springer Nature, 2024, pp. 315–344."}},{"ec_funded":1,"article_type":"original","acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility and the Lab Support Facility (LSF). Dr. Krishnendu Maji at ISTA aided in this work through XRD analysis of the crystal phase of SnSe. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411, the National Natural Science Foundation of China (NSFC) (Grants No. 22209034). M.C. received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2024","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"article_number":"e202402628","intvolume":"        63","date_published":"2024-06-17T00:00:00Z","day":"17","doi":"10.1002/anie.202402628","oa":1,"file":[{"access_level":"open_access","date_created":"2025-01-09T09:12:07Z","file_name":"2024_AngewChemieIntern_Fiedler.pdf","success":1,"file_size":16347226,"creator":"dernst","relation":"main_file","checksum":"1572a0f4d2df55751761efeb2d11c7fc","content_type":"application/pdf","file_id":"18797","date_updated":"2025-01-09T09:12:07Z"}],"ddc":["540"],"OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"publication":"Angewandte Chemie - International Edition","isi":1,"oa_version":"Published Version","file_date_updated":"2025-01-09T09:12:07Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-09-08T07:36:36Z","title":"Unveiling crucial chemical processing parameters influencing the performance of solution-processed inorganic thermoelectric materials","author":[{"first_name":"Christine","full_name":"Fiedler, Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366"},{"first_name":"Mariano","full_name":"Calcabrini, Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877"},{"full_name":"Liu, Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","first_name":"Yu"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"}],"quality_controlled":"1","pmid":1,"type":"journal_article","abstract":[{"text":"Production of thermoelectric materials from solution-processed particles involves the synthesis of particles, their purification and densification into pelletized material. Chemical changes that occur during each one of these steps render them performance determining. Particularly the purification steps, bypassed in conventional solid-state synthesis, are the cause for large discrepancies among similar solution-processed materials. In present work, the investigation focuses on a water-based surfactant free solution synthesis of SnSe, a highly relevant thermoelectric material. We show and rationalize that the number of leaching steps, purification solvent, annealing, and annealing atmosphere have significant influence on the Sn : Se ratio and impurity content in the powder. Such compositional changes that are undetectable by conventional characterization techniques lead to distinct consolidated materials with different types and concentration of defects. Additionally, the profound effect on their transport properties is demonstrated. We emphasize that understanding the chemistry and identifying key chemical species and their role throughout the process is paramount for optimizing material performance. Furthermore, we aim to demonstrate the necessity of comprehensive reporting of these steps as a standard practice to ensure material reproducibility.","lang":"eng"}],"citation":{"short":"C. Fiedler, M. Calcabrini, Y. Liu, M. Ibáñez, Angewandte Chemie - International Edition 63 (2024).","mla":"Fiedler, Christine, et al. “Unveiling Crucial Chemical Processing Parameters Influencing the Performance of Solution-Processed Inorganic Thermoelectric Materials.” <i>Angewandte Chemie - International Edition</i>, vol. 63, no. 25, e202402628, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/anie.202402628\">10.1002/anie.202402628</a>.","chicago":"Fiedler, Christine, Mariano Calcabrini, Yu Liu, and Maria Ibáñez. “Unveiling Crucial Chemical Processing Parameters Influencing the Performance of Solution-Processed Inorganic Thermoelectric Materials.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/anie.202402628\">https://doi.org/10.1002/anie.202402628</a>.","ista":"Fiedler C, Calcabrini M, Liu Y, Ibáñez M. 2024. Unveiling crucial chemical processing parameters influencing the performance of solution-processed inorganic thermoelectric materials. Angewandte Chemie - International Edition. 63(25), e202402628.","apa":"Fiedler, C., Calcabrini, M., Liu, Y., &#38; Ibáñez, M. (2024). Unveiling crucial chemical processing parameters influencing the performance of solution-processed inorganic thermoelectric materials. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202402628\">https://doi.org/10.1002/anie.202402628</a>","ieee":"C. Fiedler, M. Calcabrini, Y. Liu, and M. Ibáñez, “Unveiling crucial chemical processing parameters influencing the performance of solution-processed inorganic thermoelectric materials,” <i>Angewandte Chemie - International Edition</i>, vol. 63, no. 25. Wiley, 2024.","ama":"Fiedler C, Calcabrini M, Liu Y, Ibáñez M. Unveiling crucial chemical processing parameters influencing the performance of solution-processed inorganic thermoelectric materials. <i>Angewandte Chemie - International Edition</i>. 2024;63(25). doi:<a href=\"https://doi.org/10.1002/anie.202402628\">10.1002/anie.202402628</a>"},"publisher":"Wiley","corr_author":"1","OA_type":"hybrid","department":[{"_id":"MaIb"}],"volume":63,"external_id":{"isi":["001223768400001"],"pmid":["38623865"]},"date_created":"2024-05-26T22:00:58Z","publication_status":"published","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"scopus_import":"1","issue":"25","month":"06","_id":"17052"},{"_id":"17053","scopus_import":"1","month":"02","date_created":"2024-05-26T22:00:58Z","publication_status":"published","conference":{"name":"MBMV: Methods and Description Languages for Modeling and Verification of Circuits and Systems","location":"Kaiserslautern, Germany","start_date":"2024-02-14","end_date":"2024-02-15"},"department":[{"_id":"ToHe"}],"OA_type":"green","main_file_link":[{"url":"https://cca.informatik.uni-freiburg.de/papers/FroleyksYuBiere-MBMV24.pdf","open_access":"1"}],"quality_controlled":"1","citation":{"chicago":"Froleyks, Nils, Emily Yu, and Armin Biere. “Ternary Simulation as Abstract Interpretation (Work in Progress).” In <i>27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems</i>, 148–51, 2024.","ista":"Froleyks N, Yu E, Biere A. 2024. Ternary simulation as abstract interpretation (Work in Progress). 27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems. MBMV: Methods and Description Languages for Modeling and Verification of Circuits and Systems, 148–151.","mla":"Froleyks, Nils, et al. “Ternary Simulation as Abstract Interpretation (Work in Progress).” <i>27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems</i>, 2024, pp. 148–51.","ieee":"N. Froleyks, E. Yu, and A. Biere, “Ternary simulation as abstract interpretation (Work in Progress),” in <i>27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems</i>, Kaiserslautern, Germany, 2024, pp. 148–151.","apa":"Froleyks, N., Yu, E., &#38; Biere, A. (2024). Ternary simulation as abstract interpretation (Work in Progress). In <i>27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems</i> (pp. 148–151). Kaiserslautern, Germany.","ama":"Froleyks N, Yu E, Biere A. Ternary simulation as abstract interpretation (Work in Progress). In: <i>27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems</i>. ; 2024:148-151.","short":"N. Froleyks, E. Yu, A. Biere, in:, 27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems, 2024, pp. 148–151."},"type":"conference","abstract":[{"lang":"eng","text":"We introduce a formalization of ternary simulation as abstract interpretation along with a widening operator to speed up convergence. With the same goal, we present a subsumption algorithm that can determine termination earlier than the usual approach using hash sets. Additionally, we introduce a narrowing operator that utilizes recent advances in backbone extraction, allowing to increase the overapproximation precision in simulation at any time. The experiments evaluate the presented techniques in the context of hardware model checking."}],"page":"148-151","date_updated":"2026-01-05T14:05:35Z","author":[{"first_name":"Nils","full_name":"Froleyks, Nils","last_name":"Froleyks"},{"first_name":"Zhengqi","orcid":"0000-0002-4993-773X","full_name":"Yu, Zhengqi","last_name":"Yu","id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342"},{"last_name":"Biere","full_name":"Biere, Armin","first_name":"Armin"}],"title":"Ternary simulation as abstract interpretation (Work in Progress)","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publication":"27th Workshop on Methods and Description Languages for Modeling and Verification of Circuits and Systems","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"date_published":"2024-02-01T00:00:00Z","oa":1,"day":"01","year":"2024","acknowledgement":"This work is supported by the Austrian Science Fund (FWF) under the project W1255-N23, the LIT AI Lab funded by the State of Upper Austria, the ERC-2020-AdG 101020093 and by a gift from Intel Corporation.","publication_identifier":{"isbn":["9783800762682"]},"ec_funded":1},{"_id":"17054","issue":"5","scopus_import":"1","month":"10","date_created":"2024-05-26T22:00:58Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","department":[{"_id":"RaKl"}],"OA_type":"gold","volume":5,"publisher":"Wiley","quality_controlled":"1","citation":{"ama":"Shan Y, Sheng J, Zhang Q, Stuart MCA, Qu DH, Feringa BL. Multi-state photoluminescent properties of an overcrowded alkene-based molecular motor in aggregates. <i>Aggregate</i>. 2024;5(5). doi:<a href=\"https://doi.org/10.1002/agt2.584\">10.1002/agt2.584</a>","apa":"Shan, Y., Sheng, J., Zhang, Q., Stuart, M. C. A., Qu, D. H., &#38; Feringa, B. L. (2024). Multi-state photoluminescent properties of an overcrowded alkene-based molecular motor in aggregates. <i>Aggregate</i>. Wiley. <a href=\"https://doi.org/10.1002/agt2.584\">https://doi.org/10.1002/agt2.584</a>","ieee":"Y. Shan, J. Sheng, Q. Zhang, M. C. A. Stuart, D. H. Qu, and B. L. Feringa, “Multi-state photoluminescent properties of an overcrowded alkene-based molecular motor in aggregates,” <i>Aggregate</i>, vol. 5, no. 5. Wiley, 2024.","chicago":"Shan, Yahan, Jinyu Sheng, Qi Zhang, Marc C.A. Stuart, Da Hui Qu, and Ben L. Feringa. “Multi-State Photoluminescent Properties of an Overcrowded Alkene-Based Molecular Motor in Aggregates.” <i>Aggregate</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/agt2.584\">https://doi.org/10.1002/agt2.584</a>.","ista":"Shan Y, Sheng J, Zhang Q, Stuart MCA, Qu DH, Feringa BL. 2024. Multi-state photoluminescent properties of an overcrowded alkene-based molecular motor in aggregates. Aggregate. 5(5), e584.","mla":"Shan, Yahan, et al. “Multi-State Photoluminescent Properties of an Overcrowded Alkene-Based Molecular Motor in Aggregates.” <i>Aggregate</i>, vol. 5, no. 5, e584, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/agt2.584\">10.1002/agt2.584</a>.","short":"Y. Shan, J. Sheng, Q. Zhang, M.C.A. Stuart, D.H. Qu, B.L. Feringa, Aggregate 5 (2024)."},"type":"journal_article","abstract":[{"text":"Photoisomerization and photoluminescence are two distinct energy dissipation pathways in light-driven molecular motors. The photoisomerization properties of discrete molecular motors have been well established in solution, but their photoluminescent properties have been rarely reported—especially in aggregates. Here, it is shown that an overcrowded alkene-based molecular motor exhibits distinct dynamic properties in solution and aggregate states, for example, gel and solid states. Despite the poor emissive properties of molecular motors in solution, a bright emission is observed in the aggregate states, including in gel and the crystalline solid. The emission wavelength is highly dependent on the nature of the supramolecular packing and order in the aggregates. As a result, the fluorescent color can be readily tuned reversibly via mechanical grinding and vapor fuming, which provides a new platform for developing multi-stimuli functional materials.","lang":"eng"}],"date_updated":"2025-01-09T09:41:53Z","author":[{"first_name":"Yahan","last_name":"Shan","full_name":"Shan, Yahan"},{"first_name":"Jinyu","full_name":"Sheng, Jinyu","last_name":"Sheng","id":"639f0526-27c9-11ee-95a6-966cd7f102d8"},{"first_name":"Qi","last_name":"Zhang","full_name":"Zhang, Qi"},{"first_name":"Marc C.A.","full_name":"Stuart, Marc C.A.","last_name":"Stuart"},{"last_name":"Qu","full_name":"Qu, Da Hui","first_name":"Da Hui"},{"first_name":"Ben L.","last_name":"Feringa","full_name":"Feringa, Ben L."}],"title":"Multi-state photoluminescent properties of an overcrowded alkene-based molecular motor in aggregates","has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2025-01-09T09:38:51Z","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","publication":"Aggregate","ddc":["540"],"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-10-01T00:00:00Z","intvolume":"         5","file":[{"access_level":"open_access","date_created":"2025-01-09T09:38:51Z","success":1,"file_name":"2024_Aggregate_Shan.pdf","file_size":2299084,"creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"1e79dc81d0edf0b441ef661a1890bbf5","file_id":"18804","date_updated":"2025-01-09T09:38:51Z"}],"oa":1,"day":"01","doi":"10.1002/agt2.584","year":"2024","acknowledgement":"This work was supported by the National Natural Science Foundation of China (grant nos. 22220102004, 22025503), Shanghai Municipal Science and Technology Major Project (grant no. 2018SHZDZX03), the Innovation Program of Shanghai Municipal Education Commission (2023ZKZD40), the Fundamental Research Funds for the Central Universities, the Program of Introducing Talents of Discipline to Universities (grant no. B16017), Science and Technology Commission of Shanghai Municipality (grant no. 21JC1401700), and the Starry Night Science Fund of Zhejiang University Shanghai Institute for Advanced Study (grant no. SN-ZJU-SIAS-006), China Scholarship Council (CSC PhD Fellowship No. 202006745016 to Yahan Shan). The authors gratefully acknowledge financial support from the Dutch Ministry of Education, Culture and Science (gravitation program no. 024.001.035 to Ben L. Feringa). The authors thank Dr. Youxin Fu and Dr. Alexander Ryabchun for the help with fluorescence quantum yield measurement, Cristina Nitu for the help with photoisomerzation quantum yield measurement, Prof. Wesley R. Browne for the help with fluorescence lifetime measurement, and Dr. Jianyu Zhang for fruitful discussion and revising the manuscript.","publication_identifier":{"issn":["2766-8541"],"eissn":["2692-4560"]},"article_type":"original","article_number":"e584"},{"oa_version":"Published Version","date_updated":"2025-09-08T07:42:25Z","author":[{"first_name":"Shih Pi","full_name":"Ku, Shih Pi","last_name":"Ku"},{"full_name":"Atucha, Erika","last_name":"Atucha","first_name":"Erika"},{"last_name":"Alavi","full_name":"Alavi, Nico","first_name":"Nico"},{"last_name":"Mulla-Osman","full_name":"Mulla-Osman, Halla","first_name":"Halla"},{"full_name":"Kayumova, Rukhshona","last_name":"Kayumova","first_name":"Rukhshona"},{"first_name":"Motoharu","full_name":"Yoshida, Motoharu","last_name":"Yoshida"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"},{"first_name":"Magdalena M.","last_name":"Sauvage","full_name":"Sauvage, Magdalena M."}],"title":"Phase locking of hippocampal CA3 neurons to distal CA1 theta oscillations selectively predicts memory performance","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2024-06-03T07:12:45Z","language":[{"iso":"eng"}],"status":"public","date_published":"2024-06-25T00:00:00Z","intvolume":"        43","oa":1,"file":[{"file_id":"17096","date_updated":"2024-06-03T07:12:45Z","relation":"main_file","content_type":"application/pdf","checksum":"9b43f8ca5e5a12ae96e3fb9df06385c1","success":1,"date_created":"2024-06-03T07:12:45Z","file_name":"2024_CellReports_Ku.pdf","file_size":4371015,"creator":"dernst","access_level":"open_access"}],"doi":"10.1016/j.celrep.2024.114276","day":"25","year":"2024","article_type":"original","acknowledgement":"We would like to thank J. Maiwald for her assistance in animal behavior training, experiments, and brain slice preparation; D. Koch for her assistance in recording drive building and brain slicing; K. Kaefer and J. Wallenschus (IST Austria) for their initial technical support; S. Mikulovich for her comments on an early version of the manuscript; C. Reichert for his comments on SVM analyses; and J. Pakan for English proofreading. This project is funded by the DFG (CRC 779 and CRC 1436).","publication_identifier":{"eissn":["2211-1247"]},"article_number":"114276","isi":1,"publication":"Cell Reports","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-06-02T22:00:56Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"isi":["001252792600001"]},"_id":"17089","issue":"6","scopus_import":"1","month":"06","quality_controlled":"1","citation":{"short":"S.P. Ku, E. Atucha, N. Alavi, H. Mulla-Osman, R. Kayumova, M. Yoshida, J.L. Csicsvari, M.M. Sauvage, Cell Reports 43 (2024).","chicago":"Ku, Shih Pi, Erika Atucha, Nico Alavi, Halla Mulla-Osman, Rukhshona Kayumova, Motoharu Yoshida, Jozsef L Csicsvari, and Magdalena M. Sauvage. “Phase Locking of Hippocampal CA3 Neurons to Distal CA1 Theta Oscillations Selectively Predicts Memory Performance.” <i>Cell Reports</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.celrep.2024.114276\">https://doi.org/10.1016/j.celrep.2024.114276</a>.","ista":"Ku SP, Atucha E, Alavi N, Mulla-Osman H, Kayumova R, Yoshida M, Csicsvari JL, Sauvage MM. 2024. Phase locking of hippocampal CA3 neurons to distal CA1 theta oscillations selectively predicts memory performance. Cell Reports. 43(6), 114276.","mla":"Ku, Shih Pi, et al. “Phase Locking of Hippocampal CA3 Neurons to Distal CA1 Theta Oscillations Selectively Predicts Memory Performance.” <i>Cell Reports</i>, vol. 43, no. 6, 114276, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.celrep.2024.114276\">10.1016/j.celrep.2024.114276</a>.","apa":"Ku, S. P., Atucha, E., Alavi, N., Mulla-Osman, H., Kayumova, R., Yoshida, M., … Sauvage, M. M. (2024). Phase locking of hippocampal CA3 neurons to distal CA1 theta oscillations selectively predicts memory performance. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2024.114276\">https://doi.org/10.1016/j.celrep.2024.114276</a>","ama":"Ku SP, Atucha E, Alavi N, et al. Phase locking of hippocampal CA3 neurons to distal CA1 theta oscillations selectively predicts memory performance. <i>Cell Reports</i>. 2024;43(6). doi:<a href=\"https://doi.org/10.1016/j.celrep.2024.114276\">10.1016/j.celrep.2024.114276</a>","ieee":"S. P. Ku <i>et al.</i>, “Phase locking of hippocampal CA3 neurons to distal CA1 theta oscillations selectively predicts memory performance,” <i>Cell Reports</i>, vol. 43, no. 6. Elsevier, 2024."},"abstract":[{"lang":"eng","text":"How the coordination of neuronal spiking and brain rhythms between hippocampal subregions supports memory function remains elusive. We studied the interregional coordination of CA3 neuronal spiking with CA1 theta oscillations by recording electrophysiological signals along the proximodistal axis of the hippocampus in rats that were performing a high-memory-demand recognition memory task adapted from humans. We found that CA3 population spiking occurs preferentially at the peak of distal CA1 theta oscillations when memory was tested but only when previously encountered stimuli were presented. In addition, decoding analyses revealed that only population cell firing of proximal CA3 together with that of distal CA1 can predict performance at test in the present non-spatial task. Overall, our work demonstrates an important role for the synchronization of CA3 neuronal activity with CA1 theta oscillations during memory testing."}],"type":"journal_article","department":[{"_id":"JoCs"}],"volume":43,"publisher":"Elsevier"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","isi":1,"publication":"Science","article_type":"original","year":"2024","acknowledgement":"K.E.H. acknowledges support from Carlsberg Foundation Reintegration Fellowship grant CF21-0103. A.H. acknowledges support from the VILLUM FONDEN under grant 37459. C.A.M. acknowledges support from the VILLUM FONDEN under grant 37459 and the Carlsberg Foundation under grant CF22-1322. N.R.T. was funded through Science and Technology Facilities Council (STFC) consolidated grant ST/W000857/1. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. R.P.N. was supported by the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy under NASA contract NAS5-26555. P.A.O. received funding from the Swiss State Secretariat for Education, Research, and Innovation (SERI) under contract number MB22.00072 and from the Swiss National Science Foundation (SNSF) through project grant 200020_207349.","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa":1,"day":"24","doi":"10.1126/science.adj0343","date_published":"2024-05-24T00:00:00Z","intvolume":"       384","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Strong damped Lyman-a absorption in young star-forming galaxies at redshifts 9 to 11","author":[{"first_name":"Kasper E.","last_name":"Heintz","full_name":"Heintz, Kasper E."},{"first_name":"Darach","last_name":"Watson","full_name":"Watson, Darach"},{"first_name":"Gabriel","full_name":"Brammer, Gabriel","last_name":"Brammer"},{"full_name":"Vejlgaard, Simone","last_name":"Vejlgaard","first_name":"Simone"},{"last_name":"Hutter","full_name":"Hutter, Anne","first_name":"Anne"},{"first_name":"Victoria B.","last_name":"Strait","full_name":"Strait, Victoria B."},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"first_name":"Páll","last_name":"Jakobsson","full_name":"Jakobsson, Páll"},{"first_name":"Nial R.","last_name":"Tanvir","full_name":"Tanvir, Nial R."},{"last_name":"Laursen","full_name":"Laursen, Peter","first_name":"Peter"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"full_name":"Mason, Charlotte A.","last_name":"Mason","first_name":"Charlotte A."},{"first_name":"Meghana","full_name":"Killi, Meghana","last_name":"Killi"},{"last_name":"Jung","full_name":"Jung, Intae","first_name":"Intae"},{"full_name":"Hsiao, Tiger Yu Yang","last_name":"Hsiao","first_name":"Tiger Yu Yang"},{"first_name":"Unknown","last_name":"Abdurro’Uf","full_name":"Abdurro’Uf, Unknown"},{"full_name":"Coe, Dan","last_name":"Coe","first_name":"Dan"},{"first_name":"Pablo Arrabal","full_name":"Haro, Pablo Arrabal","last_name":"Haro"},{"first_name":"Steven L.","full_name":"Finkelstein, Steven L.","last_name":"Finkelstein"},{"full_name":"Toft, Sune","last_name":"Toft","first_name":"Sune"}],"date_updated":"2025-09-08T07:43:13Z","page":"890-894","oa_version":"Submitted Version","publisher":"AAAS","main_file_link":[{"open_access":"1","url":"https://figshare.com/articles/journal_contribution/Strong_damped_Lyman-_absorption_in_young_star-forming_galaxies_at_redshifts_9_to_11/26069122?file=47174584"}],"volume":384,"OA_type":"green","department":[{"_id":"JoMa"}],"citation":{"short":"K.E. Heintz, D. Watson, G. Brammer, S. Vejlgaard, A. Hutter, V.B. Strait, J.J. Matthee, P.A. Oesch, P. Jakobsson, N.R. Tanvir, P. Laursen, R.P. Naidu, C.A. Mason, M. Killi, I. Jung, T.Y.Y. Hsiao, U. Abdurro’Uf, D. Coe, P.A. Haro, S.L. Finkelstein, S. Toft, Science 384 (2024) 890–894.","ieee":"K. E. Heintz <i>et al.</i>, “Strong damped Lyman-a absorption in young star-forming galaxies at redshifts 9 to 11,” <i>Science</i>, vol. 384, no. 6698. AAAS, pp. 890–894, 2024.","ama":"Heintz KE, Watson D, Brammer G, et al. Strong damped Lyman-a absorption in young star-forming galaxies at redshifts 9 to 11. <i>Science</i>. 2024;384(6698):890-894. doi:<a href=\"https://doi.org/10.1126/science.adj0343\">10.1126/science.adj0343</a>","apa":"Heintz, K. E., Watson, D., Brammer, G., Vejlgaard, S., Hutter, A., Strait, V. B., … Toft, S. (2024). Strong damped Lyman-a absorption in young star-forming galaxies at redshifts 9 to 11. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adj0343\">https://doi.org/10.1126/science.adj0343</a>","mla":"Heintz, Kasper E., et al. “Strong Damped Lyman-a Absorption in Young Star-Forming Galaxies at Redshifts 9 to 11.” <i>Science</i>, vol. 384, no. 6698, AAAS, 2024, pp. 890–94, doi:<a href=\"https://doi.org/10.1126/science.adj0343\">10.1126/science.adj0343</a>.","chicago":"Heintz, Kasper E., Darach Watson, Gabriel Brammer, Simone Vejlgaard, Anne Hutter, Victoria B. Strait, Jorryt J Matthee, et al. “Strong Damped Lyman-a Absorption in Young Star-Forming Galaxies at Redshifts 9 to 11.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adj0343\">https://doi.org/10.1126/science.adj0343</a>.","ista":"Heintz KE, Watson D, Brammer G, Vejlgaard S, Hutter A, Strait VB, Matthee JJ, Oesch PA, Jakobsson P, Tanvir NR, Laursen P, Naidu RP, Mason CA, Killi M, Jung I, Hsiao TYY, Abdurro’Uf U, Coe D, Haro PA, Finkelstein SL, Toft S. 2024. Strong damped Lyman-a absorption in young star-forming galaxies at redshifts 9 to 11. Science. 384(6698), 890–894."},"pmid":1,"abstract":[{"text":"Primordial neutral atomic gas, mostly composed of hydrogen, is the raw material for star formation in galaxies. However, there are few direct constraints on the amount of neutral atomic hydrogen (H i) in galaxies at early cosmic times. We analyzed James Webb Space Telescope (JWST) near-infrared spectroscopy of distant galaxies, at redshifts ≳8. From a sample of 12 galaxies, we identified three that show strong damped Lyman-α absorption due to H i in their local surroundings. The galaxies are located at spectroscopic redshifts of 8.8, 10.2, and 11.4, corresponding to 400 to 600 million years after the Big Bang. They have H i column densities ≳1022 cm−2, which is an order of magnitude higher than expected for a fully neutral intergalactic medium, and constitute a gas-rich population of young star-forming galaxies.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","month":"05","issue":"6698","scopus_import":"1","_id":"17090","external_id":{"pmid":["38781391"],"isi":["001230029500001"]},"publication_status":"published","date_created":"2024-06-02T22:00:56Z"},{"external_id":{"isi":["001230076500007"],"pmid":["38781359"]},"date_created":"2024-06-02T22:00:57Z","publication_status":"published","issue":"6698","scopus_import":"1","month":"05","_id":"17091","quality_controlled":"1","pmid":1,"type":"journal_article","abstract":[{"lang":"eng","text":"DNA sequences are connected to genes and functions in the developing and adult brain"}],"citation":{"short":"G. Novarino, C. Bock, Science 384 (2024) 860–861.","ieee":"G. Novarino and C. Bock, “Mapping the brain’s gene-regulatory maze,” <i>Science</i>, vol. 384, no. 6698. AAAS, pp. 860–861, 2024.","apa":"Novarino, G., &#38; Bock, C. (2024). Mapping the brain’s gene-regulatory maze. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adp4663\">https://doi.org/10.1126/science.adp4663</a>","ama":"Novarino G, Bock C. Mapping the brain’s gene-regulatory maze. <i>Science</i>. 2024;384(6698):860-861. doi:<a href=\"https://doi.org/10.1126/science.adp4663\">10.1126/science.adp4663</a>","mla":"Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” <i>Science</i>, vol. 384, no. 6698, AAAS, 2024, pp. 860–61, doi:<a href=\"https://doi.org/10.1126/science.adp4663\">10.1126/science.adp4663</a>.","ista":"Novarino G, Bock C. 2024. Mapping the brain’s gene-regulatory maze. Science. 384(6698), 860–861.","chicago":"Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adp4663\">https://doi.org/10.1126/science.adp4663</a>."},"publisher":"AAAS","corr_author":"1","department":[{"_id":"GaNo"}],"volume":384,"oa_version":"None","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"page":"860-861","date_updated":"2025-09-08T07:40:10Z","title":"Mapping the brain’s gene-regulatory maze","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"}],"year":"2024","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_type":"letter_note","intvolume":"       384","date_published":"2024-05-24T00:00:00Z","doi":"10.1126/science.adp4663","day":"24","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Science","isi":1},{"ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Journal of Neuroscience","isi":1,"publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"year":"2024","article_type":"original","acknowledgement":"We thank Sadra Sadeh and Inês Completo Guerreiro for helpful comments on the manuscript, Yosif Zaki and Denise J. Cai for useful feedback and members of the Clopath lab for discussion and support. This work was supported by Biotechnology and Biological Sciences Research Council (BB/N013956/1 awarded to C.C.), Wellcome Trust (200790/Z/16/Z awarded to C.C.), the Simons Foundation (564408 awarded to C.C.), and Engineering and Physical Sciences Research Council (EP/R035806/1 awarded to C.C.).","article_number":"e0846232024","intvolume":"        44","date_published":"2024-05-22T00:00:00Z","day":"22","doi":"10.1523/JNEUROSCI.0846-23.2024","file":[{"content_type":"application/pdf","checksum":"4e19159800db605b802c721e4d4b1ffe","relation":"main_file","date_updated":"2024-06-03T06:34:21Z","file_id":"17095","access_level":"open_access","date_created":"2024-06-03T06:34:21Z","file_name":"2024_JourNeuroscience_Delamare.pdf","success":1,"creator":"dernst","file_size":920354}],"oa":1,"file_date_updated":"2024-06-03T06:34:21Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-09-08T07:40:58Z","author":[{"first_name":"Geoffroy","last_name":"Delamare","full_name":"Delamare, Geoffroy"},{"id":"0eed2d40-3d48-11ec-8d38-f789cc2e40b2","last_name":"Feitosa Tomé","full_name":"Feitosa Tomé, Douglas","first_name":"Douglas"},{"first_name":"Claudia","last_name":"Clopath","full_name":"Clopath, Claudia"}],"title":"Intrinsic neural excitability biases allocation and overlap of memory engrams","oa_version":"Published Version","publisher":"Society for Neuroscience","department":[{"_id":"TiVo"}],"volume":44,"quality_controlled":"1","pmid":1,"type":"journal_article","abstract":[{"text":"Memories are thought to be stored in neural ensembles known as engrams that are specifically reactivated during memory recall. Recent studies have found that memory engrams of two events that happened close in time tend to overlap in the hippocampus and the amygdala, and these overlaps have been shown to support memory linking. It has been hypothesized that engram overlaps arise from the mechanisms that regulate memory allocation itself, involving neural excitability, but the exact process remains unclear. Indeed, most theoretical studies focus on synaptic plasticity and little is known about the role of intrinsic plasticity, which could be mediated by neural excitability and serve as a complementary mechanism for forming memory engrams. Here, we developed a rate-based recurrent neural network that includes both synaptic plasticity and neural excitability. We obtained structural and functional overlap of memory engrams for contexts that are presented close in time, consistent with experimental and computational studies. We then investigated the role of excitability in memory allocation at the network level and unveiled competitive mechanisms driven by inhibition. This work suggests mechanisms underlying the role of intrinsic excitability in memory allocation and linking, and yields predictions regarding the formation and the overlap of memory engrams.","lang":"eng"}],"citation":{"short":"G. Delamare, D. Feitosa Tomé, C. Clopath, Journal of Neuroscience 44 (2024).","ama":"Delamare G, Feitosa Tomé D, Clopath C. Intrinsic neural excitability biases allocation and overlap of memory engrams. <i>Journal of Neuroscience</i>. 2024;44(21). doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0846-23.2024\">10.1523/JNEUROSCI.0846-23.2024</a>","apa":"Delamare, G., Feitosa Tomé, D., &#38; Clopath, C. (2024). Intrinsic neural excitability biases allocation and overlap of memory engrams. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0846-23.2024\">https://doi.org/10.1523/JNEUROSCI.0846-23.2024</a>","ieee":"G. Delamare, D. Feitosa Tomé, and C. Clopath, “Intrinsic neural excitability biases allocation and overlap of memory engrams,” <i>Journal of Neuroscience</i>, vol. 44, no. 21. Society for Neuroscience, 2024.","mla":"Delamare, Geoffroy, et al. “Intrinsic Neural Excitability Biases Allocation and Overlap of Memory Engrams.” <i>Journal of Neuroscience</i>, vol. 44, no. 21, e0846232024, Society for Neuroscience, 2024, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0846-23.2024\">10.1523/JNEUROSCI.0846-23.2024</a>.","chicago":"Delamare, Geoffroy, Douglas Feitosa Tomé, and Claudia Clopath. “Intrinsic Neural Excitability Biases Allocation and Overlap of Memory Engrams.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2024. <a href=\"https://doi.org/10.1523/JNEUROSCI.0846-23.2024\">https://doi.org/10.1523/JNEUROSCI.0846-23.2024</a>.","ista":"Delamare G, Feitosa Tomé D, Clopath C. 2024. Intrinsic neural excitability biases allocation and overlap of memory engrams. Journal of Neuroscience. 44(21), e0846232024."},"issue":"21","scopus_import":"1","month":"05","_id":"17092","external_id":{"pmid":["38561228"],"isi":["001249681000008"]},"date_created":"2024-06-02T22:00:57Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"external_id":{"arxiv":["2206.10032"]},"alternative_title":["PMLR"],"conference":{"location":"Valencia, Spain","name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2024-05-02","end_date":"2024-05-04"},"date_created":"2024-06-02T22:00:57Z","publication_status":"published","scopus_import":"1","month":"05","_id":"17093","quality_controlled":"1","citation":{"short":"H. Zakerinia, S. Talaei, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 27th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2024, pp. 3448–3456.","mla":"Zakerinia, Hossein, et al. “Communication-Efficient Federated Learning with Data and Client Heterogeneity.” <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>, vol. 238, ML Research Press, 2024, pp. 3448–56.","ista":"Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. 2024. Communication-efficient federated learning with data and client heterogeneity. Proceedings of the 27th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 238, 3448–3456.","chicago":"Zakerinia, Hossein, Shayan Talaei, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Communication-Efficient Federated Learning with Data and Client Heterogeneity.” In <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>, 238:3448–56. ML Research Press, 2024.","ama":"Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. Communication-efficient federated learning with data and client heterogeneity. In: <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>. Vol 238. ML Research Press; 2024:3448-3456.","ieee":"H. Zakerinia, S. Talaei, G. Nadiradze, and D.-A. Alistarh, “Communication-efficient federated learning with data and client heterogeneity,” in <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i>, Valencia, Spain, 2024, vol. 238, pp. 3448–3456.","apa":"Zakerinia, H., Talaei, S., Nadiradze, G., &#38; Alistarh, D.-A. (2024). Communication-efficient federated learning with data and client heterogeneity. In <i>Proceedings of the 27th International Conference on Artificial Intelligence and Statistics</i> (Vol. 238, pp. 3448–3456). Valencia, Spain: ML Research Press."},"type":"conference","abstract":[{"lang":"eng","text":"Federated Learning (FL) enables large-scale distributed training of machine learning models, while still allowing individual nodes to maintain data locally. However, executing FL at scale comes with inherent practical challenges: 1) heterogeneity of the local node data distributions, 2) heterogeneity of node computational speeds (asynchrony), but also 3) constraints in the amount of communication between the clients and the server. In this work, we present the first variant of the classic federated averaging (FedAvg) algorithm which, at the same time, supports data heterogeneity, partial client asynchrony, and communication compression. Our algorithm comes with a novel, rigorous analysis showing that, in spite of these system relaxations, it can provide similar convergence to FedAvg in interesting parameter regimes. Experimental results in the rigorous LEAF benchmark on setups of up to 300 nodes show that our algorithm ensures fast convergence for standard federated tasks, improving upon prior quantized and asynchronous approaches."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.10032","open_access":"1"}],"corr_author":"1","publisher":"ML Research Press","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"volume":238,"oa_version":"Preprint","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"page":"3448-3456","date_updated":"2024-10-09T21:08:57Z","author":[{"last_name":"Zakerinia","full_name":"Zakerinia, Hossein","id":"653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4","first_name":"Hossein"},{"first_name":"Shayan","full_name":"Talaei, Shayan","last_name":"Talaei"},{"first_name":"Giorgi","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"title":"Communication-efficient federated learning with data and client heterogeneity","year":"2024","publication_identifier":{"eissn":["2640-3498"]},"date_published":"2024-05-01T00:00:00Z","intvolume":"       238","oa":1,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 27th International Conference on Artificial Intelligence and Statistics","arxiv":1},{"scopus_import":"1","month":"07","_id":"17098","external_id":{"isi":["001275042100006"],"arxiv":["2405.02479"]},"conference":{"end_date":"2024-07-11","start_date":"2024-07-08","location":"Tallinn, Estonia","name":"LICS: Logic in Computer Science"},"date_created":"2024-06-03T07:43:15Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.02479"}],"corr_author":"1","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"quality_controlled":"1","type":"conference","abstract":[{"text":"Turn-based discounted-sum games are two-player zero-sum games played on finite directed graphs. The vertices of the graph are partitioned between player 1 and player 2. Plays are infinite walks on the graph where the next vertex is decided by a player that owns the current vertex. Each edge is assigned an integer weight and the payoff of a play is the discounted-sum of the weights of the play. The goal of player 1 is to maximize the discounted-sum payoff against the adversarial player 2. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class and the existence of a polynomial-time algorithm is a major open question. Since breaking the general exponential barrier has been a challenging problem, faster parameterized algorithms have been considered. If the discount factor is expressed in unary, then discounted-sum games can be solved in polynomial time. However, if the discount factor is arbitrary (or expressed in binary), but the weights are in unary, none of the existing approaches yield a sub-exponential bound. Our main result is a new analysis technique for a classical algorithm (namely, the strategy iteration algorithm) that present a new runtime bound which is [EQUATION] for game graphs with n vertices and absolute weights of at most W. In particular, our result yields a deterministic sub-exponential bound for games with weights that are constant or represented in unary.","lang":"eng"}],"citation":{"short":"A. Asadi, K. Chatterjee, J. Svoboda, R.J. Saona Urmeneta, in:, 39th Annual ACM/IEEE Symposium on Logic in Computer Science, Association for Computing Machinery, 2024.","mla":"Asadi, Ali, et al. “Deterministic Sub-Exponential Algorithm for Discounted-Sum Games with Unary Weights.” <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 6, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3661814.3662080\">10.1145/3661814.3662080</a>.","ista":"Asadi A, Chatterjee K, Svoboda J, Saona Urmeneta RJ. 2024. Deterministic sub-exponential algorithm for discounted-sum games with unary weights. 39th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Jakub Svoboda, and Raimundo J Saona Urmeneta. “Deterministic Sub-Exponential Algorithm for Discounted-Sum Games with Unary Weights.” In <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3661814.3662080\">https://doi.org/10.1145/3661814.3662080</a>.","apa":"Asadi, A., Chatterjee, K., Svoboda, J., &#38; Saona Urmeneta, R. J. (2024). Deterministic sub-exponential algorithm for discounted-sum games with unary weights. In <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Tallinn, Estonia: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3661814.3662080\">https://doi.org/10.1145/3661814.3662080</a>","ama":"Asadi A, Chatterjee K, Svoboda J, Saona Urmeneta RJ. Deterministic sub-exponential algorithm for discounted-sum games with unary weights. In: <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3661814.3662080\">10.1145/3661814.3662080</a>","ieee":"A. Asadi, K. Chatterjee, J. Svoboda, and R. J. Saona Urmeneta, “Deterministic sub-exponential algorithm for discounted-sum games with unary weights,” in <i>39th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Tallinn, Estonia, 2024."},"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-09-08T07:44:29Z","title":"Deterministic sub-exponential algorithm for discounted-sum games with unary weights","author":[{"full_name":"Asadi, Ali","last_name":"Asadi","id":"02d96aae-000e-11ec-b801-cadd0a5eefbb","first_name":"Ali"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","first_name":"Jakub"},{"first_name":"Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta"}],"oa_version":"Preprint","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"publication":"39th Annual ACM/IEEE Symposium on Logic in Computer Science","isi":1,"ec_funded":1,"publication_identifier":{"eissn":["1043-6871"],"isbn":["9798400706608"]},"year":"2024","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.\r\n","article_number":"6","date_published":"2024-07-08T00:00:00Z","doi":"10.1145/3661814.3662080","day":"08","oa":1},{"_id":"17099","month":"12","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2024-06-03T07:44:27Z","conference":{"start_date":"2024-12-16","location":"Gujarat, India","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","end_date":"2024-12-18"},"external_id":{"arxiv":["2405.02486"],"isi":["001537516500005"]},"alternative_title":["LIPIcs"],"volume":323,"OA_type":"gold","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","corr_author":"1","citation":{"ista":"Asadi A, Chatterjee K, Saona Urmeneta RJ, Svoboda J. 2024. Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms. 44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 323, 5.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Concurrent Stochastic Games with Stateful-Discounted and Parity Objectives: Complexity and Algorithms.” In <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 323. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5</a>.","mla":"Asadi, Ali, et al. “Concurrent Stochastic Games with Stateful-Discounted and Parity Objectives: Complexity and Algorithms.” <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 323, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">10.4230/LIPIcs.FSTTCS.2024.5</a>.","ama":"Asadi A, Chatterjee K, Saona Urmeneta RJ, Svoboda J. Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms. In: <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 323. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">10.4230/LIPIcs.FSTTCS.2024.5</a>","apa":"Asadi, A., Chatterjee, K., Saona Urmeneta, R. J., &#38; Svoboda, J. (2024). Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms. In <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 323). Gujarat, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5\">https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5</a>","ieee":"A. Asadi, K. Chatterjee, R. J. Saona Urmeneta, and J. Svoboda, “Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms,” in <i>44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Gujarat, India, 2024, vol. 323.","short":"A. Asadi, K. Chatterjee, R.J. Saona Urmeneta, J. Svoboda, in:, 44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024."},"abstract":[{"text":"We study two-player zero-sum concurrent stochastic games with finite state and action space played for an infinite number of steps. In every step, the two players simultaneously and independently choose an action. Given the current state and the chosen actions, the next state is obtained according to a stochastic transition function. An objective is a measurable function on plays (or infinite trajectories) of the game, and the value for an objective is the maximal expectation that the player can guarantee against the adversarial player. We consider: (a) stateful-discounted objectives, which are similar to the classical discounted-sum objectives, but states are associated with different discount factors rather than a single discount factor; and (b) parity objectives, which are a canonical representation for ω-regular objectives. For stateful-discounted objectives, given an ordering of the discount factors, the limit value is the limit of the value of the stateful-discounted objectives, as the discount factors approach zero according to the given order.\r\nThe computational problem we consider is the approximation of the value within an arbitrary\r\nadditive error. The above problem is known to be in EXPSPACE for the limit value of statefuldiscounted objectives and in PSPACE for parity objectives. The best-known algorithms for both the above problems are at least exponential time, with an exponential dependence on the number of states and actions. Our main results for the value approximation problem for the limit value of stateful-discounted objectives and parity objectives are as follows: (a) we establish TFNP[NP] complexity; and (b) we present algorithms that improve the dependency on the number of actions in the exponent from linear to logarithmic. In particular, if the number of states is constant, our algorithms run in polynomial time.","lang":"eng"}],"type":"conference","quality_controlled":"1","author":[{"last_name":"Asadi","full_name":"Asadi, Ali","id":"02d96aae-000e-11ec-b801-cadd0a5eefbb","first_name":"Ali"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","first_name":"Raimundo J"},{"first_name":"Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","last_name":"Svoboda"}],"title":"Concurrent stochastic games with stateful-discounted and parity objectives: Complexity and algorithms","date_updated":"2025-12-02T13:40:52Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2025-01-08T09:49:31Z","oa_version":"Published Version","isi":1,"arxiv":1,"publication":"44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"ddc":["000"],"OA_place":"publisher","oa":1,"file":[{"access_level":"open_access","success":1,"date_created":"2025-01-08T09:49:31Z","file_name":"2024_LIPIcs_Asadi.pdf","creator":"dernst","file_size":847960,"checksum":"5b544ab4692b93300b404435c036ddd4","content_type":"application/pdf","relation":"main_file","date_updated":"2025-01-08T09:49:31Z","file_id":"18777"}],"doi":"10.4230/LIPIcs.FSTTCS.2024.5","day":"05","date_published":"2024-12-05T00:00:00Z","intvolume":"       323","article_number":"5","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773553"]},"acknowledgement":"This research was partially supported by ERC CoG 863818 (ForM-SMArt), Austrian\r\nScience Fund (FWF) 10.55776/COE12, and French Agence Nationale de la Recherche (ANR)\r\nANR-21-CE40-0020 (CONVERGENCE project)","year":"2024","ec_funded":1},{"article_number":"2401.16252","acknowledgement":"This work was supported by the French Agence Nationale de la Recherche (ANR) under references ANR-21-CE40-0020 (CONVERGENCE project) and ANR-20-CE40-0002 (GrHyDy), and by Fondecyt grant 1220174. This collaboration was mainly conducted during a 1-year visit of Bruno Ziliotto to the Center for Mathematical Modeling (CMM) at University of Chile in 2023,\r\nunder the IRL program of CNRS.","year":"2024","abstract":[{"text":"This paper considers a class of two-player zero-sum games on directed graphs whose vertices are equipped with random payoffs of bounded support known by both players.\r\nStarting from a fixed vertex, players take turns to move a token along the edges of the graph.\r\nOn the one hand, for acyclic directed graphs of bounded degree and sub-exponential expansion, we show that the value of the game converges almost surely to a constant at an exponential rate dominated in terms of the expansion.\r\nOn the other hand, for the infinite d-ary tree that does not fall into the previous class of graphs, we show convergence at a double-exponential rate in terms of the expansion.","lang":"eng"}],"doi":"10.48550/arXiv.2401.16252","type":"preprint","day":"29","oa":1,"citation":{"short":"L. Attia, L. Lichev, D. Mitsche, R.J. Saona Urmeneta, B. Ziliotto, ArXiv (n.d.).","apa":"Attia, L., Lichev, L., Mitsche, D., Saona Urmeneta, R. J., &#38; Ziliotto, B. (n.d.). Zero-sum random games on directed graphs. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2401.16252\">https://doi.org/10.48550/arXiv.2401.16252</a>","ieee":"L. Attia, L. Lichev, D. Mitsche, R. J. Saona Urmeneta, and B. Ziliotto, “Zero-sum random games on directed graphs,” <i>arXiv</i>. .","ama":"Attia L, Lichev L, Mitsche D, Saona Urmeneta RJ, Ziliotto B. Zero-sum random games on directed graphs. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2401.16252\">10.48550/arXiv.2401.16252</a>","ista":"Attia L, Lichev L, Mitsche D, Saona Urmeneta RJ, Ziliotto B. Zero-sum random games on directed graphs. arXiv, 2401.16252.","chicago":"Attia, Luc, Lyuben Lichev, Dieter Mitsche, Raimundo J Saona Urmeneta, and Bruno Ziliotto. “Zero-Sum Random Games on Directed Graphs.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2401.16252\">https://doi.org/10.48550/arXiv.2401.16252</a>.","mla":"Attia, Luc, et al. “Zero-Sum Random Games on Directed Graphs.” <i>ArXiv</i>, 2401.16252, doi:<a href=\"https://doi.org/10.48550/arXiv.2401.16252\">10.48550/arXiv.2401.16252</a>."},"date_published":"2024-01-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2401.16252","open_access":"1"}],"publication":"arXiv","arxiv":1,"department":[{"_id":"KrCh"}],"external_id":{"arxiv":["2401.16252"]},"publication_status":"submitted","date_created":"2024-06-03T07:45:22Z","oa_version":"Preprint","language":[{"iso":"eng"}],"status":"public","month":"01","article_processing_charge":"No","author":[{"first_name":"Luc","last_name":"Attia","full_name":"Attia, Luc"},{"full_name":"Lichev, Lyuben","last_name":"Lichev","first_name":"Lyuben"},{"full_name":"Mitsche, Dieter","last_name":"Mitsche","first_name":"Dieter"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X","first_name":"Raimundo J"},{"last_name":"Ziliotto","full_name":"Ziliotto, Bruno","first_name":"Bruno"}],"title":"Zero-sum random games on directed graphs","date_updated":"2024-06-03T07:50:29Z","_id":"17101"},{"_id":"17103","scopus_import":"1","month":"04","date_created":"2024-06-03T08:54:50Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38653755"],"isi":["001207290500013"]},"department":[{"_id":"JiFr"}],"volume":15,"publisher":"Springer Nature","quality_controlled":"1","abstract":[{"lang":"eng","text":"Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription."}],"pmid":1,"type":"journal_article","citation":{"ieee":"L. Jiang <i>et al.</i>, “Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Jiang L, Zhang X, Zhao Y, et al. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47746-y\">10.1038/s41467-024-47746-y</a>","apa":"Jiang, L., Zhang, X., Zhao, Y., Zhu, H., Fu, Q., Lu, X., … Du, Y. (2024). Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47746-y\">https://doi.org/10.1038/s41467-024-47746-y</a>","chicago":"Jiang, Lihui, Xiaoyan Zhang, Yiting Zhao, Haiyan Zhu, Qijing Fu, Xinqi Lu, Wuying Huang, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47746-y\">https://doi.org/10.1038/s41467-024-47746-y</a>.","ista":"Jiang L, Zhang X, Zhao Y, Zhu H, Fu Q, Lu X, Huang W, Yang X, Zhou X, Wu L, Yang A, He X, Dong M, Peng Z, Yang J, Guo L, Wen J, Huang H, Xie Y, Zhu S, Li C, He X, Zhu Y, Friml J, Du Y. 2024. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature Communications. 15, 3437.","mla":"Jiang, Lihui, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” <i>Nature Communications</i>, vol. 15, 3437, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47746-y\">10.1038/s41467-024-47746-y</a>.","short":"L. Jiang, X. Zhang, Y. Zhao, H. Zhu, Q. Fu, X. Lu, W. Huang, X. Yang, X. Zhou, L. Wu, A. Yang, X. He, M. Dong, Z. Peng, J. Yang, L. Guo, J. Wen, H. Huang, Y. Xie, S. Zhu, C. Li, X. He, Y. Zhu, J. Friml, Y. Du, Nature Communications 15 (2024)."},"date_updated":"2025-09-08T07:46:24Z","author":[{"first_name":"Lihui","last_name":"Jiang","full_name":"Jiang, Lihui"},{"full_name":"Zhang, Xiaoyan","last_name":"Zhang","first_name":"Xiaoyan"},{"first_name":"Yiting","full_name":"Zhao, Yiting","last_name":"Zhao"},{"full_name":"Zhu, Haiyan","last_name":"Zhu","first_name":"Haiyan"},{"first_name":"Qijing","last_name":"Fu","full_name":"Fu, Qijing"},{"first_name":"Xinqi","full_name":"Lu, Xinqi","last_name":"Lu"},{"last_name":"Huang","full_name":"Huang, Wuying","first_name":"Wuying"},{"first_name":"Xinyue","full_name":"Yang, Xinyue","last_name":"Yang"},{"first_name":"Xuan","full_name":"Zhou, Xuan","last_name":"Zhou"},{"full_name":"Wu, Lixia","last_name":"Wu","first_name":"Lixia"},{"full_name":"Yang, Ao","last_name":"Yang","first_name":"Ao"},{"first_name":"Xie","last_name":"He","full_name":"He, Xie"},{"full_name":"Dong, Man","last_name":"Dong","first_name":"Man"},{"first_name":"Ziai","last_name":"Peng","full_name":"Peng, Ziai"},{"full_name":"Yang, Jing","last_name":"Yang","first_name":"Jing"},{"first_name":"Liwei","last_name":"Guo","full_name":"Guo, Liwei"},{"first_name":"Jiancheng","full_name":"Wen, Jiancheng","last_name":"Wen"},{"first_name":"Huichuan","full_name":"Huang, Huichuan","last_name":"Huang"},{"last_name":"Xie","full_name":"Xie, Yong","first_name":"Yong"},{"first_name":"Shusheng","full_name":"Zhu, Shusheng","last_name":"Zhu"},{"first_name":"Chengyun","last_name":"Li","full_name":"Li, Chengyun"},{"first_name":"Xiahong","full_name":"He, Xiahong","last_name":"He"},{"first_name":"Youyong","last_name":"Zhu","full_name":"Zhu, Youyong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Du, Yunlong","last_name":"Du","first_name":"Yunlong"}],"title":"Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast","file_date_updated":"2024-06-03T12:05:10Z","has_accepted_license":"1","article_processing_charge":"Yes","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","DOAJ_listed":"1","publication":"Nature Communications","isi":1,"ddc":["580"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        15","date_published":"2024-04-23T00:00:00Z","day":"23","doi":"10.1038/s41467-024-47746-y","oa":1,"file":[{"creator":"dernst","file_size":8013695,"success":1,"date_created":"2024-06-03T12:05:10Z","file_name":"2024_NatureComm_Jiang.pdf","access_level":"open_access","date_updated":"2024-06-03T12:05:10Z","file_id":"17110","content_type":"application/pdf","checksum":"80cb2f2c538e81064f4836b54bc313ca","relation":"main_file"}],"article_type":"original","year":"2024","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for his generous support with the sakuranetin measurement. We thank International Rice Research Institute (IRRI) for provision of the rice NILs. We thank Professor Zhongkai Zhang (Yunnan Academy of Agricultural Sciences) for his generous support with subcellular structure observation of rice roots. We thank Professor Barbara Valent (Kansas State University) for her generously provision of the plasmid containing the PWL2 gene. We thank Professor Zuhua He (Chinese Academy of Sciences) for the gift of the transgenic rice line expressing the Pigm gene, OsNPR1-RNAi mutant line and ROD1-overexpression rice line. We thank Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. We thank Professor Muyuan Zhu (Zhejiang University) for provision of the transgenic plants overexpressing miR393a. We thank Professor Zhengge Zhu (Hebei Normal University) for provision of the rice line overexpressing OsPIN3t-GFP. We thank Professor Yanhua Qi (Zhejiang University) for provision of the arf12 mutant line. Thanks also go to Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the fungus M. oryzae strain Guy11 (AvrCo39-mRFP). This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31760500 and 31901870), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005). The project was also sponsored by SRF for ROCS, SEM (Grant No. [2013] 1792), the Key Projects of Applied Basic Research Plan of Yunnan Province (Grant No. 2017FA018, 202301AS070082), the Major Science and Technology Project in Yunnan Province (202102AE090042, 202202AE090036 and 202102AE090017), the Young and Middle-Aged Academic and Technical Leaders Reserve Talent Program in Yunnan Province (202205AC160076), the China Postdoctoral Science Foundation (2019M653849XB) and the National Key Research and Development Program of China (2023YFE0107500).","article_number":"3437"},{"scopus_import":"1","issue":"4","month":"04","_id":"17104","external_id":{"isi":["001202370200001"],"arxiv":["2310.04272"]},"date_created":"2024-06-03T08:58:44Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","publisher":"SciPost Foundation","department":[{"_id":"EdHa"}],"volume":16,"quality_controlled":"1","citation":{"short":"J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).","chicago":"Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>. SciPost Foundation, 2024. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>.","ista":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 16(4), 097.","mla":"Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>, vol. 16, no. 4, 097, SciPost Foundation, 2024, doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>.","ieee":"J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells,” <i>SciPost Physics</i>, vol. 16, no. 4. SciPost Foundation, 2024.","apa":"Krämer, J. C., Hannezo, E. B., Gompper, G., &#38; Elgeti, J. (2024). Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>","ama":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. 2024;16(4). doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>"},"abstract":[{"text":"The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth, the regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue steady-state are still poorly understood. Here, we develop a computational model that incorporates basic assumptions of stem cell renewal into distinct populations and mechanical interactions between cells. We find that the model generates unexpected dynamic features: stem cells repel each other in the bulk tissue and are thus found rather isolated, as in a number of in vivo contexts. By mapping the system onto a gas of passive Brownian particles with effective repulsive interactions, that arise from the generated flows of differentiated cells, we show that we can quantitatively describe such stem cell distribution in tissues. The interaction potential between a pair of stem cells decays exponentially with a characteristic length that spans several cell sizes, corresponding to the volume of cells generated per stem cell division. Our findings may help understanding the dynamics of normal and cancerous epithelial tissues.","lang":"eng"}],"type":"journal_article","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2024-06-03T11:18:51Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-09-08T07:45:40Z","author":[{"first_name":"Johannes C.","full_name":"Krämer, Johannes C.","last_name":"Krämer"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"full_name":"Gompper, Gerhard","last_name":"Gompper","first_name":"Gerhard"},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"}],"title":"Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells","oa_version":"Published Version","ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"arxiv":1,"publication":"SciPost Physics","publication_identifier":{"issn":["2542-4653"]},"year":"2024","acknowledgement":"JE and JK gratefully acknowledge financial support from the Initiative and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed with computing resources granted by RWTH Aachen University under project ‘rwth0475’.","article_type":"original","article_number":"097","date_published":"2024-04-08T00:00:00Z","intvolume":"        16","oa":1,"file":[{"content_type":"application/pdf","checksum":"6fdeecd21c166db8dedb927ecc2e6025","relation":"main_file","date_updated":"2024-06-03T11:18:51Z","file_id":"17109","access_level":"open_access","success":1,"file_name":"2024_SciPostPhys_Kraemer.pdf","date_created":"2024-06-03T11:18:51Z","creator":"dernst","file_size":4973291}],"doi":"10.21468/scipostphys.16.4.097","day":"08"},{"quality_controlled":"1","citation":{"short":"J. Sheng, J. Perego, S. Bracco, P. Cieciórski, W. Danowski, A. Comotti, B.L. Feringa, Angewandte Chemie International Edition 63 (2024).","apa":"Sheng, J., Perego, J., Bracco, S., Cieciórski, P., Danowski, W., Comotti, A., &#38; Feringa, B. L. (2024). Orthogonal photoswitching in a porous organic framework. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202404878\">https://doi.org/10.1002/anie.202404878</a>","ieee":"J. Sheng <i>et al.</i>, “Orthogonal photoswitching in a porous organic framework,” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 23. Wiley, 2024.","ama":"Sheng J, Perego J, Bracco S, et al. Orthogonal photoswitching in a porous organic framework. <i>Angewandte Chemie International Edition</i>. 2024;63(23). doi:<a href=\"https://doi.org/10.1002/anie.202404878\">10.1002/anie.202404878</a>","ista":"Sheng J, Perego J, Bracco S, Cieciórski P, Danowski W, Comotti A, Feringa BL. 2024. Orthogonal photoswitching in a porous organic framework. Angewandte Chemie International Edition. 63(23), e202404878.","chicago":"Sheng, Jinyu, Jacopo Perego, Silvia Bracco, Piotr Cieciórski, Wojciech Danowski, Angiolina Comotti, and Ben L. Feringa. “Orthogonal Photoswitching in a Porous Organic Framework.” <i>Angewandte Chemie International Edition</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/anie.202404878\">https://doi.org/10.1002/anie.202404878</a>.","mla":"Sheng, Jinyu, et al. “Orthogonal Photoswitching in a Porous Organic Framework.” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 23, e202404878, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/anie.202404878\">10.1002/anie.202404878</a>."},"pmid":1,"abstract":[{"text":"The development of photoresponsive systems with non-invasive orthogonal control by distinct wavelengths of light is still in its infancy. In particular, the design of photochemically triggered-orthogonal systems integrated into solid materials that enable multiple dynamic control over their properties remains a longstanding challenge. Here, we report the orthogonal and reversible control of two types of photoswitches in an integrated solid porous framework, that is, visible-light responsive o-fluoroazobenzene and nitro-spiropyran motifs. The properties of the constructed material can be selectively controlled by different wavelengths of light thus generating four distinct states providing a basis for dynamic multifunctional materials. Solid-state NMR spectroscopy demonstrated the selective transformation of the azobenzene switch in the bulk, which in turn modulates N2 and CO2 adsorption.","lang":"eng"}],"type":"journal_article","publisher":"Wiley","department":[{"_id":"RaKl"}],"volume":63,"external_id":{"pmid":["38530132"]},"date_created":"2024-06-03T09:00:01Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","issue":"23","scopus_import":"1","month":"03","_id":"17105","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"acknowledgement":"This work was supported from the following sources: China Scholarship Council (CSC PhD Fellowship No. 201808330459 to J.S.), the Ministry of Education, Culture and Science of the Netherlands (Gravitation Program No. 024.001.035 to BLF), Financial support from The Netherlands Organization for Scientific Research (NWO-CW), the European Research Council (ERC; advanced Grant No. 694345 to B.L.F.). PRIN (SHERPA 2020 No. H45F21003430001) and PRIN (HySTAR 2022 No. H53D23004720006) and Lombardy Region for “Enhancing Photosynthesis” grant (2021-2023 No. H45F21002830007). W.D. is grateful for financial support from Marie Skłodowska-Curie Actions (Individual Fellowship No. 101027639). P.C. is grateful for the financial support provided by the PRELUDIUM grant from the National Science Center Poland (Reg. No: 2023/49/N/ST5/01864).","year":"2024","article_type":"original","article_number":"e202404878","date_published":"2024-03-26T00:00:00Z","intvolume":"        63","oa":1,"file":[{"success":1,"date_created":"2024-06-03T10:33:17Z","file_name":"2024_AngChemieInt_Sheng.pdf","creator":"dernst","file_size":2363206,"access_level":"open_access","date_updated":"2024-06-03T10:33:17Z","file_id":"17107","checksum":"7ecb0892051f6ed8f6a6f25baa47543a","content_type":"application/pdf","relation":"main_file"}],"doi":"10.1002/anie.202404878","day":"26","ddc":["540"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Angewandte Chemie International Edition","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2024-06-03T10:33:17Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-04-23T07:48:28Z","author":[{"first_name":"Jinyu","last_name":"Sheng","full_name":"Sheng, Jinyu","id":"639f0526-27c9-11ee-95a6-966cd7f102d8"},{"first_name":"Jacopo","full_name":"Perego, Jacopo","last_name":"Perego"},{"full_name":"Bracco, Silvia","last_name":"Bracco","first_name":"Silvia"},{"full_name":"Cieciórski, Piotr","last_name":"Cieciórski","first_name":"Piotr"},{"first_name":"Wojciech","full_name":"Danowski, Wojciech","last_name":"Danowski"},{"first_name":"Angiolina","full_name":"Comotti, Angiolina","last_name":"Comotti"},{"first_name":"Ben L.","full_name":"Feringa, Ben L.","last_name":"Feringa"}],"title":"Orthogonal photoswitching in a porous organic framework"},{"article_type":"original","publication_identifier":{"issn":["0006-3495"]},"year":"2024","date_published":"2024-06-04T00:00:00Z","intvolume":"       123","day":"04","doi":"10.1016/j.bpj.2024.03.015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Biophysical Journal","oa_version":"None","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-01-13T11:03:41Z","page":"1494-1507","title":"Lipid droplets as substrates for protein phase separation","author":[{"first_name":"Advika","full_name":"Kamatar, Advika","last_name":"Kamatar"},{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","first_name":"Jack Peter Kelly"},{"full_name":"Yuan, Feng","last_name":"Yuan","first_name":"Feng"},{"first_name":"Liping","last_name":"Wang","full_name":"Wang, Liping"},{"full_name":"Lafer, Eileen M.","last_name":"Lafer","first_name":"Eileen M."},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."},{"first_name":"Jeanne C.","full_name":"Stachowiak, Jeanne C.","last_name":"Stachowiak"},{"full_name":"Parekh, Sapun H.","last_name":"Parekh","first_name":"Sapun H."}],"quality_controlled":"1","citation":{"ieee":"A. Kamatar <i>et al.</i>, “Lipid droplets as substrates for protein phase separation,” <i>Biophysical Journal</i>, vol. 123, no. 11. Elsevier, pp. 1494–1507, 2024.","ama":"Kamatar A, Bravo JPK, Yuan F, et al. Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. 2024;123(11):1494-1507. doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>","apa":"Kamatar, A., Bravo, J. P. K., Yuan, F., Wang, L., Lafer, E. M., Taylor, D. W., … Parekh, S. H. (2024). Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>","mla":"Kamatar, Advika, et al. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>, vol. 123, no. 11, Elsevier, 2024, pp. 1494–507, doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>.","chicago":"Kamatar, Advika, Jack Peter Kelly Bravo, Feng Yuan, Liping Wang, Eileen M. Lafer, David W. Taylor, Jeanne C. Stachowiak, and Sapun H. Parekh. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>.","ista":"Kamatar A, Bravo JPK, Yuan F, Wang L, Lafer EM, Taylor DW, Stachowiak JC, Parekh SH. 2024. Lipid droplets as substrates for protein phase separation. Biophysical Journal. 123(11), 1494–1507.","short":"A. Kamatar, J.P.K. Bravo, F. Yuan, L. Wang, E.M. Lafer, D.W. Taylor, J.C. Stachowiak, S.H. Parekh, Biophysical Journal 123 (2024) 1494–1507."},"pmid":1,"type":"journal_article","abstract":[{"text":"Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets.","lang":"eng"}],"extern":"1","publisher":"Elsevier","volume":123,"external_id":{"pmid":["38462838"]},"date_created":"2024-06-04T06:41:03Z","publication_status":"published","issue":"11","scopus_import":"1","month":"06","_id":"17111"},{"publication":"Science","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-02-01T00:00:00Z","intvolume":"       383","oa":1,"day":"01","doi":"10.1126/science.adk0378","year":"2024","acknowledgement":"We thank R. Fregoso Ocampo for assistance with negative-stain EM imaging. This work was funded by Dutch Research Council (NWO) VIDI grant VI.Vidi.203.074 (R.H.J.S.), NWO Spinoza grant SPI 93-537 (J.v.d.O.), European Research Council (ERC) Advanced grant ERC-AdG-834279 (J.v.d.O.), ERC CoG grant 817834 (T.J.G.E.), NWO VICI grant VI.C.192.016 (T.J.G.E.), Volkswagen Foundation grant 96725 (T.J.G.E.), National Institute of General Medical Sciences of the National Institutes of Health grant R35GM138348 (D.W.T.), Welch Foundation research grant F-1938 (D.W.T.), a Robert J. Kleberg, Jr. And Helen C. Kleberg Foundation medical research grant (D.W.T.), and American Cancer Society Research Scholar grant RSG-21-050-01-DMC (D.W.T.).","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_type":"original","date_updated":"2025-09-24T08:31:45Z","page":"512-519","author":[{"first_name":"Jurre A.","full_name":"Steens, Jurre A.","last_name":"Steens"},{"first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","orcid":"0000-0003-0456-0753"},{"first_name":"Carl Raymund P.","full_name":"Salazar, Carl Raymund P.","last_name":"Salazar"},{"first_name":"Caglar","full_name":"Yildiz, Caglar","last_name":"Yildiz"},{"full_name":"Amieiro, Afonso M.","last_name":"Amieiro","first_name":"Afonso M."},{"last_name":"Köstlbacher","full_name":"Köstlbacher, Stephan","first_name":"Stephan"},{"full_name":"Prinsen, Stijn H.P.","last_name":"Prinsen","first_name":"Stijn H.P."},{"full_name":"Patinios, Constantinos","last_name":"Patinios","first_name":"Constantinos"},{"first_name":"Andreas","full_name":"Bardis, Andreas","last_name":"Bardis"},{"first_name":"Arjan","last_name":"Barendregt","full_name":"Barendregt, Arjan"},{"last_name":"Scheltema","full_name":"Scheltema, Richard A.","first_name":"Richard A."},{"last_name":"Ettema","full_name":"Ettema, Thijs J.G.","first_name":"Thijs J.G."},{"first_name":"John","last_name":"van der Oost","full_name":"van der Oost, John"},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."},{"last_name":"Staals","full_name":"Staals, Raymond H.J.","first_name":"Raymond H.J."}],"title":"Type III-B CRISPR-Cas cascade of proteolytic cleavages","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","OA_type":"green","volume":383,"main_file_link":[{"url":"https://doi.org/10.1101/2023.06.23.546230","open_access":"1"}],"publisher":"American Association for the Advancement of Science","quality_controlled":"1","citation":{"mla":"Steens, Jurre A., et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” <i>Science</i>, vol. 383, no. 6682, American Association for the Advancement of Science, 2024, pp. 512–19, doi:<a href=\"https://doi.org/10.1126/science.adk0378\">10.1126/science.adk0378</a>.","ista":"Steens JA, Bravo JPK, Salazar CRP, Yildiz C, Amieiro AM, Köstlbacher S, Prinsen SHP, Patinios C, Bardis A, Barendregt A, Scheltema RA, Ettema TJG, van der Oost J, Taylor DW, Staals RHJ. 2024. Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science. 383(6682), 512–519.","chicago":"Steens, Jurre A., Jack Peter Kelly Bravo, Carl Raymund P. Salazar, Caglar Yildiz, Afonso M. Amieiro, Stephan Köstlbacher, Stijn H.P. Prinsen, et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adk0378\">https://doi.org/10.1126/science.adk0378</a>.","apa":"Steens, J. A., Bravo, J. P. K., Salazar, C. R. P., Yildiz, C., Amieiro, A. M., Köstlbacher, S., … Staals, R. H. J. (2024). Type III-B CRISPR-Cas cascade of proteolytic cleavages. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adk0378\">https://doi.org/10.1126/science.adk0378</a>","ama":"Steens JA, Bravo JPK, Salazar CRP, et al. Type III-B CRISPR-Cas cascade of proteolytic cleavages. <i>Science</i>. 2024;383(6682):512-519. doi:<a href=\"https://doi.org/10.1126/science.adk0378\">10.1126/science.adk0378</a>","ieee":"J. A. Steens <i>et al.</i>, “Type III-B CRISPR-Cas cascade of proteolytic cleavages,” <i>Science</i>, vol. 383, no. 6682. American Association for the Advancement of Science, pp. 512–519, 2024.","short":"J.A. Steens, J.P.K. Bravo, C.R.P. Salazar, C. Yildiz, A.M. Amieiro, S. Köstlbacher, S.H.P. Prinsen, C. Patinios, A. Bardis, A. Barendregt, R.A. Scheltema, T.J.G. Ettema, J. van der Oost, D.W. Taylor, R.H.J. Staals, Science 383 (2024) 512–519."},"extern":"1","type":"journal_article","pmid":1,"abstract":[{"text":"The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide–based antiphage signaling system (CBASS). Cyclic tri–adenosine monophosphate (AMP)–induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas–based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities.","lang":"eng"}],"_id":"17112","scopus_import":"1","issue":"6682","month":"02","date_created":"2024-06-04T06:41:26Z","publication_status":"published","external_id":{"pmid":["38301007"]}},{"oa_version":"Published Version","title":"Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9","author":[{"first_name":"Grace N.","full_name":"Hibshman, Grace N.","last_name":"Hibshman"},{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","first_name":"Jack Peter Kelly"},{"first_name":"Matthew M.","last_name":"Hooper","full_name":"Hooper, Matthew M."},{"last_name":"Dangerfield","full_name":"Dangerfield, Tyler L.","first_name":"Tyler L."},{"last_name":"Zhang","full_name":"Zhang, Hongshan","first_name":"Hongshan"},{"first_name":"Ilya J.","full_name":"Finkelstein, Ilya J.","last_name":"Finkelstein"},{"full_name":"Johnson, Kenneth A.","last_name":"Johnson","first_name":"Kenneth A."},{"first_name":"David W.","last_name":"Taylor","full_name":"Taylor, David W."}],"date_updated":"2024-10-14T12:34:26Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes","doi":"10.1038/s41467-024-47830-3","day":"30","oa":1,"intvolume":"        15","date_published":"2024-04-30T00:00:00Z","article_number":"3663","publication_identifier":{"issn":["2041-1723"]},"year":"2024","article_type":"original","publication":"Nature Communications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2024-06-04T06:42:07Z","external_id":{"pmid":["38688943"]},"_id":"17113","month":"04","scopus_import":"1","type":"journal_article","extern":"1","pmid":1,"abstract":[{"lang":"eng","text":"CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for <jats:italic>Streptococcus pyogenes</jats:italic> Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing."}],"citation":{"ista":"Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. 15, 3663.","chicago":"Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L. Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>.","mla":"Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>, vol. 15, 3663, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>.","ama":"Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>","apa":"Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang, H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>","ieee":"G. N. Hibshman <i>et al.</i>, “Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J. Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024)."},"quality_controlled":"1","volume":15,"publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1038/s41467-024-47830-3","open_access":"1"}]},{"month":"04","scopus_import":"1","_id":"17114","external_id":{"pmid":["38637512"]},"publication_status":"published","date_created":"2024-06-04T06:43:02Z","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1038/s41467-024-47506-y","open_access":"1"}],"volume":15,"extern":"1","type":"journal_article","abstract":[{"lang":"eng","text":"CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction<jats:sup>1–5</jats:sup>. Target RNA cleavage at regular intervals is characteristic of type III effector complexes<jats:sup>6–8</jats:sup>. Here, we determine the structures of the <jats:italic>Synechocystis</jats:italic> type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors<jats:sup>9,10</jats:sup>, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes."}],"pmid":1,"citation":{"short":"E.A. Schwartz, J.P.K. Bravo, M. Ahsan, L.A. Macias, C.L. McCafferty, T.L. Dangerfield, J.N. Walker, J.S. Brodbelt, G. Palermo, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, Nature Communications 15 (2024).","ieee":"E. A. Schwartz <i>et al.</i>, “RNA targeting and cleavage by the type III-Dv CRISPR effector complex,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Schwartz EA, Bravo JPK, Ahsan M, et al. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>","apa":"Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., … Taylor, D. W. (2024). RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>","mla":"Schwartz, Evan A., et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>, vol. 15, 3324, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>.","chicago":"Schwartz, Evan A., Jack Peter Kelly Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>.","ista":"Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. 2024. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. 15, 3324."},"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes","title":"RNA targeting and cleavage by the type III-Dv CRISPR effector complex","author":[{"last_name":"Schwartz","full_name":"Schwartz, Evan A.","first_name":"Evan A."},{"first_name":"Jack Peter Kelly","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"last_name":"Ahsan","full_name":"Ahsan, Mohd","first_name":"Mohd"},{"first_name":"Luis A.","full_name":"Macias, Luis A.","last_name":"Macias"},{"first_name":"Caitlyn L.","full_name":"McCafferty, Caitlyn L.","last_name":"McCafferty"},{"first_name":"Tyler L.","last_name":"Dangerfield","full_name":"Dangerfield, Tyler L."},{"first_name":"Jada N.","full_name":"Walker, Jada N.","last_name":"Walker"},{"full_name":"Brodbelt, Jennifer S.","last_name":"Brodbelt","first_name":"Jennifer S."},{"first_name":"Giulia","last_name":"Palermo","full_name":"Palermo, Giulia"},{"first_name":"Peter C.","full_name":"Fineran, Peter C.","last_name":"Fineran"},{"last_name":"Fagerlund","full_name":"Fagerlund, Robert D.","first_name":"Robert D."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"date_updated":"2024-06-04T07:05:26Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Nature Communications","article_number":"3324","year":"2024","publication_identifier":{"issn":["2041-1723"]},"article_type":"original","day":"18","doi":"10.1038/s41467-024-47506-y","oa":1,"intvolume":"        15","date_published":"2024-04-18T00:00:00Z"}]